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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

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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

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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

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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

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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

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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

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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

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Manganese binding site 7 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


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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

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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

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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

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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

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