Atomistry » Manganese » PDB 8iri-8k62 » 8iri
Atomistry »
  Manganese »
    PDB 8iri-8k62 »
      8iri »

Manganese in PDB 8iri: Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay

Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay

All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay:
1.10.3.9;

Protein crystallography data

The structure of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay, PDB code: 8iri was solved by H.Li, M.Suga, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.77, 231.76, 288.58, 90, 90, 90
R / Rfree (%) 14 / 17.7

Other elements in 8iri:

The structure of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Calcium (Ca) 11 atoms
Magnesium (Mg) 80 atoms
Chlorine (Cl) 8 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Manganese atom in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay (pdb code 8iri). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay, PDB code: 8iri:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in 8iri

Go back to Manganese Binding Sites List in 8iri
Manganese binding site 1 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:46.0
occ:0.51
 MN1 A:OEY401 0.0 46.0 0.5
MN1 A:OEX413 0.2 42.9 0.5
OE2 A:GLU189 1.6 52.8 0.5
O6 A:OEY401 1.7 47.2 0.5
OE2 A:GLU189 1.7 50.1 0.5
O1 A:OEY401 1.8 41.2 0.5
O1 A:OEX413 1.9 42.8 0.5
O3 A:OEY401 1.9 44.9 0.5
OD2 A:ASP342 2.0 43.2 0.5
OD2 A:ASP342 2.1 43.2 0.5
O3 A:OEX413 2.1 44.8 0.5
NE2 A:HIS332 2.1 44.9 0.5
NE2 A:HIS332 2.1 43.7 0.5
CD A:GLU189 2.7 45.2 0.5
CD A:GLU189 2.9 45.1 0.5
MN2 A:OEY401 2.9 43.2 0.5
MN2 A:OEX413 2.9 43.8 0.5
CE1 A:HIS332 3.0 39.1 0.5
CG A:ASP342 3.0 48.3 0.5
CG A:ASP342 3.0 48.4 0.5
O5 A:OEX413 3.0 49.3 0.5
CD2 A:HIS332 3.0 42.5 0.5
CE1 A:HIS332 3.1 37.3 0.5
CD2 A:HIS332 3.2 41.5 0.5
O5 A:OEY401 3.2 57.0 0.5
OD1 A:ASP342 3.3 42.3 0.5
OD1 A:ASP342 3.3 42.4 0.5
OE1 A:GLU189 3.4 48.4 0.5
OE1 A:GLU189 3.4 47.8 0.5
MN3 A:OEX413 3.4 43.6 0.5
CA1 A:OEY401 3.5 46.5 0.5
MN3 A:OEY401 3.5 44.2 0.5
O2 A:OEX413 3.6 42.4 0.5
CA1 A:OEX413 3.6 44.5 0.5
O2 A:OEY401 3.7 41.0 0.5
CG A:GLU189 3.9 43.7 0.5
NE2 A:HIS337 4.0 45.6 0.5
NE2 A:HIS337 4.1 45.7 0.5
CG A:GLU189 4.1 44.4 0.5
OE1 A:GLU333 4.1 43.3 0.5
OE1 A:GLU333 4.1 43.3 0.5
ND1 A:HIS332 4.1 42.9 0.5
CG A:HIS332 4.2 45.1 0.5
ND1 A:HIS332 4.2 42.0 0.5
O A:HOH611 4.2 58.8 0.5
OXT A:ALA344 4.2 47.8 0.5
CG A:HIS332 4.2 45.2 0.5
O A:HOH611 4.3 59.8 0.5
CB A:ASP342 4.3 44.7 0.5
CB A:ASP342 4.3 44.7 0.5
OXT A:ALA344 4.3 47.7 0.5
OE1 C:GLU354 4.6 48.1 0.5
CG1 A:VAL185 4.6 41.5 0.5
CE1 A:HIS337 4.6 46.0 0.5
CG1 A:VAL185 4.6 41.5 0.5
OE1 C:GLU354 4.6 48.1 0.5
CE1 A:HIS337 4.7 46.0 0.5
OE2 C:GLU354 4.7 46.0 0.5
O A:HOH610 4.7 42.7 0.5
OE2 C:GLU354 4.7 46.1 0.5
O A:ALA344 4.7 46.4 0.5
O A:HOH610 4.8 42.7 0.5
O A:ALA344 4.8 46.0 0.5
C A:ALA344 4.8 43.7 0.5
CD A:GLU333 4.8 44.6 0.5
C A:ALA344 4.9 43.6 0.5
CD A:GLU333 5.0 44.2 0.5

Manganese binding site 2 out of 16 in 8iri

Go back to Manganese Binding Sites List in 8iri
Manganese binding site 2 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:43.2
occ:0.51
 MN2 A:OEY401 0.0 43.2 0.5
MN2 A:OEX413 0.1 43.8 0.5
O2 A:OEX413 1.8 42.4 0.5
O1 A:OEX413 1.8 42.8 0.5
O1 A:OEY401 1.8 41.2 0.5
OXT A:ALA344 1.8 47.8 0.5
O2 A:OEY401 1.8 41.0 0.5
O3 A:OEX413 1.9 44.8 0.5
O3 A:OEY401 1.9 44.9 0.5
OXT A:ALA344 1.9 47.7 0.5
OE1 C:GLU354 2.1 48.1 0.5
OE1 C:GLU354 2.1 48.1 0.5
OD1 A:ASP342 2.1 42.3 0.5
OD1 A:ASP342 2.1 42.4 0.5
MN3 A:OEX413 2.7 43.6 0.5
C A:ALA344 2.8 43.7 0.5
MN1 A:OEX413 2.8 42.9 0.5
CD C:GLU354 2.8 51.3 0.5
MN3 A:OEY401 2.9 44.2 0.5
CD C:GLU354 2.9 51.6 0.5
MN1 A:OEY401 2.9 46.0 0.5
C A:ALA344 2.9 43.6 0.5
OE2 C:GLU354 3.0 46.1 0.5
O A:ALA344 3.0 46.4 0.5
CG A:ASP342 3.0 48.3 0.5
CG A:ASP342 3.0 48.4 0.5
OE2 C:GLU354 3.1 46.0 0.5
O A:ALA344 3.2 46.0 0.5
OD2 A:ASP342 3.2 43.2 0.5
OD2 A:ASP342 3.3 43.2 0.5
CA1 A:OEY401 3.4 46.5 0.5
CA1 A:OEX413 3.4 44.5 0.5
O6 A:OEY401 3.6 47.2 0.5
O5 A:OEX413 3.6 49.3 0.5
NE2 A:HIS337 3.8 45.6 0.5
O5 A:OEY401 3.8 57.0 0.5
NE2 A:HIS337 3.8 45.7 0.5
O C:HOH736 4.0 49.4 0.5
OE2 A:GLU189 4.1 50.1 0.5
O4 A:OEX413 4.1 45.8 0.5
O C:HOH736 4.1 49.5 0.5
OE2 A:GLU189 4.1 52.8 0.5
CA A:ALA344 4.1 46.6 0.5
O A:HOH611 4.1 58.8 0.5
CG C:GLU354 4.2 50.5 0.5
CA A:ALA344 4.2 46.7 0.5
OE1 A:GLU333 4.3 43.3 0.5
CG C:GLU354 4.3 46.9 0.5
O4 A:OEY401 4.3 49.3 0.5
N A:ALA344 4.3 51.2 0.5
OE1 A:GLU333 4.3 43.3 0.5
CD2 A:HIS337 4.3 46.0 0.5
N A:ALA344 4.4 51.5 0.5
CD2 A:HIS337 4.4 46.0 0.5
NH2 C:ARG357 4.4 42.0 0.5
CB A:ASP342 4.5 44.7 0.5
O A:HOH611 4.5 59.8 0.5
CB A:ASP342 4.5 44.7 0.5
NH2 C:ARG357 4.5 42.0 0.5
NE2 A:HIS332 4.5 43.7 0.5
NE2 A:HIS332 4.6 44.9 0.5
OD1 A:ASP170 4.7 43.0 0.5
OD1 A:ASP170 4.7 43.0 0.5
CB C:GLU354 4.8 43.0 0.5
NH1 C:ARG357 4.8 41.0 0.5
NH1 C:ARG357 4.8 41.0 0.5
CD A:GLU189 4.8 45.2 0.5
CA A:ASP342 4.9 46.9 0.5
C A:ASP342 4.9 47.3 0.5
CB C:GLU354 4.9 43.0 0.5
CA A:ASP342 4.9 46.9 0.5
CE1 A:HIS337 4.9 46.0 0.5
CZ C:ARG357 4.9 52.2 0.5
OE1 A:GLU189 4.9 48.4 0.5
C A:ASP342 4.9 47.3 0.5
CD A:GLU189 4.9 45.1 0.5
CZ C:ARG357 5.0 52.2 0.5
CE1 A:HIS337 5.0 46.0 0.5
O A:ASP342 5.0 46.0 0.5

Manganese binding site 3 out of 16 in 8iri

Go back to Manganese Binding Sites List in 8iri
Manganese binding site 3 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:44.2
occ:0.51
 MN3 A:OEY401 0.0 44.2 0.5
MN3 A:OEX413 0.2 43.6 0.5
O4 A:OEX413 1.8 45.8 0.5
O2 A:OEY401 1.8 41.0 0.5
O2 A:OEX413 1.9 42.4 0.5
O5 A:OEY401 1.9 57.0 0.5
O4 A:OEY401 1.9 49.3 0.5
OE1 A:GLU333 1.9 43.3 0.5
O5 A:OEX413 1.9 49.3 0.5
OE1 A:GLU333 2.0 43.3 0.5
OE2 C:GLU354 2.0 46.1 0.5
OE2 C:GLU354 2.0 46.0 0.5
O3 A:OEY401 2.1 44.9 0.5
O3 A:OEX413 2.2 44.8 0.5
MN4 A:OEY401 2.6 47.7 0.5
MN4 A:OEX413 2.7 47.0 0.5
CD A:GLU333 2.8 44.6 0.5
MN2 A:OEY401 2.9 43.2 0.5
CD A:GLU333 2.9 44.2 0.5
OE2 A:GLU333 2.9 45.7 0.5
MN2 A:OEX413 3.0 43.8 0.5
OE2 A:GLU333 3.0 44.1 0.5
CD C:GLU354 3.0 51.6 0.5
CD C:GLU354 3.1 51.3 0.5
O6 A:OEY401 3.1 47.2 0.5
MN1 A:OEX413 3.3 42.9 0.5
OE1 C:GLU354 3.4 48.1 0.5
OE1 C:GLU354 3.5 48.1 0.5
CA1 A:OEY401 3.5 46.5 0.5
O1 A:OEX413 3.5 42.8 0.5
MN1 A:OEY401 3.5 46.0 0.5
O1 A:OEY401 3.6 41.2 0.5
CA1 A:OEX413 3.6 44.5 0.5
OD2 A:ASP170 3.9 42.7 0.5
NH2 C:ARG357 3.9 42.0 0.5
OD2 A:ASP170 3.9 43.4 0.5
NH2 C:ARG357 3.9 42.0 0.5
OD1 A:ASP170 3.9 43.0 0.5
OD1 A:ASP170 4.0 43.0 0.5
O C:HOH682 4.0 45.5 0.5
O A:HOH522 4.1 47.4 0.5
NE2 A:HIS332 4.2 43.7 0.5
NE2 A:HIS337 4.2 45.6 0.5
CG A:GLU333 4.2 41.9 0.5
O A:HOH522 4.2 46.9 0.5
NE2 A:HIS337 4.3 45.7 0.5
CG A:GLU333 4.3 42.0 0.5
O A:HOH520 4.3 41.5 0.5
CG C:GLU354 4.3 46.9 0.5
O A:HOH520 4.3 42.3 0.5
CG C:GLU354 4.3 50.5 0.5
CG A:ASP170 4.3 40.2 0.5
CG A:ASP170 4.4 40.2 0.5
OXT A:ALA344 4.4 47.8 0.5
CD2 A:HIS332 4.4 41.5 0.5
O A:HOH518 4.4 42.2 0.5
O A:HOH518 4.4 45.1 0.5
NE2 A:HIS332 4.5 44.9 0.5
OXT A:ALA344 4.5 47.7 0.5
CD2 A:HIS332 4.5 42.5 0.5
O A:ALA344 4.6 46.4 0.5
OD1 A:ASP342 4.6 42.3 0.5
CB A:GLU333 4.7 42.3 0.5
OD1 A:ASP342 4.7 42.4 0.5
OE2 A:GLU189 4.7 52.8 0.5
O A:ALA344 4.7 46.0 0.5
O A:HOH610 4.7 42.7 0.5
CB A:GLU333 4.7 42.3 0.5
O A:HOH610 4.8 42.7 0.5
CE1 A:HIS337 4.8 46.0 0.5
OD2 A:ASP342 4.8 43.2 0.5
OD2 A:ASP342 4.9 43.2 0.5
CE1 A:HIS337 4.9 46.0 0.5
C A:ALA344 5.0 43.7 0.5
OD1 A:ASP61 5.0 42.4 0.5

Manganese binding site 4 out of 16 in 8iri

Go back to Manganese Binding Sites List in 8iri
Manganese binding site 4 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:47.7
occ:0.51
 MN4 A:OEY401 0.0 47.7 0.5
MN4 A:OEX413 0.3 47.0 0.5
O4 A:OEX413 1.8 45.8 0.5
OE2 A:GLU333 1.9 45.7 0.5
OD2 A:ASP170 1.9 42.7 0.5
OE2 A:GLU333 2.0 44.1 0.5
OD2 A:ASP170 2.0 43.4 0.5
O4 A:OEY401 2.0 49.3 0.5
O A:HOH518 2.0 45.1 0.5
O A:HOH520 2.1 42.3 0.5
O A:HOH518 2.2 42.2 0.5
O5 A:OEY401 2.2 57.0 0.5
O A:HOH520 2.3 41.5 0.5
O5 A:OEX413 2.4 49.3 0.5
MN3 A:OEY401 2.6 44.2 0.5
MN3 A:OEX413 2.8 43.6 0.5
CD A:GLU333 2.9 44.6 0.5
CD A:GLU333 2.9 44.2 0.5
CG A:ASP170 3.0 40.2 0.5
CG A:ASP170 3.1 40.2 0.5
OE1 A:GLU333 3.2 43.3 0.5
OE1 A:GLU333 3.2 43.3 0.5
O A:HOH522 3.5 47.4 0.5
OD1 A:ASP170 3.5 43.0 0.5
OD1 A:ASP170 3.5 43.0 0.5
O2 A:OEY401 3.7 41.0 0.5
O2 A:OEX413 3.7 42.4 0.5
OD1 A:ASP61 3.7 42.4 0.5
O A:HOH522 3.7 46.9 0.5
OD1 A:ASP61 3.9 42.4 0.5
O A:HOH610 4.0 42.7 0.5
O A:HOH610 4.0 42.7 0.5
O6 A:OEY401 4.1 47.2 0.5
CA1 A:OEY401 4.1 46.5 0.5
OE2 C:GLU354 4.2 46.1 0.5
O A:HOH539 4.2 47.5 0.5
CG A:GLU333 4.2 41.9 0.5
O A:SER169 4.2 43.1 0.5
OE2 C:GLU354 4.2 46.0 0.5
CA1 A:OEX413 4.2 44.5 0.5
O A:HOH539 4.3 47.6 0.5
O A:SER169 4.3 43.1 0.5
CG A:GLU333 4.3 42.0 0.5
O A:HOH626 4.3 48.3 0.5
CB A:ASP170 4.3 42.3 0.5
CB A:ASP170 4.3 42.2 0.5
NH2 C:ARG357 4.4 42.0 0.5
NH2 C:ARG357 4.4 42.0 0.5
O A:HOH626 4.4 48.4 0.5
CA A:ASP170 4.5 48.7 0.5
O3 A:OEY401 4.5 44.9 0.5
CA A:ASP170 4.5 48.6 0.5
O3 A:OEX413 4.6 44.8 0.5
CG A:ASP61 4.7 47.5 0.5
O C:HOH682 4.7 45.5 0.5
O D:HOH512 4.7 41.0 0.5
C A:SER169 4.7 47.3 0.5
CG A:ASP61 4.8 47.6 0.5
C A:SER169 4.8 47.3 0.5
O D:HOH512 4.8 40.5 0.5
OG A:SER169 4.8 48.8 0.5
N A:ASP170 4.8 42.9 0.5
N A:ASP170 4.8 42.8 0.5
OG A:SER169 4.9 48.9 0.5

Manganese binding site 5 out of 16 in 8iri

Go back to Manganese Binding Sites List in 8iri
Manganese binding site 5 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:42.9
occ:0.49
 MN1 A:OEX413 0.0 42.9 0.5
MN1 A:OEY401 0.2 46.0 0.5
O6 A:OEY401 1.6 47.2 0.5
OE2 A:GLU189 1.7 52.8 0.5
O3 A:OEY401 1.7 44.9 0.5
O1 A:OEY401 1.8 41.2 0.5
O1 A:OEX413 1.9 42.8 0.5
O3 A:OEX413 1.9 44.8 0.5
OE2 A:GLU189 1.9 50.1 0.5
NE2 A:HIS332 2.1 44.9 0.5
NE2 A:HIS332 2.1 43.7 0.5
OD2 A:ASP342 2.1 43.2 0.5
OD2 A:ASP342 2.2 43.2 0.5
MN2 A:OEY401 2.8 43.2 0.5
O5 A:OEX413 2.8 49.3 0.5
MN2 A:OEX413 2.8 43.8 0.5
CD A:GLU189 2.9 45.2 0.5
CD2 A:HIS332 3.0 42.5 0.5
CE1 A:HIS332 3.0 39.1 0.5
CD A:GLU189 3.0 45.1 0.5
O5 A:OEY401 3.0 57.0 0.5
CG A:ASP342 3.0 48.3 0.5
CG A:ASP342 3.1 48.4 0.5
CD2 A:HIS332 3.1 41.5 0.5
CE1 A:HIS332 3.2 37.3 0.5
MN3 A:OEX413 3.2 43.6 0.5
OD1 A:ASP342 3.3 42.3 0.5
OD1 A:ASP342 3.3 42.4 0.5
MN3 A:OEY401 3.3 44.2 0.5
CA1 A:OEY401 3.4 46.5 0.5
O2 A:OEX413 3.4 42.4 0.5
OE1 A:GLU189 3.5 48.4 0.5
OE1 A:GLU189 3.5 47.8 0.5
O2 A:OEY401 3.5 41.0 0.5
CA1 A:OEX413 3.6 44.5 0.5
OE1 A:GLU333 3.9 43.3 0.5
OE1 A:GLU333 3.9 43.3 0.5
NE2 A:HIS337 3.9 45.6 0.5
NE2 A:HIS337 4.0 45.7 0.5
CG A:GLU189 4.1 43.7 0.5
ND1 A:HIS332 4.1 42.9 0.5
CG A:HIS332 4.1 45.1 0.5
OXT A:ALA344 4.2 47.8 0.5
ND1 A:HIS332 4.2 42.0 0.5
CG A:HIS332 4.2 45.2 0.5
CG A:GLU189 4.3 44.4 0.5
OXT A:ALA344 4.3 47.7 0.5
O A:HOH611 4.3 58.8 0.5
O A:HOH611 4.4 59.8 0.5
CB A:ASP342 4.4 44.7 0.5
OE1 C:GLU354 4.4 48.1 0.5
CB A:ASP342 4.4 44.7 0.5
CE1 A:HIS337 4.5 46.0 0.5
OE1 C:GLU354 4.5 48.1 0.5
OE2 C:GLU354 4.5 46.0 0.5
OE2 C:GLU354 4.5 46.1 0.5
CE1 A:HIS337 4.6 46.0 0.5
CG1 A:VAL185 4.6 41.5 0.5
CG1 A:VAL185 4.6 41.5 0.5
CD A:GLU333 4.6 44.6 0.5
O A:HOH610 4.7 42.7 0.5
O A:ALA344 4.7 46.4 0.5
O A:HOH610 4.7 42.7 0.5
O A:ALA344 4.7 46.0 0.5
CD A:GLU333 4.8 44.2 0.5
C A:ALA344 4.8 43.7 0.5
C A:ALA344 4.9 43.6 0.5
CD C:GLU354 4.9 51.6 0.5
O4 A:OEX413 4.9 45.8 0.5
OE2 A:GLU333 4.9 45.7 0.5
CD C:GLU354 5.0 51.3 0.5
MN4 A:OEX413 5.0 47.0 0.5

Manganese binding site 6 out of 16 in 8iri

Go back to Manganese Binding Sites List in 8iri
Manganese binding site 6 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:43.8
occ:0.49
 MN2 A:OEX413 0.0 43.8 0.5
MN2 A:OEY401 0.1 43.2 0.5
OXT A:ALA344 1.7 47.8 0.5
O1 A:OEX413 1.8 42.8 0.5
O1 A:OEY401 1.8 41.2 0.5
O2 A:OEX413 1.8 42.4 0.5
OXT A:ALA344 1.9 47.7 0.5
O2 A:OEY401 1.9 41.0 0.5
O3 A:OEX413 2.0 44.8 0.5
O3 A:OEY401 2.0 44.9 0.5
OD1 A:ASP342 2.0 42.3 0.5
OD1 A:ASP342 2.1 42.4 0.5
OE1 C:GLU354 2.1 48.1 0.5
OE1 C:GLU354 2.1 48.1 0.5
C A:ALA344 2.7 43.7 0.5
MN3 A:OEX413 2.8 43.6 0.5
C A:ALA344 2.8 43.6 0.5
MN1 A:OEX413 2.8 42.9 0.5
CD C:GLU354 2.9 51.3 0.5
CD C:GLU354 2.9 51.6 0.5
MN1 A:OEY401 2.9 46.0 0.5
MN3 A:OEY401 3.0 44.2 0.5
CG A:ASP342 3.0 48.3 0.5
CG A:ASP342 3.0 48.4 0.5
O A:ALA344 3.0 46.4 0.5
OE2 C:GLU354 3.1 46.1 0.5
OE2 C:GLU354 3.1 46.0 0.5
O A:ALA344 3.1 46.0 0.5
OD2 A:ASP342 3.2 43.2 0.5
OD2 A:ASP342 3.2 43.2 0.5
CA1 A:OEY401 3.4 46.5 0.5
CA1 A:OEX413 3.5 44.5 0.5
O6 A:OEY401 3.7 47.2 0.5
O5 A:OEX413 3.7 49.3 0.5
NE2 A:HIS337 3.8 45.6 0.5
NE2 A:HIS337 3.8 45.7 0.5
O5 A:OEY401 3.9 57.0 0.5
O C:HOH736 3.9 49.4 0.5
O C:HOH736 4.0 49.5 0.5
CA A:ALA344 4.0 46.6 0.5
O A:HOH611 4.1 58.8 0.5
OE2 A:GLU189 4.1 50.1 0.5
OE2 A:GLU189 4.1 52.8 0.5
CA A:ALA344 4.2 46.7 0.5
O4 A:OEX413 4.2 45.8 0.5
N A:ALA344 4.2 51.2 0.5
CG C:GLU354 4.2 50.5 0.5
N A:ALA344 4.3 51.5 0.5
CG C:GLU354 4.3 46.9 0.5
CD2 A:HIS337 4.3 46.0 0.5
CD2 A:HIS337 4.4 46.0 0.5
O4 A:OEY401 4.4 49.3 0.5
OE1 A:GLU333 4.4 43.3 0.5
CB A:ASP342 4.4 44.7 0.5
CB A:ASP342 4.4 44.7 0.5
O A:HOH611 4.4 59.8 0.5
OE1 A:GLU333 4.4 43.3 0.5
NH2 C:ARG357 4.5 42.0 0.5
NH2 C:ARG357 4.5 42.0 0.5
NE2 A:HIS332 4.6 43.7 0.5
NE2 A:HIS332 4.6 44.9 0.5
C A:ASP342 4.8 47.3 0.5
OD1 A:ASP170 4.8 43.0 0.5
CA A:ASP342 4.8 46.9 0.5
CB C:GLU354 4.8 43.0 0.5
CA A:ASP342 4.8 46.9 0.5
OD1 A:ASP170 4.8 43.0 0.5
NH1 C:ARG357 4.8 41.0 0.5
C A:ASP342 4.8 47.3 0.5
NH1 C:ARG357 4.8 41.0 0.5
CB C:GLU354 4.8 43.0 0.5
CD A:GLU189 4.9 45.2 0.5
O A:ASP342 4.9 46.0 0.5
CE1 A:HIS337 4.9 46.0 0.5
CZ C:ARG357 4.9 52.2 0.5
OE1 A:GLU189 5.0 48.4 0.5
CD A:GLU189 5.0 45.1 0.5
CZ C:ARG357 5.0 52.2 0.5
CE1 A:HIS337 5.0 46.0 0.5

Manganese binding site 7 out of 16 in 8iri

Go back to Manganese Binding Sites List in 8iri
Manganese binding site 7 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:43.6
occ:0.49
 MN3 A:OEX413 0.0 43.6 0.5
MN3 A:OEY401 0.2 44.2 0.5
O2 A:OEY401 1.7 41.0 0.5
O2 A:OEX413 1.8 42.4 0.5
O4 A:OEX413 1.9 45.8 0.5
O3 A:OEY401 1.9 44.9 0.5
OE2 C:GLU354 2.0 46.1 0.5
O5 A:OEY401 2.0 57.0 0.5
OE2 C:GLU354 2.0 46.0 0.5
OE1 A:GLU333 2.0 43.3 0.5
O5 A:OEX413 2.0 49.3 0.5
O3 A:OEX413 2.0 44.8 0.5
O4 A:OEY401 2.1 49.3 0.5
OE1 A:GLU333 2.1 43.3 0.5
MN2 A:OEY401 2.7 43.2 0.5
MN4 A:OEY401 2.8 47.7 0.5
MN2 A:OEX413 2.8 43.8 0.5
MN4 A:OEX413 2.8 47.0 0.5
CD A:GLU333 2.9 44.6 0.5
CD C:GLU354 2.9 51.6 0.5
CD A:GLU333 3.0 44.2 0.5
CD C:GLU354 3.0 51.3 0.5
O6 A:OEY401 3.1 47.2 0.5
OE2 A:GLU333 3.1 45.7 0.5
OE2 A:GLU333 3.2 44.1 0.5
MN1 A:OEX413 3.2 42.9 0.5
OE1 C:GLU354 3.3 48.1 0.5
OE1 C:GLU354 3.3 48.1 0.5
O1 A:OEX413 3.4 42.8 0.5
MN1 A:OEY401 3.4 46.0 0.5
O1 A:OEY401 3.5 41.2 0.5
CA1 A:OEY401 3.5 46.5 0.5
CA1 A:OEX413 3.6 44.5 0.5
NH2 C:ARG357 3.9 42.0 0.5
NH2 C:ARG357 3.9 42.0 0.5
OD1 A:ASP170 4.0 43.0 0.5
OD2 A:ASP170 4.0 42.7 0.5
OD2 A:ASP170 4.0 43.4 0.5
OD1 A:ASP170 4.0 43.0 0.5
O C:HOH682 4.1 45.5 0.5
NE2 A:HIS337 4.1 45.6 0.5
NE2 A:HIS332 4.1 43.7 0.5
NE2 A:HIS337 4.1 45.7 0.5
O A:HOH522 4.2 47.4 0.5
CG C:GLU354 4.2 46.9 0.5
CG C:GLU354 4.3 50.5 0.5
OXT A:ALA344 4.3 47.8 0.5
CG A:GLU333 4.3 41.9 0.5
O A:HOH522 4.3 46.9 0.5
OXT A:ALA344 4.4 47.7 0.5
CG A:GLU333 4.4 42.0 0.5
NE2 A:HIS332 4.4 44.9 0.5
CD2 A:HIS332 4.4 41.5 0.5
O A:HOH520 4.4 41.5 0.5
CG A:ASP170 4.4 40.2 0.5
O A:HOH520 4.5 42.3 0.5
OD1 A:ASP342 4.5 42.3 0.5
CG A:ASP170 4.5 40.2 0.5
O A:ALA344 4.5 46.4 0.5
OD1 A:ASP342 4.5 42.4 0.5
CD2 A:HIS332 4.5 42.5 0.5
O A:HOH518 4.6 42.2 0.5
O A:HOH518 4.6 45.1 0.5
OE2 A:GLU189 4.6 52.8 0.5
O A:ALA344 4.6 46.0 0.5
CB A:GLU333 4.7 42.3 0.5
OD2 A:ASP342 4.7 43.2 0.5
OD2 A:ASP342 4.7 43.2 0.5
CE1 A:HIS337 4.7 46.0 0.5
CB A:GLU333 4.8 42.3 0.5
O A:HOH610 4.8 42.7 0.5
CE1 A:HIS337 4.8 46.0 0.5
O A:HOH610 4.8 42.7 0.5
C A:ALA344 4.9 43.7 0.5
C A:ALA344 5.0 43.6 0.5
OE2 A:GLU189 5.0 50.1 0.5

Manganese binding site 8 out of 16 in 8iri

Go back to Manganese Binding Sites List in 8iri
Manganese binding site 8 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:47.0
occ:0.49
 MN4 A:OEX413 0.0 47.0 0.5
MN4 A:OEY401 0.3 47.7 0.5
O A:HOH520 1.9 42.3 0.5
OD2 A:ASP170 1.9 42.7 0.5
OE2 A:GLU333 1.9 45.7 0.5
OD2 A:ASP170 1.9 43.4 0.5
O5 A:OEY401 2.0 57.0 0.5
OE2 A:GLU333 2.0 44.1 0.5
O4 A:OEX413 2.0 45.8 0.5
O A:HOH520 2.1 41.5 0.5
O5 A:OEX413 2.2 49.3 0.5
O A:HOH518 2.2 45.1 0.5
O4 A:OEY401 2.3 49.3 0.5
O A:HOH518 2.4 42.2 0.5
MN3 A:OEY401 2.7 44.2 0.5
MN3 A:OEX413 2.8 43.6 0.5
CD A:GLU333 2.9 44.6 0.5
CG A:ASP170 3.0 40.2 0.5
CD A:GLU333 3.0 44.2 0.5
CG A:ASP170 3.0 40.2 0.5
OE1 A:GLU333 3.2 43.3 0.5
OE1 A:GLU333 3.3 43.3 0.5
OD1 A:ASP170 3.4 43.0 0.5
OD1 A:ASP170 3.4 43.0 0.5
O2 A:OEY401 3.7 41.0 0.5
O A:HOH610 3.7 42.7 0.5
O A:HOH610 3.7 42.7 0.5
O2 A:OEX413 3.7 42.4 0.5
O A:HOH522 3.8 47.4 0.5
O6 A:OEY401 3.9 47.2 0.5
CA1 A:OEY401 3.9 46.5 0.5
OD1 A:ASP61 4.0 42.4 0.5
O A:HOH539 4.0 47.5 0.5
O A:HOH626 4.0 48.3 0.5
CA1 A:OEX413 4.1 44.5 0.5
O A:HOH522 4.1 46.9 0.5
O A:HOH539 4.1 47.6 0.5
O A:HOH626 4.2 48.4 0.5
OD1 A:ASP61 4.2 42.4 0.5
CG A:GLU333 4.2 41.9 0.5
CB A:ASP170 4.2 42.3 0.5
CB A:ASP170 4.3 42.2 0.5
O A:SER169 4.3 43.1 0.5
CG A:GLU333 4.3 42.0 0.5
OE2 C:GLU354 4.3 46.1 0.5
OE2 C:GLU354 4.4 46.0 0.5
O A:SER169 4.4 43.1 0.5
O3 A:OEY401 4.4 44.9 0.5
CA A:ASP170 4.4 48.7 0.5
CA A:ASP170 4.5 48.6 0.5
NH2 C:ARG357 4.6 42.0 0.5
NH2 C:ARG357 4.6 42.0 0.5
O3 A:OEX413 4.6 44.8 0.5
O D:HOH512 4.8 41.0 0.5
O D:HOH512 4.8 40.5 0.5
C A:SER169 4.8 47.3 0.5
C A:SER169 4.9 47.3 0.5
N A:ASP170 4.9 42.9 0.5
N A:ASP170 4.9 42.8 0.5
CG A:ASP61 4.9 47.5 0.5
MN1 A:OEX413 5.0 42.9 0.5
O A:HOH516 5.0 46.5 0.5
O C:HOH682 5.0 45.5 0.5

Manganese binding site 9 out of 16 in 8iri

Go back to Manganese Binding Sites List in 8iri
Manganese binding site 9 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:47.8
occ:0.51
 MN1 a:OEY401 0.0 47.8 0.5
MN1 a:OEX413 0.3 48.3 0.5
OE2 a:GLU189 1.6 54.7 0.5
O6 a:OEY401 1.7 59.5 0.5
O1 a:OEX413 1.7 49.9 0.5
O1 a:OEY401 1.8 50.9 0.5
OE2 a:GLU189 1.8 53.4 0.5
O3 a:OEY401 1.9 48.0 0.5
OD2 a:ASP342 1.9 51.7 0.5
OD2 a:ASP342 2.0 51.7 0.5
O3 a:OEX413 2.1 48.0 0.5
NE2 a:HIS332 2.1 48.1 0.5
NE2 a:HIS332 2.3 48.6 0.5
CD a:GLU189 2.7 50.1 0.5
MN2 a:OEY401 2.7 49.2 0.5
MN2 a:OEX413 2.8 46.7 0.5
CG a:ASP342 2.9 49.0 0.5
CD a:GLU189 2.9 49.1 0.5
O5 a:OEX413 2.9 51.1 0.5
CG a:ASP342 2.9 48.9 0.5
CE1 a:HIS332 3.0 44.3 0.5
O5 a:OEY401 3.0 51.0 0.5
CE1 a:HIS332 3.1 45.5 0.5
OD1 a:ASP342 3.1 48.5 0.5
CD2 a:HIS332 3.2 47.2 0.5
OD1 a:ASP342 3.2 48.7 0.5
OE1 a:GLU189 3.3 48.9 0.5
OE1 a:GLU189 3.3 49.4 0.5
CD2 a:HIS332 3.4 47.0 0.5
CA1 a:OEY401 3.4 52.5 0.5
MN3 a:OEX413 3.4 47.9 0.5
CA1 a:OEX413 3.5 52.3 0.5
MN3 a:OEY401 3.5 46.9 0.5
O2 a:OEX413 3.6 48.1 0.5
O2 a:OEY401 3.7 53.1 0.5
CG a:GLU189 3.9 50.2 0.5
OE1 a:GLU333 4.0 45.5 0.5
NE2 a:HIS337 4.1 47.6 0.5
ND1 a:HIS332 4.1 49.3 0.5
OE1 a:GLU333 4.1 45.6 0.5
OXT a:ALA344 4.1 51.0 0.5
O a:HOH610 4.1 69.8 0.5
NE2 a:HIS337 4.2 47.5 0.5
CG a:GLU189 4.2 50.8 0.5
OXT a:ALA344 4.2 51.2 0.5
ND1 a:HIS332 4.2 48.5 0.5
CG a:HIS332 4.2 50.1 0.5
CB a:ASP342 4.2 45.0 0.5
O a:HOH610 4.3 70.1 0.5
CB a:ASP342 4.3 45.0 0.5
CG a:HIS332 4.4 49.6 0.5
OE1 c:GLU354 4.5 50.4 0.5
OE1 c:GLU354 4.5 50.4 0.5
O a:ALA344 4.6 52.0 0.5
O a:ALA344 4.6 51.9 0.5
C a:ALA344 4.7 53.2 0.5
CG1 a:VAL185 4.7 48.5 0.5
CE1 a:HIS337 4.7 47.0 0.5
O a:HOH615 4.7 52.5 0.5
C a:ALA344 4.8 53.0 0.5
O a:HOH626 4.8 63.5 0.5
OE2 c:GLU354 4.8 47.0 0.5
O a:HOH615 4.8 51.2 0.5
CG1 a:VAL185 4.8 49.2 0.5
OE2 c:GLU354 4.9 49.0 0.5
CE1 a:HIS337 4.9 46.9 0.5
CD a:GLU333 4.9 51.7 0.5
O a:HOH519 4.9 54.7 0.5
CD a:GLU333 4.9 51.7 0.5

Manganese binding site 10 out of 16 in 8iri

Go back to Manganese Binding Sites List in 8iri
Manganese binding site 10 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:49.2
occ:0.51
 MN2 a:OEY401 0.0 49.2 0.5
MN2 a:OEX413 0.2 46.7 0.5
O1 a:OEX413 1.7 49.9 0.5
O2 a:OEX413 1.7 48.1 0.5
O1 a:OEY401 1.8 50.9 0.5
O3 a:OEX413 1.8 48.0 0.5
O2 a:OEY401 1.9 53.1 0.5
OXT a:ALA344 1.9 51.0 0.5
O3 a:OEY401 1.9 48.0 0.5
OXT a:ALA344 2.0 51.2 0.5
OE1 c:GLU354 2.1 50.4 0.5
OD1 a:ASP342 2.1 48.5 0.5
OE1 c:GLU354 2.1 50.4 0.5
OD1 a:ASP342 2.2 48.7 0.5
MN3 a:OEX413 2.6 47.9 0.5
MN3 a:OEY401 2.6 46.9 0.5
MN1 a:OEX413 2.7 48.3 0.5
MN1 a:OEY401 2.7 47.8 0.5
C a:ALA344 2.8 53.2 0.5
CD c:GLU354 2.9 47.5 0.5
CD c:GLU354 2.9 47.5 0.5
C a:ALA344 3.0 53.0 0.5
CG a:ASP342 3.0 49.0 0.5
OE2 c:GLU354 3.1 47.0 0.5
OE2 c:GLU354 3.1 49.0 0.5
O a:ALA344 3.1 52.0 0.5
CG a:ASP342 3.1 48.9 0.5
OD2 a:ASP342 3.2 51.7 0.5
O a:ALA344 3.2 51.9 0.5
CA1 a:OEY401 3.3 52.5 0.5
OD2 a:ASP342 3.3 51.7 0.5
CA1 a:OEX413 3.3 52.3 0.5
O5 a:OEY401 3.4 51.0 0.5
O6 a:OEY401 3.5 59.5 0.5
O5 a:OEX413 3.5 51.1 0.5
NE2 a:HIS337 3.9 47.6 0.5
NE2 a:HIS337 4.0 47.5 0.5
OE2 a:GLU189 4.0 54.7 0.5
OE1 a:GLU333 4.1 45.5 0.5
O4 a:OEX413 4.2 49.9 0.5
OE1 a:GLU333 4.2 45.6 0.5
OE2 a:GLU189 4.2 53.4 0.5
CA a:ALA344 4.2 52.9 0.5
O c:HOH737 4.2 53.0 0.5
O4 a:OEY401 4.2 50.8 0.5
CA a:ALA344 4.3 53.0 0.5
NE2 a:HIS332 4.3 48.1 0.5
O c:HOH737 4.3 52.9 0.5
CG c:GLU354 4.3 52.8 0.5
CG c:GLU354 4.4 52.8 0.5
CD2 a:HIS337 4.4 47.9 0.5
O a:HOH610 4.4 69.8 0.5
N a:ALA344 4.4 59.7 0.5
NE2 a:HIS332 4.4 48.6 0.5
CB a:ASP342 4.4 45.0 0.5
N a:ALA344 4.5 59.8 0.5
O a:HOH610 4.5 70.1 0.5
NH2 c:ARG357 4.5 46.5 0.5
CD2 a:HIS337 4.5 48.2 0.5
CB a:ASP342 4.5 45.0 0.5
NH2 c:ARG357 4.6 46.5 0.5
NH1 c:ARG357 4.6 50.7 0.5
OD1 a:ASP170 4.6 48.0 0.5
OD1 a:ASP170 4.7 48.0 0.5
NH1 c:ARG357 4.7 50.5 0.5
CD a:GLU189 4.8 50.1 0.5
OE1 a:GLU189 4.8 48.9 0.5
CB c:GLU354 4.9 50.8 0.5
CB c:GLU354 4.9 50.8 0.5
OE1 a:GLU189 4.9 49.4 0.5
CA a:ASP342 4.9 48.8 0.5
O a:HOH519 4.9 54.7 0.5
C a:ASP342 4.9 53.6 0.5
CZ c:ARG357 4.9 49.6 0.5
CZ c:ARG357 4.9 49.7 0.5
CA a:ASP342 5.0 48.9 0.5
CD a:GLU189 5.0 49.1 0.5

Reference:

H.Li, Y.Nakajima, E.Nango, S.Owada, D.Yamada, K.Hashimoto, F.Luo, R.Tanaka, F.Akita, K.Kato, J.M.Kang, Y.Saitoh, S.Kishi, H.Yu, N.Matsubara, H.Fujii, M.Sugahara, M.Suzuki, T.Masuda, T.Kimura, T.N.Thao, S.Yonekura, L.J.Yu, T.Tosha, K.Tono, Y.Joti, T.Hatsui, M.Yabashi, M.Kubo, S.Iwata, H.Isobe, K.Yamaguchi, M.Suga, J.R.Shen. Oxygen-Evolving Photosystem II Structures During S1-S2-S3 Transitions. Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-06987-5
Page generated: Sun Oct 6 13:20:46 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy