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Manganese in PDB 8gn1: Crystal Structure of Dbbq-Bound Photosystem II Complex

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

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

Protein crystallography data

The structure of Crystal Structure of Dbbq-Bound Photosystem II Complex, PDB code: 8gn1 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) 49.02 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 122.185, 228.462, 286.626, 90, 90, 90
R / Rfree (%) 15.7 / 19.1

Other elements in 8gn1:

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

Calcium (Ca) 7 atoms
Bromine (Br) 12 atoms
Chlorine (Cl) 4 atoms
Iron (Fe) 6 atoms
Magnesium (Mg) 72 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Dbbq-Bound Photosystem II Complex (pdb code 8gn1). 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 Dbbq-Bound Photosystem II Complex, PDB code: 8gn1:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8gn1

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Manganese binding site 1 out of 8 in the Crystal Structure of Dbbq-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 Dbbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:40.9
occ:1.00
 MN1 A:OEX401 0.0 40.9 1.0
OE2 A:GLU189 1.8 45.6 1.0
O3 A:OEX401 1.8 39.5 1.0
O1 A:OEX401 1.9 40.6 1.0
NE2 A:HIS332 2.1 39.5 1.0
OD2 A:ASP342 2.1 42.6 1.0
O5 A:OEX401 2.5 43.7 1.0
MN2 A:OEX401 2.9 42.4 1.0
CD A:GLU189 2.9 46.5 1.0
CE1 A:HIS332 3.0 37.2 1.0
CG A:ASP342 3.1 40.5 1.0
CD2 A:HIS332 3.2 38.7 1.0
MN3 A:OEX401 3.2 43.4 1.0
OE1 A:GLU189 3.5 53.5 1.0
OD1 A:ASP342 3.5 42.3 1.0
CA1 A:OEX401 3.5 46.0 1.0
O2 A:OEX401 3.7 40.4 1.0
NE2 A:HIS337 3.9 39.4 1.0
OE1 A:GLU333 4.0 41.4 1.0
O A:HOH556 4.0 57.0 1.0
CG A:GLU189 4.1 48.4 1.0
ND1 A:HIS332 4.2 39.2 1.0
CG A:HIS332 4.2 42.1 1.0
OXT A:ALA344 4.4 44.0 1.0
CG1 A:VAL185 4.5 41.5 1.0
CB A:ASP342 4.5 40.3 1.0
OE1 C:GLU354 4.5 43.4 1.0
CE1 A:HIS337 4.6 40.4 1.0
OE2 C:GLU354 4.6 43.9 1.0
CD A:GLU333 4.7 47.1 1.0
O A:HOH619 4.7 45.1 1.0
O A:ALA344 4.8 46.6 1.0
O4 A:OEX401 4.9 45.0 1.0
C A:ALA344 5.0 48.9 1.0
MN4 A:OEX401 5.0 48.3 1.0
CD C:GLU354 5.0 46.0 1.0

Manganese binding site 2 out of 8 in 8gn1

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Manganese binding site 2 out of 8 in the Crystal Structure of Dbbq-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 Dbbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:42.4
occ:1.00
 MN2 A:OEX401 0.0 42.4 1.0
OXT A:ALA344 1.9 44.0 1.0
O1 A:OEX401 2.0 40.6 1.0
O2 A:OEX401 2.0 40.4 1.0
O3 A:OEX401 2.1 39.5 1.0
OE1 C:GLU354 2.1 43.4 1.0
OD1 A:ASP342 2.1 42.3 1.0
MN3 A:OEX401 2.8 43.4 1.0
MN1 A:OEX401 2.9 40.9 1.0
C A:ALA344 2.9 48.9 1.0
CD C:GLU354 2.9 46.0 1.0
CG A:ASP342 3.0 40.5 1.0
OD2 A:ASP342 3.1 42.6 1.0
OE2 C:GLU354 3.1 43.9 1.0
O A:ALA344 3.3 46.6 1.0
CA1 A:OEX401 3.4 46.0 1.0
O5 A:OEX401 3.7 43.7 1.0
NE2 A:HIS337 3.8 39.4 1.0
O C:HOH770 4.1 44.2 1.0
O A:HOH556 4.1 57.0 1.0
O4 A:OEX401 4.2 45.0 1.0
CA A:ALA344 4.2 48.2 1.0
N A:ALA344 4.2 50.7 1.0
OE2 A:GLU189 4.3 45.6 1.0
CD2 A:HIS337 4.3 40.6 1.0
CG C:GLU354 4.4 43.9 1.0
CB A:ASP342 4.4 40.3 1.0
OE1 A:GLU333 4.4 41.4 1.0
NH2 C:ARG357 4.5 45.6 1.0
NE2 A:HIS332 4.6 39.5 1.0
CB C:GLU354 4.8 43.7 1.0
CA A:ASP342 4.8 42.2 1.0
NH1 C:ARG357 4.9 45.4 1.0
C A:ASP342 4.9 42.8 1.0

Manganese binding site 3 out of 8 in 8gn1

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Manganese binding site 3 out of 8 in the Crystal Structure of Dbbq-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 Dbbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:43.4
occ:1.00
 MN3 A:OEX401 0.0 43.4 1.0
O4 A:OEX401 1.9 45.0 1.0
O2 A:OEX401 2.0 40.4 1.0
OE1 A:GLU333 2.0 41.4 1.0
OE2 C:GLU354 2.1 43.9 1.0
O3 A:OEX401 2.2 39.5 1.0
O5 A:OEX401 2.2 43.7 1.0
MN2 A:OEX401 2.8 42.4 1.0
CD A:GLU333 3.0 47.1 1.0
MN4 A:OEX401 3.0 48.3 1.0
CD C:GLU354 3.1 46.0 1.0
OE2 A:GLU333 3.2 42.8 1.0
MN1 A:OEX401 3.2 40.9 1.0
OE1 C:GLU354 3.4 43.4 1.0
CA1 A:OEX401 3.4 46.0 1.0
O1 A:OEX401 3.4 40.6 1.0
NH2 C:ARG357 4.0 45.6 1.0
NE2 A:HIS337 4.1 39.4 1.0
NE2 A:HIS332 4.1 39.5 1.0
OD1 A:ASP170 4.2 48.1 1.0
O C:HOH712 4.2 52.5 1.0
OXT A:ALA344 4.3 44.0 1.0
O A:HOH531 4.3 48.0 1.0
CG A:GLU333 4.4 41.2 1.0
OD2 A:ASP170 4.4 48.6 1.0
CD2 A:HIS332 4.4 38.7 1.0
CG C:GLU354 4.4 43.9 1.0
O A:HOH580 4.6 50.4 1.0
OD1 A:ASP342 4.7 42.3 1.0
OD2 A:ASP342 4.7 42.6 1.0
O A:ALA344 4.7 46.6 1.0
CG A:ASP170 4.7 46.0 1.0
CE1 A:HIS337 4.7 40.4 1.0
OE2 A:GLU189 4.8 45.6 1.0
CB A:GLU333 4.8 39.2 1.0
O A:HOH558 4.8 43.4 1.0
O A:HOH619 5.0 45.1 1.0

Manganese binding site 4 out of 8 in 8gn1

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Manganese binding site 4 out of 8 in the Crystal Structure of Dbbq-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 Dbbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:48.3
occ:1.00
 MN4 A:OEX401 0.0 48.3 1.0
OD1 A:ASP170 2.1 48.1 1.0
O A:HOH580 2.1 50.4 1.0
OE2 A:GLU333 2.1 42.8 1.0
O4 A:OEX401 2.2 45.0 1.0
O A:HOH558 2.3 43.4 1.0
O5 A:OEX401 2.5 43.7 1.0
MN3 A:OEX401 3.0 43.4 1.0
CD A:GLU333 3.1 47.1 1.0
CG A:ASP170 3.2 46.0 1.0
OE1 A:GLU333 3.4 41.4 1.0
OD2 A:ASP170 3.7 48.6 1.0
O A:HOH619 3.8 45.1 1.0
CA1 A:OEX401 3.8 46.0 1.0
O A:HOH531 3.9 48.0 1.0
O2 A:OEX401 3.9 40.4 1.0
O A:HOH550 4.0 49.4 1.0
O A:HOH620 4.1 47.0 1.0
OD1 A:ASP61 4.2 40.4 1.0
O A:SER169 4.4 38.2 1.0
CG A:GLU333 4.4 41.2 1.0
CB A:ASP170 4.5 44.2 1.0
CA A:ASP170 4.5 42.9 1.0
OE2 C:GLU354 4.7 43.9 1.0
NH2 C:ARG357 4.7 45.6 1.0
O A:HOH544 4.7 47.9 1.0
O3 A:OEX401 4.8 39.5 1.0
C A:SER169 4.9 40.9 1.0
MN1 A:OEX401 5.0 40.9 1.0
N A:ASP170 5.0 34.7 1.0

Manganese binding site 5 out of 8 in 8gn1

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Manganese binding site 5 out of 8 in the Crystal Structure of Dbbq-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 5 of Crystal Structure of Dbbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn2104

b:43.6
occ:1.00
 MN1 a:OEX2104 0.0 43.6 1.0
O1 a:OEX2104 1.8 38.3 1.0
OE2 a:GLU189 1.8 47.0 1.0
O3 a:OEX2104 1.9 39.9 1.0
OD2 a:ASP342 2.1 43.5 1.0
NE2 a:HIS332 2.1 40.6 1.0
O5 a:OEX2104 2.5 52.2 1.0
MN2 a:OEX2104 2.8 45.2 1.0
CD a:GLU189 2.9 50.0 1.0
CE1 a:HIS332 3.1 38.2 1.0
CD2 a:HIS332 3.1 37.8 1.0
CG a:ASP342 3.2 46.7 1.0
MN3 a:OEX2104 3.2 43.3 1.0
OE1 a:GLU189 3.4 52.5 1.0
CA1 a:OEX2104 3.5 48.7 1.0
OD1 a:ASP342 3.5 47.4 1.0
O2 a:OEX2104 3.7 44.6 1.0
O a:HOH2206 3.8 59.5 1.0
NE2 a:HIS337 3.9 41.8 1.0
OE1 a:GLU333 4.0 43.8 1.0
CG a:GLU189 4.1 51.4 1.0
ND1 a:HIS332 4.2 44.6 1.0
CG a:HIS332 4.2 42.1 1.0
OXT a:ALA344 4.4 46.0 1.0
CG1 a:VAL185 4.5 38.5 1.0
OE1 c:GLU354 4.5 48.8 1.0
CB a:ASP342 4.5 38.5 1.0
OE2 c:GLU354 4.6 42.2 1.0
CE1 a:HIS337 4.6 44.6 1.0
O a:HOH2306 4.6 43.4 1.0
CD a:GLU333 4.7 47.9 1.0
O a:ALA344 4.8 48.9 1.0
C a:ALA344 4.9 52.3 1.0
MN4 a:OEX2104 4.9 49.2 1.0
CD c:GLU354 4.9 46.6 1.0
OE2 a:GLU333 5.0 47.1 1.0

Manganese binding site 6 out of 8 in 8gn1

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Manganese binding site 6 out of 8 in the Crystal Structure of Dbbq-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 Dbbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn2104

b:45.2
occ:1.00
 MN2 a:OEX2104 0.0 45.2 1.0
OXT a:ALA344 1.9 46.0 1.0
O2 a:OEX2104 2.0 44.6 1.0
O1 a:OEX2104 2.0 38.3 1.0
OE1 c:GLU354 2.1 48.8 1.0
O3 a:OEX2104 2.1 39.9 1.0
OD1 a:ASP342 2.2 47.4 1.0
MN3 a:OEX2104 2.7 43.3 1.0
MN1 a:OEX2104 2.8 43.6 1.0
C a:ALA344 2.9 52.3 1.0
CD c:GLU354 2.9 46.6 1.0
CG a:ASP342 2.9 46.7 1.0
OD2 a:ASP342 3.0 43.5 1.0
OE2 c:GLU354 3.1 42.2 1.0
O a:ALA344 3.2 48.9 1.0
CA1 a:OEX2104 3.3 48.7 1.0
O5 a:OEX2104 3.7 52.2 1.0
NE2 a:HIS337 3.8 41.8 1.0
O a:HOH2206 4.0 59.5 1.0
O a:HOH2308 4.0 41.9 1.0
CA a:ALA344 4.2 49.8 1.0
OE2 a:GLU189 4.2 47.0 1.0
CG c:GLU354 4.3 47.4 1.0
CD2 a:HIS337 4.3 39.2 1.0
N a:ALA344 4.3 55.3 1.0
O4 a:OEX2104 4.4 43.6 1.0
OE1 a:GLU333 4.4 43.8 1.0
CB a:ASP342 4.4 38.5 1.0
NE2 a:HIS332 4.5 40.6 1.0
NH2 c:ARG357 4.5 51.8 1.0
CB c:GLU354 4.8 45.8 1.0
CA a:ASP342 4.9 43.8 1.0
OD2 a:ASP170 4.9 50.2 1.0
CD a:GLU189 4.9 50.0 1.0

Manganese binding site 7 out of 8 in 8gn1

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Manganese binding site 7 out of 8 in the Crystal Structure of Dbbq-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 Dbbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn2104

b:43.3
occ:1.00
 MN3 a:OEX2104 0.0 43.3 1.0
O2 a:OEX2104 1.9 44.6 1.0
O4 a:OEX2104 2.0 43.6 1.0
OE1 a:GLU333 2.0 43.8 1.0
O3 a:OEX2104 2.0 39.9 1.0
OE2 c:GLU354 2.1 42.2 1.0
O5 a:OEX2104 2.3 52.2 1.0
MN2 a:OEX2104 2.7 45.2 1.0
MN4 a:OEX2104 2.9 49.2 1.0
CD a:GLU333 3.0 47.9 1.0
CD c:GLU354 3.0 46.6 1.0
MN1 a:OEX2104 3.2 43.6 1.0
OE2 a:GLU333 3.3 47.1 1.0
OE1 c:GLU354 3.3 48.8 1.0
CA1 a:OEX2104 3.4 48.7 1.0
O1 a:OEX2104 3.5 38.3 1.0
NH2 c:ARG357 3.9 51.8 1.0
O c:HOH690 4.0 52.8 1.0
OD1 a:ASP170 4.1 49.9 1.0
NE2 a:HIS337 4.2 41.8 1.0
NE2 a:HIS332 4.2 40.6 1.0
O a:HOH2204 4.2 42.4 1.0
OD2 a:ASP170 4.3 50.2 1.0
OXT a:ALA344 4.3 46.0 1.0
CG c:GLU354 4.4 47.4 1.0
CG a:GLU333 4.4 43.9 1.0
CD2 a:HIS332 4.5 37.8 1.0
O a:HOH2240 4.5 42.4 1.0
O a:ALA344 4.6 48.9 1.0
O a:HOH2254 4.6 49.9 1.0
OD2 a:ASP342 4.6 43.5 1.0
CG a:ASP170 4.6 52.2 1.0
OD1 a:ASP342 4.7 47.4 1.0
O a:HOH2306 4.8 43.4 1.0
CB a:GLU333 4.8 38.9 1.0
OE2 a:GLU189 4.8 47.0 1.0
CE1 a:HIS337 4.8 44.6 1.0
C a:ALA344 4.9 52.3 1.0

Manganese binding site 8 out of 8 in 8gn1

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Manganese binding site 8 out of 8 in the Crystal Structure of Dbbq-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 Dbbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn2104

b:49.2
occ:1.00
 MN4 a:OEX2104 0.0 49.2 1.0
O4 a:OEX2104 2.0 43.6 1.0
OD1 a:ASP170 2.0 49.9 1.0
OE2 a:GLU333 2.1 47.1 1.0
O a:HOH2254 2.1 49.9 1.0
O a:HOH2240 2.2 42.4 1.0
O5 a:OEX2104 2.5 52.2 1.0
MN3 a:OEX2104 2.9 43.3 1.0
CD a:GLU333 3.0 47.9 1.0
CG a:ASP170 3.1 52.2 1.0
OE1 a:GLU333 3.2 43.8 1.0
OD2 a:ASP170 3.6 50.2 1.0
O a:HOH2306 3.7 43.4 1.0
O2 a:OEX2104 3.8 44.6 1.0
CA1 a:OEX2104 3.9 48.7 1.0
O a:HOH2204 3.9 42.4 1.0
O a:HOH2304 4.1 49.8 1.0
O a:HOH2243 4.2 47.3 1.0
OD1 a:ASP61 4.2 46.5 1.0
CB a:ASP170 4.4 47.1 1.0
CG a:GLU333 4.4 43.9 1.0
O a:SER169 4.4 41.3 1.0
CA a:ASP170 4.5 45.6 1.0
O3 a:OEX2104 4.6 39.9 1.0
OE2 c:GLU354 4.7 42.2 1.0
NH2 c:ARG357 4.7 51.8 1.0
O a:HOH2232 4.7 47.4 1.0
MN1 a:OEX2104 4.9 43.6 1.0
C a:SER169 4.9 42.5 1.0
N a:ASP170 5.0 39.0 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 12:25:14 2024

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