Chlorine in PDB 8gn0: Crystal Structure of Dcbq-Bound Photosystem II Complex

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

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

Protein crystallography data

The structure of Crystal Structure of Dcbq-Bound Photosystem II Complex, PDB code: 8gn0 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) 49.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 121.223, 228.205, 286.997, 90, 90, 90
R / Rfree (%) 15.2 / 18.5

Other elements in 8gn0:

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

Calcium (Ca) 7 atoms
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Magnesium (Mg) 74 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Dcbq-Bound Photosystem II Complex (pdb code 8gn0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Crystal Structure of Dcbq-Bound Photosystem II Complex, PDB code: 8gn0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 8gn0

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Chlorine binding site 1 out of 12 in the Crystal Structure of Dcbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:47.0
occ:1.00
 O D:HOH2470 3.1 41.9 1.0
NZ D:LYS317 3.2 49.6 1.0
O A:HOH584 3.2 48.7 1.0
ND2 A:ASN181 3.3 37.0 1.0
N A:GLU333 3.4 40.1 1.0
CB A:HIS332 3.8 39.6 1.0
CA A:HIS332 3.8 37.3 1.0
CE D:LYS317 3.9 43.0 1.0
CG A:GLU333 4.0 45.0 1.0
C A:HIS332 4.1 44.2 1.0
OD1 A:ASN181 4.1 40.3 1.0
CG A:ASN181 4.1 42.7 1.0
CG2 A:VAL185 4.3 38.7 1.0
CD2 D:LEU321 4.3 37.2 1.0
CB D:LYS317 4.4 43.0 1.0
CD1 D:LEU321 4.4 35.2 1.0
CA A:GLU333 4.4 40.8 1.0
O A:HOH534 4.5 49.6 1.0
O A:HOH537 4.5 44.2 1.0
CG D:LEU321 4.6 43.4 1.0
CG D:LYS317 4.7 44.0 1.0
CG A:HIS332 4.8 42.5 1.0
CB A:GLU333 4.8 36.9 1.0
O D:LYS317 4.8 41.0 1.0
CD A:GLU333 4.9 45.7 1.0
OE2 A:GLU333 4.9 47.1 1.0
CD D:LYS317 4.9 46.8 1.0

Chlorine binding site 2 out of 12 in 8gn0

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Chlorine binding site 2 out of 12 in the Crystal Structure of Dcbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:43.1
occ:1.00
 O A:HOH589 3.0 46.3 1.0
O C:HOH698 3.1 45.0 1.0
N A:ASN338 3.2 39.4 1.0
N C:GLU354 3.3 42.4 1.0
CD2 A:PHE339 3.7 42.2 1.0
CA A:HIS337 3.7 43.3 1.0
N A:PHE339 3.8 45.7 1.0
CA C:GLY353 3.8 42.5 1.0
C A:HIS337 4.0 44.5 1.0
C C:GLY353 4.0 43.7 1.0
CA A:ASN338 4.1 40.2 1.0
CB C:GLU354 4.1 40.6 1.0
O A:ALA336 4.2 45.2 1.0
CB A:HIS337 4.3 38.6 1.0
CA C:GLU354 4.3 48.2 1.0
CB A:ASN338 4.3 40.2 1.0
O C:HOH672 4.4 44.6 1.0
CB A:PHE339 4.4 44.4 1.0
C A:ASN338 4.4 46.4 1.0
CG A:PHE339 4.4 44.9 1.0
CE2 A:PHE339 4.5 44.9 1.0
O A:HOH622 4.5 44.3 1.0
CG C:GLU354 4.6 48.7 1.0
CA A:PHE339 4.6 44.7 1.0
O A:PHE339 4.6 44.3 1.0
N C:THR355 4.9 40.5 1.0
N A:HIS337 4.9 36.5 1.0
O C:HOH606 5.0 42.9 1.0
C A:ALA336 5.0 44.6 1.0
CD2 A:HIS337 5.0 44.2 1.0
O C:GLY352 5.0 46.2 1.0

Chlorine binding site 3 out of 12 in 8gn0

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Chlorine binding site 3 out of 12 in the Crystal Structure of Dcbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl418

b:94.3
occ:1.00
 CL A:JOX418 0.0 94.3 1.0
C3 A:JOX418 1.8 86.7 1.0
C4 A:JOX418 2.8 83.0 1.0
C2 A:JOX418 2.8 75.5 1.0
O A:JOX418 3.0 65.6 1.0
CD1 A:LEU271 3.6 62.6 1.0
N A:HIS215 3.7 49.8 1.0
CG A:MET214 3.9 68.1 1.0
CA A:HIS215 3.9 49.2 1.0
CB A:MET214 4.0 54.2 1.0
CB A:HIS215 4.0 46.6 1.0
C5 A:JOX418 4.1 87.1 1.0
C1 A:JOX418 4.2 87.5 1.0
CD1 A:LEU218 4.2 60.8 1.0
C A:MET214 4.2 50.2 1.0
O A:PHE211 4.4 49.4 1.0
ND1 A:HIS215 4.5 51.5 1.0
CD2 A:LEU275 4.6 41.9 1.0
C A:JOX418 4.7 88.0 1.0
O A:MET214 4.7 51.6 1.0
CG A:HIS215 4.7 53.0 1.0
CA A:MET214 4.8 51.2 1.0
CG A:LEU271 4.9 62.6 1.0
CD2 A:LEU271 5.0 64.0 1.0

Chlorine binding site 4 out of 12 in 8gn0

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Chlorine binding site 4 out of 12 in the Crystal Structure of Dcbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl418

b:88.9
occ:1.00
 CL1 A:JOX418 0.0 88.9 1.0
C1 A:JOX418 1.8 87.5 1.0
C2 A:JOX418 2.8 75.5 1.0
C A:JOX418 2.8 88.0 1.0
O A:JOX418 2.9 65.6 1.0
CD2 A:LEU271 3.8 64.0 1.0
CB A:ALA251 3.9 61.4 1.0
CG1 A:ILE248 4.0 73.8 1.0
CB A:LEU218 4.1 58.9 1.0
C5 A:JOX418 4.1 87.1 1.0
C3 A:JOX418 4.2 86.7 1.0
CE2 A:TYR246 4.3 70.8 1.0
ND1 A:HIS215 4.4 51.5 1.0
CG2 A:VAL219 4.4 51.1 1.0
CD1 A:ILE248 4.4 73.4 1.0
CD1 A:LEU218 4.6 60.8 1.0
CE1 A:HIS215 4.6 53.2 1.0
C4 A:JOX418 4.7 83.0 1.0
OH A:TYR246 4.7 83.4 1.0
N A:VAL219 4.9 49.2 1.0
CZ A:TYR246 4.9 80.2 1.0
C A:LEU218 4.9 55.0 1.0
CG A:LEU218 5.0 62.8 1.0

Chlorine binding site 5 out of 12 in 8gn0

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Chlorine binding site 5 out of 12 in the Crystal Structure of Dcbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl419

b:65.3
occ:0.90
 CL A:JOX419 0.0 65.3 0.9
C3 A:JOX419 1.8 66.3 0.9
C2 A:JOX419 2.6 70.3 0.9
O A:JOX419 2.6 78.0 0.9
C4 A:JOX419 2.9 60.4 0.9
O A:LEU200 3.2 50.2 1.0
N A:GLY204 3.4 45.7 1.0
CB A:ALA203 3.6 43.7 1.0
CA A:GLY282 3.7 49.9 1.0
CA A:GLY204 3.7 44.8 1.0
C A:ALA203 3.7 45.7 1.0
CE2 A:TRP278 3.8 48.9 1.0
CZ2 A:TRP278 3.8 42.4 1.0
NE1 A:TRP278 3.9 43.9 1.0
C1 A:JOX419 4.0 70.4 0.9
C5 A:JOX419 4.1 76.5 0.9
O A:ALA203 4.1 43.7 1.0
N A:GLY282 4.2 44.8 1.0
C A:LEU200 4.2 48.3 1.0
O A:TRP278 4.2 47.3 1.0
CA A:ALA203 4.3 43.1 1.0
CD2 A:TRP278 4.5 49.7 1.0
CH2 A:TRP278 4.5 47.8 1.0
CA A:LEU200 4.5 48.8 1.0
CD2 A:LEU200 4.5 44.3 1.0
C A:JOX419 4.6 68.6 0.9
CD1 A:TRP278 4.6 45.8 1.0
CB A:LEU200 4.7 42.5 1.0
CG A:TRP278 4.9 51.4 1.0

Chlorine binding site 6 out of 12 in 8gn0

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Chlorine binding site 6 out of 12 in the Crystal Structure of Dcbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl419

b:69.3
occ:0.90
 CL1 A:JOX419 0.0 69.3 0.9
C1 A:JOX419 1.8 70.4 0.9
C2 A:JOX419 2.7 70.3 0.9
O A:JOX419 2.8 78.0 0.9
C A:JOX419 2.9 68.6 0.9
CB A:VAL281 3.8 46.6 1.0
CE3 A:TRP278 3.8 54.8 1.0
CG1 A:VAL281 3.9 42.7 1.0
CA A:TRP278 4.0 51.5 1.0
C12 A:SQD412 4.0 86.3 1.0
C3 A:JOX419 4.1 66.3 0.9
CG2 A:VAL281 4.2 47.7 1.0
C5 A:JOX419 4.2 76.5 0.9
O A:ALA277 4.2 55.1 1.0
C14 A:SQD412 4.3 89.0 1.0
CZ3 A:TRP278 4.4 58.4 1.0
CD2 A:TRP278 4.4 49.7 1.0
O A:TRP278 4.5 47.3 1.0
N A:TRP278 4.5 54.0 1.0
C A:ALA277 4.5 52.5 1.0
C13 A:SQD412 4.6 85.7 1.0
C4 A:JOX419 4.7 60.4 0.9
CB A:TRP278 4.7 47.0 1.0
C A:TRP278 4.8 56.6 1.0
CG A:TRP278 4.8 51.4 1.0

Chlorine binding site 7 out of 12 in 8gn0

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Chlorine binding site 7 out of 12 in the Crystal Structure of Dcbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl2606

b:48.7
occ:1.00
 O d:HOH553 3.1 48.5 1.0
O a:HOH2731 3.2 49.1 1.0
NZ d:LYS317 3.2 48.7 1.0
ND2 a:ASN181 3.3 41.5 1.0
N a:GLU333 3.4 40.4 1.0
CB a:HIS332 3.7 40.4 1.0
CA a:HIS332 3.7 41.9 1.0
CE d:LYS317 4.0 44.4 1.0
CG a:GLU333 4.0 43.7 1.0
C a:HIS332 4.0 40.8 1.0
OD1 a:ASN181 4.2 45.8 1.0
CG2 a:VAL185 4.2 35.9 1.0
CG a:ASN181 4.2 45.3 1.0
CD2 d:LEU321 4.2 41.3 1.0
O d:HOH535 4.4 49.7 1.0
CA a:GLU333 4.4 48.8 1.0
CB d:LYS317 4.4 40.7 1.0
CD1 d:LEU321 4.4 34.7 1.0
O a:HOH2757 4.5 50.8 1.0
CG d:LEU321 4.6 44.6 1.0
CG a:HIS332 4.7 45.6 1.0
CG d:LYS317 4.7 41.5 1.0
CB a:GLU333 4.8 39.1 1.0
O d:LYS317 4.9 44.9 1.0
OE2 a:GLU333 4.9 47.5 1.0
CD a:GLU333 4.9 47.7 1.0
CD2 a:HIS332 5.0 42.3 1.0
O d:HOH554 5.0 54.9 1.0

Chlorine binding site 8 out of 12 in 8gn0

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Chlorine binding site 8 out of 12 in the Crystal Structure of Dcbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl2607

b:46.8
occ:1.00
 O a:HOH2782 3.0 52.7 1.0
N a:ASN338 3.1 44.0 1.0
O c:HOH649 3.1 47.2 1.0
N c:GLU354 3.3 42.7 1.0
CA a:HIS337 3.6 46.1 1.0
N a:PHE339 3.7 50.4 1.0
CD2 a:PHE339 3.8 46.8 1.0
CA c:GLY353 3.8 49.4 1.0
C a:HIS337 3.8 47.9 1.0
CA a:ASN338 4.1 45.2 1.0
C c:GLY353 4.1 51.0 1.0
O a:ALA336 4.1 44.9 1.0
CB c:GLU354 4.2 52.1 1.0
CB a:HIS337 4.2 45.6 1.0
CB a:ASN338 4.3 45.8 1.0
CA c:GLU354 4.4 48.2 1.0
C a:ASN338 4.4 45.9 1.0
CG a:PHE339 4.4 52.3 1.0
CB a:PHE339 4.4 47.4 1.0
CE2 a:PHE339 4.5 54.4 1.0
O c:HOH677 4.5 46.4 1.0
O c:HOH745 4.5 44.5 1.0
CA a:PHE339 4.6 51.4 1.0
CG c:GLU354 4.6 50.4 1.0
O a:PHE339 4.6 50.6 1.0
N a:HIS337 4.7 43.2 1.0
C a:ALA336 4.9 50.1 1.0
N c:THR355 4.9 39.2 1.0
CG a:ASN338 4.9 50.5 1.0
CG a:HIS337 4.9 46.0 1.0
CD2 a:HIS337 5.0 44.1 1.0

Chlorine binding site 9 out of 12 in 8gn0

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Chlorine binding site 9 out of 12 in the Crystal Structure of Dcbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl2617

b:71.2
occ:1.00
 CL a:JOX2617 0.0 71.2 1.0
C3 a:JOX2617 1.8 67.6 1.0
C2 a:JOX2617 2.6 71.2 1.0
O a:JOX2617 2.7 91.9 1.0
C4 a:JOX2617 2.9 64.4 1.0
CE3 a:TRP278 3.9 49.5 1.0
CB a:VAL281 3.9 45.8 1.0
CG1 a:VAL281 3.9 46.6 1.0
C36 d:LHG403 4.0 96.2 1.0
C1 a:JOX2617 4.0 68.1 1.0
CA a:TRP278 4.1 48.6 1.0
C5 a:JOX2617 4.1 81.8 1.0
C14 a:SQD2615 4.2 106.2 1.0
CG2 a:VAL281 4.3 54.1 1.0
C13 a:SQD2615 4.3 108.9 1.0
O a:ALA277 4.3 51.4 1.0
CZ3 a:TRP278 4.4 53.5 1.0
CD2 a:TRP278 4.4 51.7 1.0
O a:TRP278 4.6 45.9 1.0
N a:TRP278 4.6 48.8 1.0
C a:JOX2617 4.6 69.5 1.0
C38 d:LHG403 4.6 86.0 1.0
C a:ALA277 4.7 45.0 1.0
CB a:TRP278 4.8 50.9 1.0
CG a:TRP278 4.8 46.9 1.0
C37 d:LHG403 4.9 92.0 1.0
C a:TRP278 4.9 46.2 1.0
C35 d:LHG403 4.9 90.8 1.0

Chlorine binding site 10 out of 12 in 8gn0

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Chlorine binding site 10 out of 12 in the Crystal Structure of Dcbq-Bound Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl2617

b:69.2
occ:1.00
 CL1 a:JOX2617 0.0 69.2 1.0
C1 a:JOX2617 1.8 68.1 1.0
C2 a:JOX2617 2.6 71.2 1.0
O a:JOX2617 2.7 91.9 1.0
C a:JOX2617 2.9 69.5 1.0
O a:LEU200 3.3 46.5 1.0
N a:GLY204 3.4 47.4 1.0
CA a:GLY282 3.6 42.2 1.0
CA a:GLY204 3.6 40.4 1.0
CB a:ALA203 3.7 40.5 1.0
C a:ALA203 3.7 47.1 1.0
CE2 a:TRP278 3.8 52.6 1.0
NE1 a:TRP278 3.8 51.1 1.0
CZ2 a:TRP278 3.8 48.7 1.0
C3 a:JOX2617 4.0 67.6 1.0
N a:GLY282 4.0 46.2 1.0
O a:TRP278 4.1 45.9 1.0
C5 a:JOX2617 4.1 81.8 1.0
O a:ALA203 4.2 46.3 1.0
C a:LEU200 4.3 45.9 1.0
CA a:ALA203 4.3 46.1 1.0
CD2 a:TRP278 4.4 51.7 1.0
CD1 a:TRP278 4.5 45.2 1.0
CH2 a:TRP278 4.5 53.9 1.0
CD2 a:LEU200 4.6 45.5 1.0
C4 a:JOX2617 4.6 64.4 1.0
CA a:LEU200 4.6 44.3 1.0
CB a:LEU200 4.8 40.3 1.0
CG a:TRP278 4.8 46.9 1.0
C a:GLY282 5.0 44.7 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: Tue Jul 30 10:05:11 2024

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