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Chlorine in PDB 5v2c: Re-Refinement of Crystal Structure of Photosystem II Complex

Enzymatic activity of Re-Refinement of Crystal Structure of Photosystem II Complex

All present enzymatic activity of Re-Refinement of Crystal Structure of Photosystem II Complex:
1.10.3.9;

Protein crystallography data

The structure of Re-Refinement of Crystal Structure of Photosystem II Complex, PDB code: 5v2c was solved by J.Wang, J.M.Wiwczar, G.W.Brudvig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 178.62 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 122.190, 228.510, 286.400, 90.00, 90.00, 90.00
R / Rfree (%) 9.2 / 16.3

Other elements in 5v2c:

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

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Re-Refinement of Crystal Structure of Photosystem II Complex (pdb code 5v2c). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Re-Refinement of Crystal Structure of Photosystem II Complex, PDB code: 5v2c:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5v2c

Go back to Chlorine Binding Sites List in 5v2c
Chlorine binding site 1 out of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl603

b:23.7
occ:1.00
 O D:HOH514 2.9 77.8 1.0
O D:HOH580 3.1 25.3 1.0
NZ D:LYS317 3.3 25.1 1.0
ND2 A:ASN181 3.3 19.3 1.0
N A:GLU333 3.4 17.7 1.0
O A:HOH789 3.4 33.0 1.0
CB A:HIS332 3.8 18.6 1.0
CA A:HIS332 3.8 19.4 1.0
CG A:GLU333 3.9 20.1 1.0
CE D:LYS317 3.9 21.5 1.0
OD1 A:ASN181 4.1 22.1 1.0
C A:HIS332 4.1 18.6 1.0
CG A:ASN181 4.1 19.2 1.0
CD2 D:LEU321 4.2 20.7 1.0
CG2 A:VAL185 4.2 20.2 1.0
CA A:GLU333 4.3 18.1 1.0
CB D:LYS317 4.4 17.9 1.0
CD1 D:LEU321 4.4 21.9 1.0
O A:HOH732 4.5 22.4 1.0
O A:HOH761 4.6 21.7 1.0
CG D:LEU321 4.6 18.4 1.0
CG D:LYS317 4.7 18.7 1.0
CB A:GLU333 4.7 20.0 1.0
CG A:HIS332 4.8 17.4 1.0
O D:LYS317 4.9 19.1 1.0
OE2 A:GLU333 4.9 20.7 1.0
CD A:GLU333 4.9 20.4 1.0
CD D:LYS317 4.9 20.0 1.0

Chlorine binding site 2 out of 6 in 5v2c

Go back to Chlorine Binding Sites List in 5v2c
Chlorine binding site 2 out of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl604

b:21.7
occ:1.00
 O C:HOH750 3.0 21.2 1.0
O A:HOH823 3.1 23.5 1.0
N A:ASN338 3.2 20.0 1.0
N C:GLU354 3.4 21.9 1.0
CA A:HIS337 3.7 19.8 1.0
CD2 A:PHE339 3.7 21.5 1.0
CA C:GLY353 3.7 23.0 1.0
N A:PHE339 3.8 21.4 1.0
C A:HIS337 3.9 20.4 1.0
C C:GLY353 4.0 22.7 1.0
O A:ALA336 4.1 21.1 1.0
CA A:ASN338 4.2 21.8 1.0
CB C:GLU354 4.3 26.4 1.0
CB A:HIS337 4.3 20.4 1.0
CB A:ASN338 4.3 22.8 1.0
CB A:PHE339 4.3 22.8 1.0
CG A:PHE339 4.4 22.1 1.0
CA C:GLU354 4.4 23.1 1.0
O C:HOH687 4.4 23.1 1.0
CE2 A:PHE339 4.5 22.8 1.0
C A:ASN338 4.5 21.3 1.0
CG C:GLU354 4.5 22.9 1.0
O C:HOH838 4.5 26.0 1.0
CA A:PHE339 4.6 21.6 1.0
O A:PHE339 4.7 23.0 1.0
N A:HIS337 4.8 17.9 1.0
C A:ALA336 4.9 18.6 1.0
N C:THR355 4.9 21.4 1.0
O C:GLY352 4.9 25.0 1.0
CG A:ASN338 4.9 22.3 1.0
CD2 A:HIS337 4.9 21.5 1.0
CG A:HIS337 5.0 19.3 1.0
N C:GLY353 5.0 21.1 1.0

Chlorine binding site 3 out of 6 in 5v2c

Go back to Chlorine Binding Sites List in 5v2c
Chlorine binding site 3 out of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cl202

b:68.3
occ:1.00
 O V:HOH390 2.3 54.6 1.0
O V:HOH330 2.7 32.9 1.0
O V:HOH393 2.7 67.3 1.0
O B:HOH1068 2.8 64.2 1.0
O V:HOH447 3.0 62.4 1.0
O V:HOH392 3.2 60.8 1.0
NZ U:LYS104 4.1 28.3 1.0
O D:HOH615 4.2 0.2 1.0
O V:HOH306 4.3 71.9 1.0
O V:HOH395 4.3 29.7 1.0
OD2 V:ASP53 4.5 25.6 1.0
O1 V:GOL201 4.5 39.5 1.0
O2 V:GOL201 4.6 35.5 1.0
O V:HOH360 4.8 27.6 1.0
NH1 V:ARG55 5.0 35.5 0.5

Chlorine binding site 4 out of 6 in 5v2c

Go back to Chlorine Binding Sites List in 5v2c
Chlorine binding site 4 out of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl404

b:28.1
occ:1.00
 O d:HOH596 3.0 33.0 1.0
NZ d:LYS317 3.2 30.9 1.0
O a:HOH545 3.2 28.5 1.0
N a:GLU333 3.4 21.9 1.0
ND2 a:ASN181 3.5 21.4 1.0
CB a:HIS332 3.7 21.6 1.0
CA a:HIS332 3.7 20.3 1.0
CE d:LYS317 3.9 25.9 1.0
CG a:GLU333 4.0 24.9 1.0
C a:HIS332 4.1 21.2 1.0
OD1 a:ASN181 4.1 23.7 1.0
CG a:ASN181 4.2 22.5 1.0
CD2 d:LEU321 4.2 22.2 1.0
CG2 a:VAL185 4.2 22.6 1.0
CA a:GLU333 4.3 24.3 1.0
CB d:LYS317 4.4 19.5 1.0
CD1 d:LEU321 4.4 20.5 1.0
O a:HOH523 4.5 24.5 1.0
O a:HOH601 4.6 22.0 1.0
CG d:LEU321 4.6 18.9 1.0
CG a:HIS332 4.7 24.1 1.0
CB a:GLU333 4.7 25.2 1.0
CG d:LYS317 4.8 22.1 1.0
OE2 a:GLU333 4.8 24.1 1.0
CD a:GLU333 4.9 25.9 1.0
O d:LYS317 4.9 21.7 1.0
CD2 a:HIS332 5.0 23.5 1.0
CD d:LYS317 5.0 24.0 1.0

Chlorine binding site 5 out of 6 in 5v2c

Go back to Chlorine Binding Sites List in 5v2c
Chlorine binding site 5 out of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl405

b:25.6
occ:1.00
 O c:HOH736 3.1 23.9 1.0
O a:HOH637 3.1 28.9 1.0
N a:ASN338 3.2 21.4 1.0
N c:GLU354 3.4 23.0 1.0
CA a:HIS337 3.6 23.7 1.0
N a:PHE339 3.7 24.8 1.0
CD2 a:PHE339 3.7 25.1 1.0
CA c:GLY353 3.8 23.9 1.0
C a:HIS337 3.9 22.1 1.0
C c:GLY353 4.1 24.0 1.0
O a:ALA336 4.1 22.1 1.0
CA a:ASN338 4.1 22.4 1.0
CB a:HIS337 4.2 26.5 1.0
CB c:GLU354 4.2 26.0 1.0
CB a:ASN338 4.3 24.4 1.0
CB a:PHE339 4.3 26.6 1.0
O c:HOH734 4.4 24.6 1.0
CA c:GLU354 4.4 22.3 1.0
CG a:PHE339 4.4 24.9 1.0
C a:ASN338 4.4 24.8 1.0
CE2 a:PHE339 4.5 25.5 1.0
CG c:GLU354 4.5 27.3 1.0
O c:HOH824 4.5 29.8 1.0
CA a:PHE339 4.6 27.6 1.0
O a:PHE339 4.7 27.6 1.0
O c:HOH602 4.8 97.5 1.0
N a:HIS337 4.8 21.7 1.0
CD2 a:HIS337 4.9 20.7 1.0
C a:ALA336 4.9 23.0 1.0
CG a:HIS337 4.9 22.3 1.0
N c:THR355 4.9 24.1 1.0
CG a:ASN338 4.9 26.4 1.0
O c:GLY352 5.0 25.1 1.0

Chlorine binding site 6 out of 6 in 5v2c

Go back to Chlorine Binding Sites List in 5v2c
Chlorine binding site 6 out of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Cl201

b:72.9
occ:1.00
 O b:HOH753 2.5 53.9 1.0
O v:HOH450 2.6 90.2 1.0
O u:HOH391 2.7 58.7 1.0
O v:HOH324 2.9 45.8 1.0
O b:HOH1077 3.0 79.3 1.0
O v:HOH451 3.1 75.8 1.0
O v:HOH357 3.4 0.3 1.0
O v:HOH394 3.9 62.2 1.0
NZ u:LYS104 4.1 31.3 1.0
O v:HOH402 4.3 34.1 1.0
OD2 v:ASP53 4.4 31.4 1.0
O1 b:GOL628 4.5 44.8 1.0
O v:HOH352 4.7 32.6 1.0
NH1 v:ARG55 4.7 34.0 0.5
O2 b:GOL628 4.7 34.6 1.0
O v:HOH348 4.9 58.6 1.0

Reference:

J.M.Wiwczar, A.M.Lafountain, J.Wang, H.A.Frank, G.W.Brudvig. Chlorophyll A with A Farnesyl Tail in Thermophilic Cyanobacteria. Photosyn. Res. V. 134 175 2017.
ISSN: ISSN 1573-5079
PubMed: 28741056
DOI: 10.1007/S11120-017-0425-4
Page generated: Sat Jul 12 09:41:50 2025

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