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Manganese in PDB 9eh5: Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation

Enzymatic activity of Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation

All present enzymatic activity of Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation:
1.10.3.9;

Other elements in 9eh5:

The structure of Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Calcium (Ca) 8 atoms
Magnesium (Mg) 70 atoms
Iron (Fe) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation (pdb code 9eh5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation, PDB code: 9eh5:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 9eh5

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Manganese binding site 1 out of 8 in the Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:17.3
occ:1.00
 MN1 A:OEX401 0.0 17.3 1.0
OE2 A:GLU189 1.7 13.6 1.0
O3 A:OEX401 1.8 11.3 1.0
OD2 A:ASP342 2.0 12.8 1.0
O1 A:OEX401 2.1 8.7 1.0
NE2 A:HIS332 2.2 7.1 1.0
O5 A:OEX401 2.6 5.7 1.0
CD A:GLU189 2.8 5.8 1.0
CE1 A:HIS332 2.9 4.3 1.0
CG A:ASP342 3.0 11.0 1.0
MN2 A:OEX401 3.1 22.0 1.0
CD2 A:HIS332 3.3 3.4 1.0
MN3 A:OEX401 3.4 16.1 1.0
OD1 A:ASP342 3.4 10.8 1.0
OE1 A:GLU189 3.4 7.0 1.0
CA1 A:OEX401 3.7 14.2 1.0
O2 A:OEX401 3.8 10.9 1.0
OE2 A:GLU329 3.9 15.1 1.0
O A:HOH512 3.9 19.6 1.0
NE2 A:HIS337 3.9 9.3 1.0
CG A:GLU189 4.0 3.7 1.0
ND1 A:HIS332 4.1 4.2 1.0
OE1 A:GLU333 4.1 8.7 1.0
O A:ALA344 4.2 15.3 1.0
CG A:HIS332 4.3 5.2 1.0
CB A:ASP342 4.4 8.1 1.0
OE1 C:GLU341 4.5 5.9 1.0
CE1 A:HIS337 4.6 6.3 1.0
OE1 A:GLU329 4.6 11.7 1.0
CD A:GLU329 4.6 9.5 1.0
CD A:GLU333 4.7 8.9 1.0
CG1 A:VAL185 4.7 2.6 1.0
OE2 A:GLU333 4.8 13.5 1.0
O A:HOH602 5.0 7.6 1.0

Manganese binding site 2 out of 8 in 9eh5

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Manganese binding site 2 out of 8 in the Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:22.0
occ:1.00
 MN2 A:OEX401 0.0 22.0 1.0
O A:ALA344 1.6 15.3 1.0
OD1 A:ASP342 2.1 10.8 1.0
O3 A:OEX401 2.1 11.3 1.0
OE1 C:GLU341 2.2 5.9 1.0
O1 A:OEX401 2.4 8.7 1.0
O2 A:OEX401 2.5 10.9 1.0
C A:ALA344 2.8 11.9 1.0
CG A:ASP342 2.9 11.0 1.0
MN3 A:OEX401 3.0 16.1 1.0
MN1 A:OEX401 3.1 17.3 1.0
O C:HOH634 3.1 15.8 1.0
OD2 A:ASP342 3.2 12.8 1.0
CD C:GLU341 3.2 11.2 1.0
OXT A:ALA344 3.4 11.5 1.0
CA1 A:OEX401 3.5 14.2 1.0
O A:HOH512 3.5 19.6 1.0
OE2 C:GLU341 3.7 14.0 1.0
CA A:ALA344 4.0 11.9 1.0
N A:ALA344 4.0 14.7 1.0
NE2 A:HIS337 4.0 9.3 1.0
O5 A:OEX401 4.3 5.7 1.0
CB A:ASP342 4.3 8.1 1.0
CD2 A:HIS337 4.4 6.8 1.0
OE2 A:GLU189 4.5 13.6 1.0
CG C:GLU341 4.5 7.0 1.0
CA A:ASP342 4.7 7.2 1.0
OE1 A:GLU333 4.7 8.7 1.0
CB C:GLU341 4.8 5.1 1.0
C A:ASP342 4.8 8.1 1.0
O4 A:OEX401 4.9 7.6 1.0
NE2 A:HIS332 4.9 7.1 1.0
CB A:ALA344 5.0 11.8 1.0
N A:LEU343 5.0 9.4 1.0

Manganese binding site 3 out of 8 in 9eh5

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Manganese binding site 3 out of 8 in the Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:16.1
occ:1.00
 MN3 A:OEX401 0.0 16.1 1.0
O2 A:OEX401 1.9 10.9 1.0
O3 A:OEX401 2.0 11.3 1.0
OE1 A:GLU333 2.0 8.7 1.0
O4 A:OEX401 2.1 7.6 1.0
OE2 C:GLU341 2.2 14.0 1.0
O5 A:OEX401 2.6 5.7 1.0
MN4 A:OEX401 2.9 31.9 1.0
CD C:GLU341 3.0 11.2 1.0
CD A:GLU333 3.0 8.9 1.0
MN2 A:OEX401 3.0 22.0 1.0
OE1 C:GLU341 3.1 5.9 1.0
OE2 A:GLU333 3.3 13.5 1.0
MN1 A:OEX401 3.4 17.3 1.0
CA1 A:OEX401 3.5 14.2 1.0
O1 A:OEX401 3.7 8.7 1.0
NE2 A:HIS332 4.1 7.1 1.0
NH2 C:ARG344 4.2 5.5 1.0
NE2 A:HIS337 4.2 9.3 1.0
OD1 A:ASP170 4.2 6.6 1.0
O A:ALA344 4.2 15.3 1.0
O C:HOH623 4.2 13.0 1.0
CG A:GLU333 4.4 8.6 1.0
CG C:GLU341 4.4 7.0 1.0
CD2 A:HIS332 4.6 3.4 1.0
O A:HOH517 4.7 16.2 1.0
OD1 A:ASP342 4.7 10.8 1.0
CB A:GLU333 4.7 5.9 1.0
OD2 A:ASP342 4.8 12.8 1.0
OE2 A:GLU189 4.8 13.6 1.0
OXT A:ALA344 4.8 11.5 1.0
OD2 A:ASP170 4.9 10.5 1.0
CE1 A:HIS337 4.9 6.3 1.0
CG A:ASP170 5.0 4.6 1.0
O A:HOH600 5.0 17.1 1.0
C A:ALA344 5.0 11.9 1.0

Manganese binding site 4 out of 8 in 9eh5

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Manganese binding site 4 out of 8 in the Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:31.9
occ:1.00
 MN4 A:OEX401 0.0 31.9 1.0
O4 A:OEX401 1.8 7.6 1.0
OE2 A:GLU333 2.3 13.5 1.0
OD1 A:ASP170 2.3 6.6 1.0
O A:HOH600 2.5 17.1 1.0
O5 A:OEX401 2.6 5.7 1.0
O A:HOH627 2.9 13.3 1.0
O A:HOH501 2.9 30.0 1.0
MN3 A:OEX401 2.9 16.1 1.0
CD A:GLU333 3.1 8.9 1.0
OE1 A:GLU333 3.2 8.7 1.0
O2 A:OEX401 3.4 10.9 1.0
CG A:ASP170 3.5 4.6 1.0
O A:HOH517 3.8 16.2 1.0
CA1 A:OEX401 3.9 14.2 1.0
O A:HOH602 4.1 7.6 1.0
OD2 A:ASP170 4.2 10.5 1.0
O A:HOH554 4.3 3.6 1.0
O A:SER169 4.4 1.3 1.0
CG A:GLU333 4.4 8.6 1.0
NH2 C:ARG344 4.5 5.5 1.0
CA A:ASP170 4.5 0.7 1.0
O A:HOH583 4.5 6.4 1.0
OD1 A:ASP61 4.5 12.6 1.0
O3 A:OEX401 4.5 11.3 1.0
O A:HOH593 4.6 14.4 1.0
CB A:ASP170 4.6 1.2 1.0
OE2 C:GLU341 4.6 14.0 1.0
C A:SER169 4.8 0.6 1.0
OG A:SER169 4.9 5.0 1.0
N A:ASP170 5.0 0.6 1.0
O A:HOH536 5.0 3.9 1.0

Manganese binding site 5 out of 8 in 9eh5

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Manganese binding site 5 out of 8 in the Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:17.3
occ:1.00
 MN1 a:OEX401 0.0 17.3 1.0
OE2 a:GLU189 1.7 13.6 1.0
O3 a:OEX401 1.8 11.3 1.0
OD2 a:ASP342 2.0 12.8 1.0
O1 a:OEX401 2.1 8.7 1.0
NE2 a:HIS332 2.2 7.1 1.0
O5 a:OEX401 2.6 5.7 1.0
CD a:GLU189 2.8 5.8 1.0
CE1 a:HIS332 2.9 4.3 1.0
CG a:ASP342 3.0 11.0 1.0
MN2 a:OEX401 3.1 22.0 1.0
CD2 a:HIS332 3.3 3.4 1.0
MN3 a:OEX401 3.4 16.1 1.0
OD1 a:ASP342 3.4 10.8 1.0
OE1 a:GLU189 3.4 7.0 1.0
CA1 a:OEX401 3.7 14.2 1.0
O2 a:OEX401 3.8 10.9 1.0
OE2 a:GLU329 3.9 15.1 1.0
O a:HOH512 3.9 19.6 1.0
NE2 a:HIS337 3.9 9.3 1.0
CG a:GLU189 4.0 3.7 1.0
ND1 a:HIS332 4.1 4.2 1.0
OE1 a:GLU333 4.1 8.7 1.0
O a:ALA344 4.2 15.3 1.0
CG a:HIS332 4.3 5.2 1.0
CB a:ASP342 4.4 8.1 1.0
OE1 c:GLU341 4.5 5.9 1.0
CE1 a:HIS337 4.6 6.3 1.0
OE1 a:GLU329 4.6 11.7 1.0
CD a:GLU329 4.6 9.5 1.0
CD a:GLU333 4.7 8.9 1.0
CG1 a:VAL185 4.7 2.6 1.0
OE2 a:GLU333 4.8 13.5 1.0
O a:HOH602 5.0 7.6 1.0

Manganese binding site 6 out of 8 in 9eh5

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Manganese binding site 6 out of 8 in the Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:22.0
occ:1.00
 MN2 a:OEX401 0.0 22.0 1.0
O a:ALA344 1.6 15.3 1.0
OD1 a:ASP342 2.1 10.8 1.0
O3 a:OEX401 2.1 11.3 1.0
OE1 c:GLU341 2.2 5.9 1.0
O1 a:OEX401 2.4 8.7 1.0
O2 a:OEX401 2.5 10.9 1.0
C a:ALA344 2.8 11.9 1.0
CG a:ASP342 2.9 11.0 1.0
MN3 a:OEX401 3.0 16.1 1.0
MN1 a:OEX401 3.1 17.3 1.0
O c:HOH634 3.1 15.8 1.0
OD2 a:ASP342 3.2 12.8 1.0
CD c:GLU341 3.2 11.2 1.0
OXT a:ALA344 3.4 11.5 1.0
CA1 a:OEX401 3.5 14.2 1.0
O a:HOH512 3.5 19.6 1.0
OE2 c:GLU341 3.7 14.0 1.0
CA a:ALA344 4.0 11.9 1.0
N a:ALA344 4.0 14.7 1.0
NE2 a:HIS337 4.0 9.3 1.0
O5 a:OEX401 4.3 5.7 1.0
CB a:ASP342 4.3 8.1 1.0
CD2 a:HIS337 4.4 6.8 1.0
OE2 a:GLU189 4.5 13.6 1.0
CG c:GLU341 4.5 7.0 1.0
CA a:ASP342 4.7 7.2 1.0
OE1 a:GLU333 4.7 8.7 1.0
CB c:GLU341 4.8 5.1 1.0
C a:ASP342 4.8 8.1 1.0
O4 a:OEX401 4.9 7.6 1.0
NE2 a:HIS332 4.9 7.1 1.0
CB a:ALA344 5.0 11.8 1.0
N a:LEU343 5.0 9.4 1.0

Manganese binding site 7 out of 8 in 9eh5

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Manganese binding site 7 out of 8 in the Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:16.1
occ:1.00
 MN3 a:OEX401 0.0 16.1 1.0
O2 a:OEX401 1.9 10.9 1.0
O3 a:OEX401 2.0 11.3 1.0
OE1 a:GLU333 2.0 8.7 1.0
O4 a:OEX401 2.1 7.6 1.0
OE2 c:GLU341 2.2 14.0 1.0
O5 a:OEX401 2.6 5.7 1.0
MN4 a:OEX401 2.9 31.9 1.0
CD c:GLU341 3.0 11.2 1.0
CD a:GLU333 3.0 8.9 1.0
MN2 a:OEX401 3.0 22.0 1.0
OE1 c:GLU341 3.1 5.9 1.0
OE2 a:GLU333 3.3 13.5 1.0
MN1 a:OEX401 3.4 17.3 1.0
CA1 a:OEX401 3.5 14.2 1.0
O1 a:OEX401 3.7 8.7 1.0
NE2 a:HIS332 4.1 7.1 1.0
NH2 c:ARG344 4.2 5.5 1.0
NE2 a:HIS337 4.2 9.3 1.0
OD1 a:ASP170 4.2 6.6 1.0
O a:ALA344 4.2 15.3 1.0
O c:HOH623 4.2 13.0 1.0
CG a:GLU333 4.4 8.6 1.0
CG c:GLU341 4.4 7.0 1.0
CD2 a:HIS332 4.6 3.4 1.0
O a:HOH517 4.7 16.2 1.0
OD1 a:ASP342 4.7 10.8 1.0
CB a:GLU333 4.7 5.9 1.0
OD2 a:ASP342 4.8 12.8 1.0
OE2 a:GLU189 4.8 13.6 1.0
OXT a:ALA344 4.8 11.5 1.0
OD2 a:ASP170 4.9 10.5 1.0
CE1 a:HIS337 4.9 6.3 1.0
CG a:ASP170 5.0 4.6 1.0
O a:HOH600 5.0 17.1 1.0
C a:ALA344 5.0 11.9 1.0

Manganese binding site 8 out of 8 in 9eh5

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Manganese binding site 8 out of 8 in the Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn401

b:31.9
occ:1.00
 MN4 a:OEX401 0.0 31.9 1.0
O4 a:OEX401 1.8 7.6 1.0
OE2 a:GLU333 2.3 13.5 1.0
OD1 a:ASP170 2.3 6.6 1.0
O a:HOH600 2.5 17.1 1.0
O5 a:OEX401 2.6 5.7 1.0
O a:HOH628 2.9 13.3 1.0
O a:HOH501 2.9 30.0 1.0
MN3 a:OEX401 2.9 16.1 1.0
CD a:GLU333 3.1 8.9 1.0
OE1 a:GLU333 3.2 8.7 1.0
O2 a:OEX401 3.4 10.9 1.0
CG a:ASP170 3.5 4.6 1.0
O a:HOH517 3.8 16.2 1.0
CA1 a:OEX401 3.9 14.2 1.0
O a:HOH602 4.1 7.6 1.0
OD2 a:ASP170 4.1 10.5 1.0
O a:HOH555 4.3 3.6 1.0
O a:SER169 4.4 1.3 1.0
CG a:GLU333 4.4 8.6 1.0
NH2 c:ARG344 4.5 5.5 1.0
CA a:ASP170 4.5 0.7 1.0
O a:HOH583 4.5 6.4 1.0
OD1 a:ASP61 4.5 12.6 1.0
O3 a:OEX401 4.5 11.3 1.0
CB a:ASP170 4.6 1.2 1.0
O a:HOH593 4.6 14.4 1.0
OE2 c:GLU341 4.6 14.0 1.0
C a:SER169 4.8 0.6 1.0
OG a:SER169 4.9 5.0 1.0
N a:ASP170 5.0 0.6 1.0
O a:HOH536 5.0 3.9 1.0

Reference:

D.A.Flesher, J.Shin, R.J.Debus, G.W.Brudvig. Structure of A Mutated Photosystem II Complex Reveals Changes to the Hydrogen-Bonding Network That Affect Proton Egress During O-O Bond Formation. J.Biol.Chem. 08272 2025.
ISSN: ESSN 1083-351X
PubMed: 39922494
DOI: 10.1016/J.JBC.2025.108272
Page generated: Tue Feb 25 11:30:10 2025

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