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Calcium 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
Magnesium (Mg) 70 atoms
Iron (Fe) 6 atoms
Manganese (Mn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 8 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 9eh5

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Calcium 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 Calcium with other atoms in the Ca 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:Ca401

b:14.2
occ:1.00
 CA1 A:OEX401 0.0 14.2 1.0
O2 A:OEX401 2.2 10.9 1.0
O1 A:OEX401 2.3 8.7 1.0
O A:HOH521 2.6 12.4 1.0
OXT A:ALA344 2.6 11.5 1.0
OD2 A:ASP170 2.7 10.5 1.0
O A:HOH602 2.8 7.6 1.0
O5 A:OEX401 3.1 5.7 1.0
CG A:ASP170 3.3 4.6 1.0
C A:ALA344 3.3 11.9 1.0
O A:ALA344 3.4 15.3 1.0
OD1 A:ASP170 3.4 6.6 1.0
MN2 A:OEX401 3.5 22.0 1.0
OE1 A:GLU189 3.5 7.0 1.0
MN3 A:OEX401 3.5 16.1 1.0
MN1 A:OEX401 3.7 17.3 1.0
O3 A:OEX401 3.8 11.3 1.0
MN4 A:OEX401 3.9 31.9 1.0
O A:HOH512 4.1 19.6 1.0
OE2 A:GLU189 4.1 13.6 1.0
O4 A:OEX401 4.2 7.6 1.0
CD A:GLU189 4.2 5.8 1.0
O A:HOH544 4.3 15.8 1.0
OE1 A:GLN165 4.3 7.7 1.0
NH1 C:ARG344 4.3 3.6 1.0
NH2 C:ARG344 4.4 5.5 1.0
CB A:ASP170 4.6 1.2 1.0
OH A:TYR161 4.6 1.8 1.0
CA A:ALA344 4.7 11.9 1.0
CZ C:ARG344 4.8 4.3 1.0
CG A:GLN165 4.9 1.1 1.0
CB A:GLN165 5.0 1.2 1.0

Calcium binding site 2 out of 8 in 9eh5

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Calcium 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 Calcium with other atoms in the Ca 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
K:Ca101

b:43.4
occ:1.00
 OE1 Y:GLU64 2.0 20.9 1.0
OD2 K:ASP22 2.0 21.0 1.0
OD2 K:ASP18 2.5 22.3 1.0
CG K:ASP18 3.2 18.7 1.0
CG K:ASP22 3.2 16.2 1.0
CD Y:GLU64 3.2 20.9 1.0
OD1 K:ASP18 3.5 19.2 1.0
OD1 K:ASP22 3.8 20.7 1.0
NE2 Y:GLN68 3.8 19.9 1.0
OE2 Y:GLU64 3.9 24.1 1.0
O K:ASP18 4.1 18.0 1.0
CG Y:GLU64 4.3 18.7 1.0
CB K:ASP18 4.4 19.0 1.0
C K:ASP18 4.4 16.4 1.0
CB K:ASP22 4.4 13.3 1.0
N K:PRO19 4.7 15.5 1.0
CA K:PRO19 4.8 16.6 1.0
NE2 C:HIS61 4.8 11.4 1.0
O3 J:LMG101 4.8 20.0 1.0
CD Y:GLN68 4.9 20.8 1.0

Calcium binding site 3 out of 8 in 9eh5

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Calcium 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 Calcium with other atoms in the Ca 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
U:Ca201

b:30.7
occ:1.00
 OD2 U:ASP59 2.4 20.2 1.0
O B:SER386 2.4 18.2 1.0
OD1 U:ASP62 2.5 20.5 1.0
OD2 U:ASP62 2.6 21.4 1.0
CG U:ASP62 2.8 17.0 1.0
CG U:ASP59 3.3 17.7 1.0
OD1 U:ASP59 3.5 18.4 1.0
C B:SER386 3.6 15.8 1.0
O B:HOH814 4.0 29.1 1.0
CB U:ASP62 4.3 12.0 1.0
CA B:GLU387 4.5 15.9 1.0
N B:GLU387 4.5 12.7 1.0
CA B:SER386 4.5 13.3 1.0
O U:HOH309 4.5 17.8 1.0
CB U:ASP59 4.7 12.2 1.0
N U:ASP59 4.7 14.7 1.0
OE2 B:GLU387 4.8 20.5 1.0
CG B:GLU387 4.9 21.1 1.0
CB B:SER386 4.9 18.6 1.0

Calcium binding site 4 out of 8 in 9eh5

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Calcium 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 Calcium with other atoms in the Ca 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
V:Ca202

b:21.6
occ:1.00
 OE2 C:GLU70 2.2 19.0 1.0
OE1 V:GLN64 2.4 17.7 1.0
OE1 V:GLU128 2.4 18.1 1.0
O V:HOH311 2.6 30.0 1.0
OE2 V:GLU128 2.7 20.5 1.0
CD C:GLU70 2.9 12.1 1.0
OE1 C:GLU70 2.9 15.5 1.0
CD V:GLU128 2.9 17.8 1.0
O C:HOH606 3.4 20.3 1.0
CD V:GLN64 3.6 11.2 1.0
NE2 C:HIS385 4.3 7.9 1.0
CE1 C:HIS385 4.3 8.7 1.0
CG C:GLU70 4.4 10.7 1.0
CG V:GLU128 4.4 17.0 1.0
NE2 V:GLN64 4.4 7.9 1.0
O V:ASP60 4.5 14.3 1.0
CG V:GLN64 4.5 8.2 1.0
CE C:LYS66 4.5 11.2 1.0
O V:THR61 4.6 14.6 1.0
O V:HOH328 4.7 25.9 1.0
OE1 C:GLU381 4.8 10.8 1.0

Calcium binding site 5 out of 8 in 9eh5

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Calcium 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 Calcium with other atoms in the Ca 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:Ca401

b:14.2
occ:1.00
 CA1 a:OEX401 0.0 14.2 1.0
O2 a:OEX401 2.2 10.9 1.0
O1 a:OEX401 2.3 8.7 1.0
O a:HOH521 2.6 12.4 1.0
OXT a:ALA344 2.6 11.5 1.0
OD2 a:ASP170 2.7 10.5 1.0
O a:HOH602 2.8 7.6 1.0
O5 a:OEX401 3.1 5.7 1.0
CG a:ASP170 3.3 4.6 1.0
C a:ALA344 3.3 11.9 1.0
O a:ALA344 3.4 15.3 1.0
OD1 a:ASP170 3.4 6.6 1.0
MN2 a:OEX401 3.5 22.0 1.0
OE1 a:GLU189 3.5 7.0 1.0
MN3 a:OEX401 3.5 16.1 1.0
MN1 a:OEX401 3.7 17.3 1.0
O3 a:OEX401 3.8 11.3 1.0
MN4 a:OEX401 3.9 31.9 1.0
O a:HOH512 4.1 19.6 1.0
OE2 a:GLU189 4.1 13.6 1.0
O4 a:OEX401 4.2 7.6 1.0
CD a:GLU189 4.2 5.8 1.0
O a:HOH544 4.3 15.8 1.0
OE1 a:GLN165 4.3 7.7 1.0
NH1 c:ARG344 4.3 3.6 1.0
NH2 c:ARG344 4.4 5.5 1.0
CB a:ASP170 4.6 1.2 1.0
OH a:TYR161 4.6 1.8 1.0
CA a:ALA344 4.7 11.9 1.0
CZ c:ARG344 4.8 4.3 1.0
CG a:GLN165 4.9 1.1 1.0
CB a:GLN165 5.0 1.2 1.0

Calcium binding site 6 out of 8 in 9eh5

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Calcium 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 Calcium with other atoms in the Ca 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
k:Ca101

b:43.4
occ:1.00
 OE1 y:GLU64 2.0 20.9 1.0
OD2 k:ASP22 2.0 21.0 1.0
OD2 k:ASP18 2.5 22.3 1.0
CG k:ASP18 3.2 18.7 1.0
CG k:ASP22 3.2 16.2 1.0
CD y:GLU64 3.2 20.9 1.0
OD1 k:ASP18 3.5 19.2 1.0
OD1 k:ASP22 3.8 20.7 1.0
NE2 y:GLN68 3.8 19.9 1.0
OE2 y:GLU64 3.9 24.1 1.0
O k:ASP18 4.1 18.0 1.0
CG y:GLU64 4.3 18.7 1.0
CB k:ASP18 4.4 19.0 1.0
C k:ASP18 4.4 16.4 1.0
CB k:ASP22 4.4 13.3 1.0
N k:PRO19 4.7 15.5 1.0
CA k:PRO19 4.8 16.6 1.0
NE2 c:HIS61 4.8 11.4 1.0
O3 j:LMG101 4.8 20.0 1.0
CD y:GLN68 4.9 20.8 1.0

Calcium binding site 7 out of 8 in 9eh5

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Calcium 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 Calcium with other atoms in the Ca 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
u:Ca201

b:30.7
occ:1.00
 OD2 u:ASP59 2.4 20.2 1.0
O b:SER386 2.4 18.2 1.0
OD1 u:ASP62 2.5 20.5 1.0
OD2 u:ASP62 2.6 21.4 1.0
CG u:ASP62 2.8 17.0 1.0
CG u:ASP59 3.3 17.7 1.0
OD1 u:ASP59 3.5 18.4 1.0
C b:SER386 3.6 15.8 1.0
O b:HOH814 4.0 29.1 1.0
CB u:ASP62 4.3 12.0 1.0
CA b:GLU387 4.5 15.9 1.0
N b:GLU387 4.5 12.7 1.0
CA b:SER386 4.5 13.3 1.0
O u:HOH309 4.5 17.8 1.0
CB u:ASP59 4.7 12.2 1.0
N u:ASP59 4.7 14.7 1.0
OE2 b:GLU387 4.8 20.5 1.0
CG b:GLU387 4.9 21.1 1.0
CB b:SER386 4.9 18.6 1.0

Calcium binding site 8 out of 8 in 9eh5

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Calcium 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 Calcium with other atoms in the Ca 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
v:Ca202

b:21.6
occ:1.00
 OE2 c:GLU70 2.2 19.0 1.0
OE1 v:GLN64 2.4 17.7 1.0
OE1 v:GLU128 2.4 18.1 1.0
O v:HOH311 2.6 30.0 1.0
OE2 v:GLU128 2.7 20.5 1.0
CD c:GLU70 2.9 12.1 1.0
OE1 c:GLU70 2.9 15.5 1.0
CD v:GLU128 2.9 17.8 1.0
O c:HOH606 3.4 20.3 1.0
CD v:GLN64 3.6 11.2 1.0
NE2 c:HIS385 4.3 7.9 1.0
CE1 c:HIS385 4.3 8.7 1.0
CG c:GLU70 4.4 10.7 1.0
CG v:GLU128 4.4 17.0 1.0
NE2 v:GLN64 4.4 7.9 1.0
O v:ASP60 4.5 14.3 1.0
CG v:GLN64 4.5 8.2 1.0
CE c:LYS66 4.5 11.2 1.0
O v:THR61 4.6 14.6 1.0
O v:HOH328 4.7 25.9 1.0
OE1 c:GLU381 4.8 10.8 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 08:41:05 2025

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