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Manganese in PDB 8irb: Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay

Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay

All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay:
1.10.3.9;

Protein crystallography data

The structure of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay, PDB code: 8irb 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) 19.98 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.75, 231.6, 288.28, 90, 90, 90
R / Rfree (%) 14 / 17.7

Other elements in 8irb:

The structure of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms
Magnesium (Mg) 80 atoms
Calcium (Ca) 11 atoms
Iron (Fe) 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 One Flash (1F) with A 5-Millisecond Delay (pdb code 8irb). 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 One Flash (1F) with A 5-Millisecond Delay, PDB code: 8irb:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in 8irb

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Manganese binding site 1 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) 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 One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:41.0
occ:0.40
 MN1 A:OEX413 0.0 41.0 0.4
MN1 A:OEX413 0.1 45.3 0.6
O1 A:OEX413 1.7 43.1 0.6
O1 A:OEX413 1.8 42.8 0.4
OE2 A:GLU189 1.8 44.6 0.4
OE2 A:GLU189 1.8 45.1 0.6
O3 A:OEX413 1.8 46.4 0.6
O3 A:OEX413 1.9 47.3 0.4
OD2 A:ASP342 2.1 40.8 0.6
NE2 A:HIS332 2.1 45.6 0.4
NE2 A:HIS332 2.1 47.3 0.6
OD2 A:ASP342 2.2 39.9 0.4
O5 A:OEX413 2.6 47.2 0.6
O5 A:OEX413 2.6 46.9 0.4
MN2 A:OEX413 2.7 47.8 0.6
MN2 A:OEX413 2.8 44.6 0.4
CD A:GLU189 2.9 47.9 0.4
CD A:GLU189 3.0 47.9 0.6
CE1 A:HIS332 3.0 42.9 0.4
CD2 A:HIS332 3.0 43.5 0.6
CG A:ASP342 3.1 45.2 0.6
CG A:ASP342 3.1 45.0 0.4
CD2 A:HIS332 3.1 43.3 0.4
MN3 A:OEX413 3.1 47.0 0.6
CE1 A:HIS332 3.2 43.1 0.6
MN3 A:OEX413 3.2 45.8 0.4
OD1 A:ASP342 3.3 41.8 0.4
OD1 A:ASP342 3.3 42.0 0.6
O2 A:OEX413 3.4 43.6 0.6
CA1 A:OEX413 3.4 52.6 0.6
CA1 A:OEX413 3.5 47.1 0.4
OE1 A:GLU189 3.5 47.9 0.4
O2 A:OEX413 3.5 43.4 0.4
OE1 A:GLU189 3.6 52.5 0.6
OE1 A:GLU333 3.8 44.4 0.6
OE1 A:GLU333 3.9 44.6 0.4
NE2 A:HIS337 3.9 43.9 0.6
NE2 A:HIS337 4.0 44.0 0.4
CG A:GLU189 4.1 45.7 0.4
O A:HOH587 4.1 42.4 0.4
ND1 A:HIS332 4.1 41.4 0.4
CG A:GLU189 4.2 45.0 0.6
CG A:HIS332 4.2 44.5 0.6
CG A:HIS332 4.2 44.4 0.4
ND1 A:HIS332 4.2 41.5 0.6
OXT A:ALA344 4.3 47.5 0.6
OE1 C:GLU354 4.3 52.4 0.6
OXT A:ALA344 4.4 47.3 0.4
CB A:ASP342 4.4 43.3 0.6
CB A:ASP342 4.4 43.2 0.4
OE1 C:GLU354 4.5 51.2 0.4
OE2 C:GLU354 4.5 48.4 0.6
OE2 C:GLU354 4.5 46.8 0.4
CD A:GLU333 4.5 43.8 0.6
CE1 A:HIS337 4.6 45.2 0.6
CG1 A:VAL185 4.6 41.7 0.6
CG1 A:VAL185 4.6 41.6 0.4
CE1 A:HIS337 4.6 45.2 0.4
O A:ALA344 4.6 53.4 0.6
CD A:GLU333 4.7 43.7 0.4
O A:HOH620 4.7 48.8 0.4
O A:HOH587 4.7 60.5 0.6
O A:ALA344 4.7 51.6 0.4
O A:HOH620 4.8 49.5 0.6
C A:ALA344 4.8 42.6 0.6
O4 A:OEX413 4.8 41.4 0.6
MN4 A:OEX413 4.8 51.5 0.6
CD C:GLU354 4.9 54.4 0.6
MN4 A:OEX413 4.9 46.0 0.4
OE2 A:GLU333 4.9 48.4 0.6
C A:ALA344 4.9 42.5 0.4
CD C:GLU354 4.9 53.9 0.4
O4 A:OEX413 5.0 41.9 0.4
OE2 A:GLU333 5.0 47.1 0.4

Manganese binding site 2 out of 16 in 8irb

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Manganese binding site 2 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) 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 One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:45.3
occ:0.60
 MN1 A:OEX413 0.0 45.3 0.6
MN1 A:OEX413 0.1 41.0 0.4
OE2 A:GLU189 1.7 44.6 0.4
O1 A:OEX413 1.8 43.1 0.6
OE2 A:GLU189 1.8 45.1 0.6
O1 A:OEX413 1.8 42.8 0.4
O3 A:OEX413 1.9 46.4 0.6
O3 A:OEX413 2.0 47.3 0.4
NE2 A:HIS332 2.0 45.6 0.4
OD2 A:ASP342 2.0 40.8 0.6
NE2 A:HIS332 2.1 47.3 0.6
OD2 A:ASP342 2.1 39.9 0.4
O5 A:OEX413 2.7 47.2 0.6
O5 A:OEX413 2.7 46.9 0.4
MN2 A:OEX413 2.8 47.8 0.6
MN2 A:OEX413 2.9 44.6 0.4
CD A:GLU189 2.9 47.9 0.4
CE1 A:HIS332 2.9 42.9 0.4
CD A:GLU189 3.0 47.9 0.6
CD2 A:HIS332 3.0 43.5 0.6
CG A:ASP342 3.0 45.2 0.6
CG A:ASP342 3.0 45.0 0.4
CD2 A:HIS332 3.1 43.3 0.4
CE1 A:HIS332 3.1 43.1 0.6
MN3 A:OEX413 3.2 47.0 0.6
MN3 A:OEX413 3.3 45.8 0.4
OD1 A:ASP342 3.3 41.8 0.4
OD1 A:ASP342 3.3 42.0 0.6
O2 A:OEX413 3.5 43.6 0.6
CA1 A:OEX413 3.5 52.6 0.6
OE1 A:GLU189 3.5 47.9 0.4
CA1 A:OEX413 3.6 47.1 0.4
O2 A:OEX413 3.6 43.4 0.4
OE1 A:GLU189 3.6 52.5 0.6
OE1 A:GLU333 3.9 44.4 0.6
OE1 A:GLU333 3.9 44.6 0.4
NE2 A:HIS337 3.9 43.9 0.6
NE2 A:HIS337 3.9 44.0 0.4
CG A:GLU189 4.0 45.7 0.4
ND1 A:HIS332 4.1 41.4 0.4
O A:HOH587 4.1 42.4 0.4
CG A:GLU189 4.1 45.0 0.6
CG A:HIS332 4.1 44.5 0.6
ND1 A:HIS332 4.1 41.5 0.6
CG A:HIS332 4.2 44.4 0.4
OXT A:ALA344 4.3 47.5 0.6
CB A:ASP342 4.4 43.3 0.6
OE1 C:GLU354 4.4 52.4 0.6
CB A:ASP342 4.4 43.2 0.4
OXT A:ALA344 4.4 47.3 0.4
OE1 C:GLU354 4.5 51.2 0.4
CE1 A:HIS337 4.5 45.2 0.6
OE2 C:GLU354 4.5 48.4 0.6
CE1 A:HIS337 4.5 45.2 0.4
CG1 A:VAL185 4.6 41.7 0.6
OE2 C:GLU354 4.6 46.8 0.4
CG1 A:VAL185 4.6 41.6 0.4
CD A:GLU333 4.6 43.8 0.6
O A:HOH587 4.7 60.5 0.6
O A:ALA344 4.7 53.4 0.6
CD A:GLU333 4.7 43.7 0.4
O A:HOH620 4.7 48.8 0.4
O A:ALA344 4.8 51.6 0.4
O A:HOH620 4.8 49.5 0.6
C A:ALA344 4.9 42.6 0.6
O4 A:OEX413 4.9 41.4 0.6
OE2 A:GLU333 4.9 48.4 0.6
CD C:GLU354 4.9 54.4 0.6
MN4 A:OEX413 4.9 51.5 0.6
MN4 A:OEX413 4.9 46.0 0.4
C A:ALA344 5.0 42.5 0.4
CD C:GLU354 5.0 53.9 0.4

Manganese binding site 3 out of 16 in 8irb

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Manganese binding site 3 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) 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 One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:44.6
occ:0.40
 MN2 A:OEX413 0.0 44.6 0.4
MN2 A:OEX413 0.1 47.8 0.6
OXT A:ALA344 1.8 47.5 0.6
O1 A:OEX413 1.8 42.8 0.4
O2 A:OEX413 1.8 43.6 0.6
O1 A:OEX413 1.9 43.1 0.6
O2 A:OEX413 1.9 43.4 0.4
OXT A:ALA344 1.9 47.3 0.4
O3 A:OEX413 1.9 47.3 0.4
O3 A:OEX413 2.0 46.4 0.6
OE1 C:GLU354 2.1 52.4 0.6
OD1 A:ASP342 2.1 41.8 0.4
OE1 C:GLU354 2.1 51.2 0.4
OD1 A:ASP342 2.1 42.0 0.6
C A:ALA344 2.8 42.6 0.6
MN3 A:OEX413 2.8 47.0 0.6
CD C:GLU354 2.8 54.4 0.6
MN3 A:OEX413 2.8 45.8 0.4
MN1 A:OEX413 2.8 41.0 0.4
C A:ALA344 2.8 42.5 0.4
CD C:GLU354 2.9 53.9 0.4
MN1 A:OEX413 2.9 45.3 0.6
CG A:ASP342 3.0 45.2 0.6
OE2 C:GLU354 3.0 48.4 0.6
CG A:ASP342 3.0 45.0 0.4
O A:ALA344 3.1 53.4 0.6
OE2 C:GLU354 3.1 46.8 0.4
O A:ALA344 3.1 51.6 0.4
OD2 A:ASP342 3.2 40.8 0.6
OD2 A:ASP342 3.3 39.9 0.4
CA1 A:OEX413 3.4 47.1 0.4
CA1 A:OEX413 3.4 52.6 0.6
O5 A:OEX413 3.5 46.9 0.4
O5 A:OEX413 3.6 47.2 0.6
NE2 A:HIS337 3.9 44.0 0.4
NE2 A:HIS337 3.9 43.9 0.6
O C:HOH738 4.0 48.5 0.4
O C:HOH738 4.1 49.0 0.6
O A:HOH587 4.1 42.4 0.4
CA A:ALA344 4.1 48.7 0.6
CG C:GLU354 4.1 51.6 0.6
OE2 A:GLU189 4.1 45.1 0.6
OE2 A:GLU189 4.2 44.6 0.4
CA A:ALA344 4.2 48.8 0.4
O4 A:OEX413 4.2 41.4 0.6
CG C:GLU354 4.2 51.0 0.4
N A:ALA344 4.2 53.3 0.6
N A:ALA344 4.3 52.9 0.4
O4 A:OEX413 4.3 41.9 0.4
OE1 A:GLU333 4.3 44.4 0.6
OE1 A:GLU333 4.4 44.6 0.4
CD2 A:HIS337 4.4 47.6 0.6
CD2 A:HIS337 4.4 47.6 0.4
CB A:ASP342 4.4 43.3 0.6
CB A:ASP342 4.4 43.2 0.4
NH2 C:ARG357 4.5 43.3 0.6
NH2 C:ARG357 4.6 43.7 0.4
NE2 A:HIS332 4.6 45.6 0.4
O A:HOH587 4.6 60.5 0.6
NE2 A:HIS332 4.6 47.3 0.6
OD1 A:ASP170 4.7 48.9 0.6
NH1 C:ARG357 4.8 42.3 0.6
NH1 C:ARG357 4.8 42.5 0.4
C A:ASP342 4.8 48.3 0.6
CA A:ASP342 4.8 42.6 0.6
CA A:ASP342 4.8 42.6 0.4
CB C:GLU354 4.8 41.1 0.6
CB C:GLU354 4.9 41.1 0.4
OD1 A:ASP170 4.9 44.8 0.4
O A:ASP342 4.9 52.2 0.6
C A:ASP342 4.9 48.2 0.4
CD A:GLU189 4.9 47.9 0.4
CZ C:ARG357 4.9 54.0 0.6
CD A:GLU189 4.9 47.9 0.6
CZ C:ARG357 4.9 53.8 0.4

Manganese binding site 4 out of 16 in 8irb

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Manganese binding site 4 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) 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 One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:47.8
occ:0.60
 MN2 A:OEX413 0.0 47.8 0.6
MN2 A:OEX413 0.1 44.6 0.4
O1 A:OEX413 1.8 42.8 0.4
O1 A:OEX413 1.8 43.1 0.6
OXT A:ALA344 1.9 47.5 0.6
O2 A:OEX413 1.9 43.6 0.6
O3 A:OEX413 1.9 47.3 0.4
O3 A:OEX413 1.9 46.4 0.6
O2 A:OEX413 1.9 43.4 0.4
OXT A:ALA344 1.9 47.3 0.4
OD1 A:ASP342 2.1 41.8 0.4
OD1 A:ASP342 2.1 42.0 0.6
OE1 C:GLU354 2.1 52.4 0.6
OE1 C:GLU354 2.1 51.2 0.4
MN1 A:OEX413 2.7 41.0 0.4
MN3 A:OEX413 2.8 47.0 0.6
MN3 A:OEX413 2.8 45.8 0.4
C A:ALA344 2.8 42.6 0.6
CD C:GLU354 2.8 54.4 0.6
MN1 A:OEX413 2.8 45.3 0.6
C A:ALA344 2.9 42.5 0.4
CD C:GLU354 2.9 53.9 0.4
CG A:ASP342 2.9 45.2 0.6
CG A:ASP342 3.0 45.0 0.4
OE2 C:GLU354 3.0 48.4 0.6
OE2 C:GLU354 3.1 46.8 0.4
O A:ALA344 3.1 53.4 0.6
OD2 A:ASP342 3.1 40.8 0.6
O A:ALA344 3.2 51.6 0.4
OD2 A:ASP342 3.2 39.9 0.4
CA1 A:OEX413 3.4 47.1 0.4
CA1 A:OEX413 3.4 52.6 0.6
O5 A:OEX413 3.5 46.9 0.4
O5 A:OEX413 3.5 47.2 0.6
NE2 A:HIS337 3.8 44.0 0.4
NE2 A:HIS337 3.8 43.9 0.6
O C:HOH738 4.0 48.5 0.4
O A:HOH587 4.1 42.4 0.4
OE2 A:GLU189 4.1 45.1 0.6
O C:HOH738 4.1 49.0 0.6
OE2 A:GLU189 4.1 44.6 0.4
CA A:ALA344 4.1 48.7 0.6
CG C:GLU354 4.2 51.6 0.6
O4 A:OEX413 4.2 41.4 0.6
CA A:ALA344 4.2 48.8 0.4
CG C:GLU354 4.3 51.0 0.4
N A:ALA344 4.3 53.3 0.6
N A:ALA344 4.3 52.9 0.4
O4 A:OEX413 4.3 41.9 0.4
OE1 A:GLU333 4.3 44.4 0.6
OE1 A:GLU333 4.3 44.6 0.4
CB A:ASP342 4.3 43.3 0.6
CD2 A:HIS337 4.4 47.6 0.6
CD2 A:HIS337 4.4 47.6 0.4
CB A:ASP342 4.4 43.2 0.4
NE2 A:HIS332 4.5 45.6 0.4
NH2 C:ARG357 4.5 43.3 0.6
NE2 A:HIS332 4.6 47.3 0.6
O A:HOH587 4.6 60.5 0.6
NH2 C:ARG357 4.6 43.7 0.4
OD1 A:ASP170 4.7 48.9 0.6
CA A:ASP342 4.8 42.6 0.6
C A:ASP342 4.8 48.3 0.6
CA A:ASP342 4.8 42.6 0.4
NH1 C:ARG357 4.8 42.3 0.6
O A:ASP342 4.8 52.2 0.6
NH1 C:ARG357 4.8 42.5 0.4
CD A:GLU189 4.8 47.9 0.4
CB C:GLU354 4.8 41.1 0.6
CD A:GLU189 4.9 47.9 0.6
C A:ASP342 4.9 48.2 0.4
OD1 A:ASP170 4.9 44.8 0.4
CB C:GLU354 4.9 41.1 0.4
OE1 A:GLU189 5.0 52.5 0.6
OE1 A:GLU189 5.0 47.9 0.4
CZ C:ARG357 5.0 54.0 0.6
CE1 A:HIS337 5.0 45.2 0.4
CE1 A:HIS337 5.0 45.2 0.6

Manganese binding site 5 out of 16 in 8irb

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Manganese binding site 5 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) 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 One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:45.8
occ:0.40
 MN3 A:OEX413 0.0 45.8 0.4
MN3 A:OEX413 0.1 47.0 0.6
O2 A:OEX413 1.8 43.6 0.6
O2 A:OEX413 1.8 43.4 0.4
O4 A:OEX413 1.8 41.4 0.6
OE2 C:GLU354 1.9 48.4 0.6
O4 A:OEX413 1.9 41.9 0.4
O5 A:OEX413 2.0 46.9 0.4
OE1 A:GLU333 2.0 44.6 0.4
OE1 A:GLU333 2.0 44.4 0.6
O5 A:OEX413 2.0 47.2 0.6
OE2 C:GLU354 2.0 46.8 0.4
O3 A:OEX413 2.1 47.3 0.4
O3 A:OEX413 2.1 46.4 0.6
MN4 A:OEX413 2.8 46.0 0.4
MN4 A:OEX413 2.8 51.5 0.6
MN2 A:OEX413 2.8 47.8 0.6
MN2 A:OEX413 2.8 44.6 0.4
CD A:GLU333 2.9 43.8 0.6
CD A:GLU333 2.9 43.7 0.4
CD C:GLU354 2.9 54.4 0.6
CD C:GLU354 3.0 53.9 0.4
OE2 A:GLU333 3.1 48.4 0.6
OE2 A:GLU333 3.1 47.1 0.4
MN1 A:OEX413 3.2 41.0 0.4
MN1 A:OEX413 3.3 45.3 0.6
OE1 C:GLU354 3.3 52.4 0.6
OE1 C:GLU354 3.3 51.2 0.4
O1 A:OEX413 3.4 42.8 0.4
O1 A:OEX413 3.5 43.1 0.6
CA1 A:OEX413 3.5 47.1 0.4
CA1 A:OEX413 3.6 52.6 0.6
NH2 C:ARG357 3.9 43.3 0.6
OD1 A:ASP170 3.9 48.9 0.6
NH2 C:ARG357 3.9 43.7 0.4
OD2 A:ASP170 4.0 40.7 0.6
NE2 A:HIS337 4.1 44.0 0.4
OD2 A:ASP170 4.1 41.9 0.4
NE2 A:HIS337 4.1 43.9 0.6
O C:HOH688 4.1 36.1 0.4
NE2 A:HIS332 4.2 45.6 0.4
O A:HOH514 4.2 50.3 0.6
CG C:GLU354 4.2 51.6 0.6
OD1 A:ASP170 4.2 44.8 0.4
CG C:GLU354 4.2 51.0 0.4
O A:HOH514 4.3 43.5 0.4
CG A:GLU333 4.3 45.2 0.6
OXT A:ALA344 4.3 47.5 0.6
CG A:GLU333 4.3 44.9 0.4
NE2 A:HIS332 4.3 47.3 0.6
CG A:ASP170 4.4 44.8 0.6
OXT A:ALA344 4.4 47.3 0.4
O A:HOH544 4.4 43.2 0.4
CD2 A:HIS332 4.5 43.3 0.4
O A:HOH549 4.5 43.5 0.6
O A:HOH544 4.5 45.3 0.6
CD2 A:HIS332 4.5 43.5 0.6
OD1 A:ASP342 4.5 42.0 0.6
OD1 A:ASP342 4.5 41.8 0.4
O A:HOH549 4.6 43.1 0.4
CG A:ASP170 4.6 42.8 0.4
O A:ALA344 4.6 51.6 0.4
O A:ALA344 4.6 53.4 0.6
OE2 A:GLU189 4.6 44.6 0.4
OD2 A:ASP342 4.7 40.8 0.6
CB A:GLU333 4.7 44.3 0.6
CB A:GLU333 4.7 44.3 0.4
OE2 A:GLU189 4.7 45.1 0.6
OD2 A:ASP342 4.8 39.9 0.4
CE1 A:HIS337 4.8 45.2 0.4
O A:HOH620 4.8 48.8 0.4
O A:HOH620 4.8 49.5 0.6
CE1 A:HIS337 4.8 45.2 0.6
C A:ALA344 4.9 42.6 0.6
CZ C:ARG357 4.9 53.8 0.4
CZ C:ARG357 5.0 54.0 0.6
C A:ALA344 5.0 42.5 0.4

Manganese binding site 6 out of 16 in 8irb

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Manganese binding site 6 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) 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 One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:47.0
occ:0.60
 MN3 A:OEX413 0.0 47.0 0.6
MN3 A:OEX413 0.1 45.8 0.4
O2 A:OEX413 1.8 43.6 0.6
O2 A:OEX413 1.9 43.4 0.4
O4 A:OEX413 1.9 41.4 0.6
O5 A:OEX413 1.9 46.9 0.4
OE2 C:GLU354 1.9 48.4 0.6
OE1 A:GLU333 1.9 44.6 0.4
OE1 A:GLU333 1.9 44.4 0.6
O5 A:OEX413 2.0 47.2 0.6
O3 A:OEX413 2.0 47.3 0.4
O3 A:OEX413 2.0 46.4 0.6
O4 A:OEX413 2.0 41.9 0.4
OE2 C:GLU354 2.1 46.8 0.4
MN2 A:OEX413 2.8 47.8 0.6
MN2 A:OEX413 2.8 44.6 0.4
MN4 A:OEX413 2.8 51.5 0.6
MN4 A:OEX413 2.8 46.0 0.4
CD A:GLU333 2.8 43.8 0.6
CD A:GLU333 2.9 43.7 0.4
CD C:GLU354 2.9 54.4 0.6
CD C:GLU354 3.0 53.9 0.4
OE2 A:GLU333 3.1 48.4 0.6
MN1 A:OEX413 3.1 41.0 0.4
OE2 A:GLU333 3.1 47.1 0.4
MN1 A:OEX413 3.2 45.3 0.6
OE1 C:GLU354 3.3 52.4 0.6
OE1 C:GLU354 3.4 51.2 0.4
O1 A:OEX413 3.4 42.8 0.4
O1 A:OEX413 3.4 43.1 0.6
CA1 A:OEX413 3.5 47.1 0.4
CA1 A:OEX413 3.6 52.6 0.6
OD1 A:ASP170 3.9 48.9 0.6
NH2 C:ARG357 3.9 43.3 0.6
NH2 C:ARG357 4.0 43.7 0.4
OD2 A:ASP170 4.0 40.7 0.6
NE2 A:HIS332 4.1 45.6 0.4
NE2 A:HIS337 4.1 44.0 0.4
NE2 A:HIS337 4.1 43.9 0.6
OD2 A:ASP170 4.2 41.9 0.4
O C:HOH688 4.2 36.1 0.4
OD1 A:ASP170 4.2 44.8 0.4
O A:HOH514 4.2 50.3 0.6
NE2 A:HIS332 4.2 47.3 0.6
CG C:GLU354 4.2 51.6 0.6
CG A:GLU333 4.2 45.2 0.6
CG A:GLU333 4.3 44.9 0.4
OXT A:ALA344 4.3 47.5 0.6
CG C:GLU354 4.3 51.0 0.4
O A:HOH514 4.3 43.5 0.4
OXT A:ALA344 4.4 47.3 0.4
CD2 A:HIS332 4.4 43.3 0.4
CG A:ASP170 4.4 44.8 0.6
CD2 A:HIS332 4.4 43.5 0.6
O A:HOH544 4.4 43.2 0.4
OD1 A:ASP342 4.5 42.0 0.6
OD1 A:ASP342 4.5 41.8 0.4
O A:HOH544 4.5 45.3 0.6
O A:HOH549 4.5 43.5 0.6
OE2 A:GLU189 4.6 44.6 0.4
OD2 A:ASP342 4.6 40.8 0.6
O A:HOH549 4.6 43.1 0.4
O A:ALA344 4.6 51.6 0.4
OE2 A:GLU189 4.6 45.1 0.6
O A:ALA344 4.6 53.4 0.6
CG A:ASP170 4.6 42.8 0.4
CB A:GLU333 4.7 44.3 0.6
CB A:GLU333 4.7 44.3 0.4
OD2 A:ASP342 4.7 39.9 0.4
CE1 A:HIS337 4.7 45.2 0.4
CE1 A:HIS337 4.8 45.2 0.6
O A:HOH620 4.8 48.8 0.4
O A:HOH620 4.8 49.5 0.6
C A:ALA344 4.9 42.6 0.6
C A:ALA344 5.0 42.5 0.4
CG A:ASP342 5.0 45.2 0.6

Manganese binding site 7 out of 16 in 8irb

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Manganese binding site 7 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) 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 One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:46.0
occ:0.40
 MN4 A:OEX413 0.0 46.0 0.4
MN4 A:OEX413 0.2 51.5 0.6
OD2 A:ASP170 1.7 40.7 0.6
O4 A:OEX413 1.8 41.4 0.6
O4 A:OEX413 1.9 41.9 0.4
OE2 A:GLU333 2.0 48.4 0.6
OD2 A:ASP170 2.0 41.9 0.4
OE2 A:GLU333 2.1 47.1 0.4
O A:HOH544 2.1 43.2 0.4
O A:HOH544 2.1 45.3 0.6
O A:HOH549 2.2 43.5 0.6
O A:HOH549 2.3 43.1 0.4
O5 A:OEX413 2.3 46.9 0.4
O5 A:OEX413 2.3 47.2 0.6
MN3 A:OEX413 2.8 45.8 0.4
MN3 A:OEX413 2.8 47.0 0.6
CG A:ASP170 2.8 44.8 0.6
CD A:GLU333 2.9 43.8 0.6
CD A:GLU333 3.0 43.7 0.4
CG A:ASP170 3.1 42.8 0.4
OD1 A:ASP170 3.2 48.9 0.6
OE1 A:GLU333 3.2 44.6 0.4
OE1 A:GLU333 3.2 44.4 0.6
OD1 A:ASP170 3.5 44.8 0.4
O A:HOH620 3.6 49.5 0.6
O2 A:OEX413 3.6 43.6 0.6
O A:HOH620 3.7 48.8 0.4
O2 A:OEX413 3.7 43.4 0.4
O A:HOH514 3.8 43.5 0.4
CA1 A:OEX413 3.8 47.1 0.4
O A:HOH514 3.9 50.3 0.6
CA1 A:OEX413 3.9 52.6 0.6
OD1 A:ASP61 4.1 46.2 0.6
CB A:ASP170 4.1 40.6 0.6
O A:HOH565 4.1 44.5 0.4
O A:HOH625 4.1 50.5 0.6
O A:HOH625 4.2 49.5 0.4
OD1 A:ASP61 4.2 45.9 0.4
O A:SER169 4.2 47.7 0.6
OE2 C:GLU354 4.3 48.4 0.6
CG A:GLU333 4.3 45.2 0.6
O A:HOH565 4.3 46.1 0.6
CA A:ASP170 4.3 50.5 0.6
CG A:GLU333 4.4 44.9 0.4
CB A:ASP170 4.4 41.8 0.4
OE2 C:GLU354 4.4 46.8 0.4
NH2 C:ARG357 4.4 43.7 0.4
O A:SER169 4.5 46.3 0.4
NH2 C:ARG357 4.5 43.3 0.6
CA A:ASP170 4.6 49.2 0.4
O3 A:OEX413 4.6 46.4 0.6
O3 A:OEX413 4.6 47.3 0.4
C A:SER169 4.8 49.6 0.6
N A:ASP170 4.8 45.3 0.6
MN1 A:OEX413 4.9 41.0 0.4
O D:HOH512 4.9 45.2 0.4
CG A:ASP61 4.9 49.7 0.6
MN1 A:OEX413 4.9 45.3 0.6
O D:HOH512 5.0 45.2 0.6
OG A:SER169 5.0 46.2 0.6
C A:SER169 5.0 49.1 0.4

Manganese binding site 8 out of 16 in 8irb

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Manganese binding site 8 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) 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 One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn413

b:51.5
occ:0.60
 MN4 A:OEX413 0.0 51.5 0.6
MN4 A:OEX413 0.2 46.0 0.4
OE2 A:GLU333 1.8 48.4 0.6
OE2 A:GLU333 1.9 47.1 0.4
O4 A:OEX413 1.9 41.4 0.6
OD2 A:ASP170 1.9 40.7 0.6
O4 A:OEX413 1.9 41.9 0.4
O A:HOH544 2.0 45.3 0.6
O A:HOH544 2.0 43.2 0.4
O A:HOH549 2.1 43.5 0.6
OD2 A:ASP170 2.2 41.9 0.4
O A:HOH549 2.2 43.1 0.4
O5 A:OEX413 2.3 46.9 0.4
O5 A:OEX413 2.3 47.2 0.6
MN3 A:OEX413 2.8 45.8 0.4
CD A:GLU333 2.8 43.8 0.6
MN3 A:OEX413 2.8 47.0 0.6
CD A:GLU333 2.8 43.7 0.4
CG A:ASP170 3.0 44.8 0.6
OE1 A:GLU333 3.1 44.6 0.4
OE1 A:GLU333 3.1 44.4 0.6
CG A:ASP170 3.3 42.8 0.4
OD1 A:ASP170 3.4 48.9 0.6
O A:HOH620 3.7 49.5 0.6
OD1 A:ASP170 3.7 44.8 0.4
O2 A:OEX413 3.7 43.6 0.6
O A:HOH620 3.8 48.8 0.4
O2 A:OEX413 3.8 43.4 0.4
O A:HOH514 3.8 43.5 0.4
O A:HOH514 3.9 50.3 0.6
CA1 A:OEX413 3.9 47.1 0.4
OD1 A:ASP61 4.0 46.2 0.6
O A:HOH565 4.0 44.5 0.4
CA1 A:OEX413 4.1 52.6 0.6
CG A:GLU333 4.1 45.2 0.6
OD1 A:ASP61 4.1 45.9 0.4
CG A:GLU333 4.2 44.9 0.4
O A:HOH625 4.2 50.5 0.6
O A:HOH565 4.2 46.1 0.6
OE2 C:GLU354 4.3 48.4 0.6
O A:HOH625 4.3 49.5 0.4
CB A:ASP170 4.3 40.6 0.6
O A:SER169 4.3 47.7 0.6
OE2 C:GLU354 4.4 46.8 0.4
CA A:ASP170 4.5 50.5 0.6
O A:SER169 4.5 46.3 0.4
O3 A:OEX413 4.5 46.4 0.6
NH2 C:ARG357 4.6 43.7 0.4
O3 A:OEX413 4.6 47.3 0.4
CB A:ASP170 4.6 41.8 0.4
NH2 C:ARG357 4.6 43.3 0.6
CA A:ASP170 4.7 49.2 0.4
O D:HOH512 4.7 45.2 0.4
CG A:ASP61 4.8 49.7 0.6
O D:HOH512 4.8 45.2 0.6
MN1 A:OEX413 4.8 41.0 0.4
C A:SER169 4.9 49.6 0.6
N A:ASP170 4.9 45.3 0.6
MN1 A:OEX413 4.9 45.3 0.6

Manganese binding site 9 out of 16 in 8irb

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Manganese binding site 9 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) 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 One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn412

b:48.4
occ:0.40
 MN1 a:OEX412 0.0 48.4 0.4
MN1 a:OEX412 0.1 48.4 0.6
O1 a:OEX412 1.7 47.3 0.6
OE2 a:GLU189 1.8 51.3 0.4
O1 a:OEX412 1.8 47.1 0.4
O3 a:OEX412 1.8 45.1 0.6
OE2 a:GLU189 1.8 51.6 0.6
O3 a:OEX412 1.9 45.1 0.4
OD2 a:ASP342 2.1 51.8 0.6
NE2 a:HIS332 2.1 50.2 0.4
OD2 a:ASP342 2.1 51.4 0.4
NE2 a:HIS332 2.2 50.4 0.6
O5 a:OEX412 2.6 50.8 0.6
O5 a:OEX412 2.6 50.8 0.4
MN2 a:OEX412 2.7 50.2 0.6
MN2 a:OEX412 2.8 50.2 0.4
CD a:GLU189 2.9 50.1 0.4
CE1 a:HIS332 2.9 51.6 0.4
CD a:GLU189 2.9 50.2 0.6
CG a:ASP342 2.9 50.6 0.6
CE1 a:HIS332 3.0 52.0 0.6
CG a:ASP342 3.1 50.4 0.4
OD1 a:ASP342 3.1 52.8 0.6
CD2 a:HIS332 3.2 50.4 0.4
CD2 a:HIS332 3.2 50.5 0.6
MN3 a:OEX412 3.3 50.1 0.6
OD1 a:ASP342 3.3 52.9 0.4
MN3 a:OEX412 3.3 47.8 0.4
O2 a:OEX412 3.3 46.0 0.6
OE1 a:GLU189 3.4 51.1 0.4
OE1 a:GLU189 3.4 57.9 0.6
CA1 a:OEX412 3.4 58.0 0.6
CA1 a:OEX412 3.5 53.1 0.4
O2 a:OEX412 3.6 43.9 0.4
OE1 a:GLU333 3.7 51.4 0.6
OE1 a:GLU333 3.9 49.6 0.4
NE2 a:HIS337 4.0 52.2 0.4
NE2 a:HIS337 4.0 52.8 0.6
ND1 a:HIS332 4.1 46.6 0.4
CG a:GLU189 4.1 54.1 0.4
O a:HOH591 4.1 47.5 0.4
ND1 a:HIS332 4.2 46.5 0.6
CG a:GLU189 4.2 54.1 0.6
CG a:HIS332 4.2 49.9 0.4
OXT a:ALA344 4.3 55.4 0.6
CG a:HIS332 4.3 50.0 0.6
OXT a:ALA344 4.3 54.5 0.4
CB a:ASP342 4.3 47.1 0.6
CB a:ASP342 4.4 48.1 0.4
OE1 c:GLU354 4.5 50.8 0.4
OE1 c:GLU354 4.5 50.8 0.6
O a:HOH591 4.6 61.2 0.6
OE2 c:GLU354 4.6 50.6 0.6
CD a:GLU333 4.6 49.8 0.6
CG1 a:VAL185 4.6 45.4 0.4
OE2 c:GLU354 4.6 47.5 0.4
CG1 a:VAL185 4.7 45.4 0.6
CD a:GLU333 4.7 49.6 0.4
CE1 a:HIS337 4.7 49.1 0.4
O a:ALA344 4.7 53.8 0.4
O a:ALA344 4.7 53.8 0.6
CE1 a:HIS337 4.8 49.1 0.6
O a:HOH623 4.8 54.2 0.4
MN4 a:OEX412 4.8 44.0 0.4
C a:ALA344 4.8 53.0 0.6
C a:ALA344 4.9 53.0 0.4
O a:HOH623 4.9 55.8 0.6
MN4 a:OEX412 4.9 53.1 0.6
CD c:GLU354 5.0 52.1 0.6
OE2 a:GLU333 5.0 49.4 0.6
CD c:GLU354 5.0 50.9 0.4

Manganese binding site 10 out of 16 in 8irb

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Manganese binding site 10 out of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) 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 One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn412

b:48.4
occ:0.60
 MN1 a:OEX412 0.0 48.4 0.6
MN1 a:OEX412 0.1 48.4 0.4
O1 a:OEX412 1.8 47.3 0.6
OE2 a:GLU189 1.8 51.3 0.4
O3 a:OEX412 1.8 45.1 0.6
OE2 a:GLU189 1.8 51.6 0.6
O3 a:OEX412 1.9 45.1 0.4
O1 a:OEX412 1.9 47.1 0.4
NE2 a:HIS332 2.0 50.2 0.4
OD2 a:ASP342 2.1 51.8 0.6
NE2 a:HIS332 2.1 50.4 0.6
OD2 a:ASP342 2.2 51.4 0.4
O5 a:OEX412 2.6 50.8 0.6
O5 a:OEX412 2.6 50.8 0.4
MN2 a:OEX412 2.8 50.2 0.6
MN2 a:OEX412 2.8 50.2 0.4
CE1 a:HIS332 2.8 51.6 0.4
CD a:GLU189 2.9 50.1 0.4
CE1 a:HIS332 2.9 52.0 0.6
CD a:GLU189 3.0 50.2 0.6
CG a:ASP342 3.0 50.6 0.6
CG a:ASP342 3.1 50.4 0.4
CD2 a:HIS332 3.1 50.4 0.4
CD2 a:HIS332 3.1 50.5 0.6
OD1 a:ASP342 3.2 52.8 0.6
MN3 a:OEX412 3.3 50.1 0.6
MN3 a:OEX412 3.3 47.8 0.4
OD1 a:ASP342 3.3 52.9 0.4
O2 a:OEX412 3.4 46.0 0.6
OE1 a:GLU189 3.4 51.1 0.4
OE1 a:GLU189 3.5 57.9 0.6
CA1 a:OEX412 3.5 58.0 0.6
CA1 a:OEX412 3.6 53.1 0.4
O2 a:OEX412 3.6 43.9 0.4
OE1 a:GLU333 3.7 51.4 0.6
OE1 a:GLU333 3.8 49.6 0.4
NE2 a:HIS337 4.0 52.2 0.4
NE2 a:HIS337 4.0 52.8 0.6
ND1 a:HIS332 4.0 46.6 0.4
ND1 a:HIS332 4.1 46.5 0.6
CG a:GLU189 4.1 54.1 0.4
CG a:HIS332 4.1 49.9 0.4
CG a:HIS332 4.2 50.0 0.6
O a:HOH591 4.2 47.5 0.4
CG a:GLU189 4.2 54.1 0.6
OXT a:ALA344 4.3 55.4 0.6
CB a:ASP342 4.4 47.1 0.6
OXT a:ALA344 4.4 54.5 0.4
CB a:ASP342 4.5 48.1 0.4
OE1 c:GLU354 4.5 50.8 0.4
OE1 c:GLU354 4.5 50.8 0.6
CD a:GLU333 4.6 49.8 0.6
CG1 a:VAL185 4.6 45.4 0.4
OE2 c:GLU354 4.6 50.6 0.6
CG1 a:VAL185 4.6 45.4 0.6
CD a:GLU333 4.6 49.6 0.4
O a:HOH591 4.6 61.2 0.6
CE1 a:HIS337 4.6 49.1 0.4
OE2 c:GLU354 4.7 47.5 0.4
CE1 a:HIS337 4.7 49.1 0.6
O a:ALA344 4.8 53.8 0.4
O a:HOH623 4.8 54.2 0.4
MN4 a:OEX412 4.8 44.0 0.4
O a:ALA344 4.8 53.8 0.6
MN4 a:OEX412 4.9 53.1 0.6
O a:HOH623 4.9 55.8 0.6
C a:ALA344 4.9 53.0 0.6
OE2 a:GLU333 4.9 49.4 0.6
C a:ALA344 5.0 53.0 0.4
CD c:GLU354 5.0 52.1 0.6
CD c:GLU354 5.0 50.9 0.4
CD2 a:HIS337 5.0 49.9 0.6

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 12:37:43 2024

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