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Manganese in PDB 8gn2: Crystal Structure of Ppbq-Bound Photosystem II Complex

Enzymatic activity of Crystal Structure of Ppbq-Bound Photosystem II Complex

All present enzymatic activity of Crystal Structure of Ppbq-Bound Photosystem II Complex:
1.10.3.9;

Protein crystallography data

The structure of Crystal Structure of Ppbq-Bound Photosystem II Complex, PDB code: 8gn2 was solved by S.Kamada, Y.Nakajima, J.-R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.22 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.018, 229.579, 287.18, 90, 90, 90
R / Rfree (%) 15.3 / 18.1

Other elements in 8gn2:

The structure of Crystal Structure of Ppbq-Bound Photosystem II Complex also contains other interesting chemical elements:

Iron (Fe) 6 atoms
Calcium (Ca) 9 atoms
Chlorine (Cl) 4 atoms
Magnesium (Mg) 72 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Ppbq-Bound Photosystem II Complex (pdb code 8gn2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Ppbq-Bound Photosystem II Complex, PDB code: 8gn2:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8gn2

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Manganese binding site 1 out of 8 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:35.4
occ:1.00
 MN1 A:OEX401 0.0 35.4 1.0
OE2 A:GLU189 1.8 40.9 1.0
O3 A:OEX401 1.9 35.9 1.0
O1 A:OEX401 1.9 36.7 1.0
NE2 A:HIS332 2.1 34.6 1.0
OD2 A:ASP342 2.2 37.2 1.0
O5 A:OEX401 2.7 40.3 1.0
MN2 A:OEX401 2.9 37.9 1.0
CD A:GLU189 2.9 40.7 1.0
CE1 A:HIS332 3.1 35.0 1.0
CG A:ASP342 3.1 35.6 1.0
CD2 A:HIS332 3.1 35.6 1.0
MN3 A:OEX401 3.3 37.8 1.0
OD1 A:ASP342 3.4 35.0 1.0
OE1 A:GLU189 3.5 41.8 1.0
CA1 A:OEX401 3.6 39.9 1.0
O2 A:OEX401 3.7 39.1 1.0
NE2 A:HIS337 4.0 34.2 1.0
O A:HOH530 4.0 52.3 1.0
OE1 A:GLU333 4.0 36.5 1.0
CG A:GLU189 4.1 36.7 1.0
ND1 A:HIS332 4.2 37.2 1.0
CG A:HIS332 4.3 35.1 1.0
OXT A:ALA344 4.5 38.8 1.0
CG1 A:VAL185 4.5 35.4 1.0
CB A:ASP342 4.5 35.5 1.0
OE1 C:GLU354 4.5 41.7 1.0
CE1 A:HIS337 4.6 34.9 1.0
OE2 C:GLU354 4.7 38.2 1.0
O A:HOH639 4.7 39.5 1.0
CD A:GLU333 4.7 39.8 1.0
O A:ALA344 4.8 39.0 1.0
MN4 A:OEX401 4.9 41.6 1.0
O A:HOH539 5.0 40.8 1.0
C A:ALA344 5.0 39.6 1.0

Manganese binding site 2 out of 8 in 8gn2

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Manganese binding site 2 out of 8 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:37.9
occ:1.00
 MN2 A:OEX401 0.0 37.9 1.0
OXT A:ALA344 1.9 38.8 1.0
O2 A:OEX401 2.0 39.1 1.0
O3 A:OEX401 2.1 35.9 1.0
O1 A:OEX401 2.1 36.7 1.0
OE1 C:GLU354 2.1 41.7 1.0
OD1 A:ASP342 2.1 35.0 1.0
MN3 A:OEX401 2.9 37.8 1.0
C A:ALA344 2.9 39.6 1.0
MN1 A:OEX401 2.9 35.4 1.0
CD C:GLU354 3.0 39.5 1.0
CG A:ASP342 3.0 35.6 1.0
O A:ALA344 3.1 39.0 1.0
OE2 C:GLU354 3.2 38.2 1.0
OD2 A:ASP342 3.2 37.2 1.0
CA1 A:OEX401 3.4 39.9 1.0
O5 A:OEX401 3.7 40.3 1.0
NE2 A:HIS337 3.9 34.2 1.0
O C:HOH807 4.0 40.4 1.0
CA A:ALA344 4.2 44.0 1.0
O A:HOH530 4.2 52.3 1.0
N A:ALA344 4.2 45.3 1.0
OE2 A:GLU189 4.3 40.9 1.0
O4 A:OEX401 4.4 42.1 1.0
CD2 A:HIS337 4.4 33.6 1.0
CG C:GLU354 4.4 38.5 1.0
CB A:ASP342 4.5 35.5 1.0
OE1 A:GLU333 4.5 36.5 1.0
NH2 C:ARG357 4.6 42.5 1.0
NE2 A:HIS332 4.6 34.6 1.0
CB C:GLU354 4.8 35.0 1.0
CA A:ASP342 4.8 35.4 1.0
O A:HOH539 4.9 40.8 1.0
NH1 C:ARG357 4.9 41.8 1.0
C A:ASP342 4.9 39.1 1.0

Manganese binding site 3 out of 8 in 8gn2

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Manganese binding site 3 out of 8 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:37.8
occ:1.00
 MN3 A:OEX401 0.0 37.8 1.0
O2 A:OEX401 2.0 39.1 1.0
O4 A:OEX401 2.0 42.1 1.0
OE1 A:GLU333 2.0 36.5 1.0
O3 A:OEX401 2.1 35.9 1.0
OE2 C:GLU354 2.1 38.2 1.0
O5 A:OEX401 2.2 40.3 1.0
MN2 A:OEX401 2.9 37.9 1.0
MN4 A:OEX401 2.9 41.6 1.0
CD A:GLU333 3.0 39.8 1.0
CD C:GLU354 3.1 39.5 1.0
OE2 A:GLU333 3.3 39.9 1.0
MN1 A:OEX401 3.3 35.4 1.0
OE1 C:GLU354 3.4 41.7 1.0
CA1 A:OEX401 3.5 39.9 1.0
O1 A:OEX401 3.6 36.7 1.0
NH2 C:ARG357 4.0 42.5 1.0
O C:HOH707 4.1 44.9 1.0
NE2 A:HIS337 4.1 34.2 1.0
OD1 A:ASP170 4.2 42.3 1.0
NE2 A:HIS332 4.2 34.6 1.0
O A:HOH504 4.3 37.5 1.0
CG A:GLU333 4.4 35.1 1.0
OXT A:ALA344 4.4 38.8 1.0
OD2 A:ASP170 4.4 40.5 1.0
CG C:GLU354 4.4 38.5 1.0
CD2 A:HIS332 4.5 35.6 1.0
O A:HOH588 4.6 40.6 1.0
OD1 A:ASP342 4.7 35.0 1.0
O A:ALA344 4.7 39.0 1.0
CE1 A:HIS337 4.7 34.9 1.0
O A:HOH558 4.7 40.2 1.0
CB A:GLU333 4.8 33.4 1.0
CG A:ASP170 4.8 40.2 1.0
OD2 A:ASP342 4.8 37.2 1.0
OE2 A:GLU189 4.9 40.9 1.0
O A:HOH639 5.0 39.5 1.0

Manganese binding site 4 out of 8 in 8gn2

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Manganese binding site 4 out of 8 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:41.6
occ:1.00
 MN4 A:OEX401 0.0 41.6 1.0
O A:HOH588 2.1 40.6 1.0
OE2 A:GLU333 2.1 39.9 1.0
OD1 A:ASP170 2.1 42.3 1.0
O4 A:OEX401 2.1 42.1 1.0
O A:HOH558 2.3 40.2 1.0
O5 A:OEX401 2.3 40.3 1.0
MN3 A:OEX401 2.9 37.8 1.0
CD A:GLU333 3.0 39.8 1.0
CG A:ASP170 3.3 40.2 1.0
OE1 A:GLU333 3.3 36.5 1.0
OD2 A:ASP170 3.8 40.5 1.0
O A:HOH639 3.8 39.5 1.0
CA1 A:OEX401 3.8 39.9 1.0
O2 A:OEX401 3.9 39.1 1.0
O A:HOH504 3.9 37.5 1.0
O A:HOH580 4.0 44.3 1.0
OD1 A:ASP61 4.2 41.2 1.0
O A:HOH594 4.3 42.0 1.0
CG A:GLU333 4.4 35.1 1.0
O A:SER169 4.4 35.8 1.0
CB A:ASP170 4.5 34.2 1.0
CA A:ASP170 4.6 33.9 1.0
O3 A:OEX401 4.7 35.9 1.0
NH2 C:ARG357 4.7 42.5 1.0
OE2 C:GLU354 4.7 38.2 1.0
O D:HOH509 4.8 41.1 1.0
MN1 A:OEX401 4.9 35.4 1.0
C A:SER169 5.0 38.7 1.0

Manganese binding site 5 out of 8 in 8gn2

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Manganese binding site 5 out of 8 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn403

b:40.4
occ:1.00
 MN1 a:OEX403 0.0 40.4 1.0
OE2 a:GLU189 1.8 44.9 1.0
O1 a:OEX403 1.9 39.4 1.0
O3 a:OEX403 1.9 39.4 1.0
NE2 a:HIS332 2.1 38.6 1.0
OD2 a:ASP342 2.2 40.8 1.0
O5 a:OEX403 2.6 42.2 1.0
MN2 a:OEX403 2.9 39.9 1.0
CD a:GLU189 2.9 44.6 1.0
CE1 a:HIS332 3.0 40.1 1.0
CG a:ASP342 3.1 40.5 1.0
CD2 a:HIS332 3.2 36.7 1.0
MN3 a:OEX403 3.3 40.7 1.0
OE1 a:GLU189 3.4 42.7 1.0
OD1 a:ASP342 3.4 42.4 1.0
CA1 a:OEX403 3.5 42.9 1.0
O2 a:OEX403 3.7 41.7 1.0
O a:HOH527 4.0 52.1 1.0
NE2 a:HIS337 4.0 38.1 1.0
O a:HOH626 4.0 56.8 1.0
OE1 a:GLU333 4.0 41.3 1.0
CG a:GLU189 4.1 41.5 1.0
ND1 a:HIS332 4.2 41.4 1.0
CG a:HIS332 4.3 39.6 1.0
OXT a:ALA344 4.5 42.9 1.0
OE1 c:GLU354 4.5 38.8 1.0
CB a:ASP342 4.5 38.8 1.0
CG1 a:VAL185 4.5 36.2 1.0
OE2 c:GLU354 4.6 39.6 1.0
CE1 a:HIS337 4.6 38.2 1.0
O a:HOH616 4.6 44.4 1.0
CD a:GLU333 4.8 42.5 1.0
O a:ALA344 4.8 43.8 1.0
CD c:GLU354 4.9 40.7 1.0
MN4 a:OEX403 4.9 41.9 1.0
C a:ALA344 5.0 46.2 1.0

Manganese binding site 6 out of 8 in 8gn2

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Manganese binding site 6 out of 8 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn403

b:39.9
occ:1.00
 MN2 a:OEX403 0.0 39.9 1.0
OXT a:ALA344 1.9 42.9 1.0
O1 a:OEX403 2.0 39.4 1.0
O3 a:OEX403 2.0 39.4 1.0
O2 a:OEX403 2.0 41.7 1.0
OE1 c:GLU354 2.1 38.8 1.0
OD1 a:ASP342 2.2 42.4 1.0
MN1 a:OEX403 2.9 40.4 1.0
C a:ALA344 2.9 46.2 1.0
MN3 a:OEX403 2.9 40.7 1.0
CD c:GLU354 3.0 40.7 1.0
CG a:ASP342 3.0 40.5 1.0
O a:ALA344 3.1 43.8 1.0
OE2 c:GLU354 3.1 39.6 1.0
OD2 a:ASP342 3.2 40.8 1.0
CA1 a:OEX403 3.3 42.9 1.0
O5 a:OEX403 3.8 42.2 1.0
NE2 a:HIS337 3.8 38.1 1.0
O c:HOH791 3.9 43.8 1.0
O a:HOH527 4.2 52.1 1.0
CA a:ALA344 4.2 46.9 1.0
N a:ALA344 4.3 46.7 1.0
OE2 a:GLU189 4.4 44.9 1.0
CD2 a:HIS337 4.4 38.2 1.0
CG c:GLU354 4.4 39.1 1.0
CB a:ASP342 4.4 38.8 1.0
O4 a:OEX403 4.5 38.4 1.0
OE1 a:GLU333 4.5 41.3 1.0
NE2 a:HIS332 4.6 38.6 1.0
NH2 c:ARG357 4.7 48.2 1.0
CB c:GLU354 4.8 45.3 1.0
CA a:ASP342 4.8 38.8 1.0
NH1 c:ARG357 4.9 42.4 1.0
O a:HOH555 4.9 42.6 1.0
C a:ASP342 4.9 42.2 1.0

Manganese binding site 7 out of 8 in 8gn2

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Manganese binding site 7 out of 8 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn403

b:40.7
occ:1.00
 MN3 a:OEX403 0.0 40.7 1.0
O2 a:OEX403 1.9 41.7 1.0
O4 a:OEX403 2.0 38.4 1.0
OE1 a:GLU333 2.0 41.3 1.0
O3 a:OEX403 2.0 39.4 1.0
OE2 c:GLU354 2.1 39.6 1.0
O5 a:OEX403 2.2 42.2 1.0
MN2 a:OEX403 2.9 39.9 1.0
MN4 a:OEX403 2.9 41.9 1.0
CD a:GLU333 3.0 42.5 1.0
CD c:GLU354 3.1 40.7 1.0
OE2 a:GLU333 3.3 39.8 1.0
MN1 a:OEX403 3.3 40.4 1.0
OE1 c:GLU354 3.4 38.8 1.0
CA1 a:OEX403 3.4 42.9 1.0
O1 a:OEX403 3.6 39.4 1.0
O c:HOH704 4.0 44.4 1.0
NH2 c:ARG357 4.0 48.2 1.0
OD1 a:ASP170 4.1 39.5 1.0
NE2 a:HIS337 4.1 38.1 1.0
NE2 a:HIS332 4.2 38.6 1.0
O a:HOH505 4.2 38.0 1.0
CG a:GLU333 4.4 40.8 1.0
OD2 a:ASP170 4.4 45.8 1.0
OXT a:ALA344 4.4 42.9 1.0
CG c:GLU354 4.4 39.1 1.0
CD2 a:HIS332 4.5 36.7 1.0
O a:HOH574 4.6 41.3 1.0
O a:HOH580 4.6 41.6 1.0
O a:ALA344 4.7 43.8 1.0
CG a:ASP170 4.7 43.1 1.0
OD1 a:ASP342 4.7 42.4 1.0
CE1 a:HIS337 4.7 38.2 1.0
CB a:GLU333 4.8 38.9 1.0
OD2 a:ASP342 4.8 40.8 1.0
O a:HOH616 4.8 44.4 1.0
OE2 a:GLU189 4.9 44.9 1.0

Manganese binding site 8 out of 8 in 8gn2

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Manganese binding site 8 out of 8 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn403

b:41.9
occ:1.00
 MN4 a:OEX403 0.0 41.9 1.0
O4 a:OEX403 2.0 38.4 1.0
O a:HOH580 2.1 41.6 1.0
OD1 a:ASP170 2.1 39.5 1.0
OE2 a:GLU333 2.1 39.8 1.0
O a:HOH574 2.2 41.3 1.0
O5 a:OEX403 2.4 42.2 1.0
MN3 a:OEX403 2.9 40.7 1.0
CD a:GLU333 3.0 42.5 1.0
CG a:ASP170 3.2 43.1 1.0
OE1 a:GLU333 3.3 41.3 1.0
O a:HOH616 3.7 44.4 1.0
OD2 a:ASP170 3.8 45.8 1.0
CA1 a:OEX403 3.8 42.9 1.0
O2 a:OEX403 3.9 41.7 1.0
O a:HOH505 3.9 38.0 1.0
O a:HOH592 4.0 46.0 1.0
OD1 a:ASP61 4.2 43.3 1.0
O a:HOH607 4.3 48.2 1.0
O a:SER169 4.4 35.3 1.0
CG a:GLU333 4.4 40.8 1.0
CB a:ASP170 4.5 36.4 1.0
CA a:ASP170 4.5 34.2 1.0
O3 a:OEX403 4.6 39.4 1.0
O a:HOH508 4.6 44.3 1.0
OE2 c:GLU354 4.7 39.6 1.0
NH2 c:ARG357 4.8 48.2 1.0
C a:SER169 4.9 39.2 1.0
MN1 a:OEX403 4.9 40.4 1.0
N a:ASP170 5.0 33.9 1.0

Reference:

S.Kamada, Y.Nakajima, J.R.Shen. Structural Insights Into the Action Mechanisms of Artificial Electron Acceptors in Photosystem II. J.Biol.Chem. V. 299 04839 2023.
ISSN: ESSN 1083-351X
PubMed: 37209822
DOI: 10.1016/J.JBC.2023.104839
Page generated: Sun Oct 6 12:25:19 2024

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