Chlorine in PDB 8gn1: 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;

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

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
Manganese	(Mn)	8 atoms
Iron	(Fe)	6 atoms
Magnesium	(Mg)	72 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Dbbq-Bound Photosystem II Complex, PDB code: 8gn1:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Dbbq-Bound 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 Crystal Structure of Dbbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:42.3 occ:1.00 O D:HOH591 3.0 40.5 1.0 ND2 A:ASN181 3.3 36.8 1.0 NZ D:LYS317 3.3 43.4 1.0 O A:HOH550 3.3 49.4 1.0 N A:GLU333 3.4 39.9 1.0 CB A:HIS332 3.7 35.2 1.0 CA A:HIS332 3.8 37.0 1.0 CE D:LYS317 4.0 44.2 1.0 CG A:GLU333 4.1 41.2 1.0 OD1 A:ASN181 4.1 42.1 1.0 C A:HIS332 4.1 40.3 1.0 CG A:ASN181 4.1 38.0 1.0 CG2 A:VAL185 4.2 37.1 1.0 CD1 D:LEU321 4.3 32.5 1.0 CD2 D:LEU321 4.4 38.6 1.0 CB D:LYS317 4.4 39.5 1.0 CA A:GLU333 4.4 43.1 1.0 O A:HOH544 4.5 47.9 1.0 O A:HOH526 4.5 41.1 1.0 CG D:LEU321 4.6 42.9 1.0 CG D:LYS317 4.7 40.9 1.0 CG A:HIS332 4.7 42.1 1.0 CB A:GLU333 4.8 39.2 1.0 O D:LYS317 4.8 37.4 1.0 CD2 A:HIS332 5.0 38.7 1.0 O D:HOH575 5.0 51.8 1.0 CD A:GLU333 5.0 47.1 1.0 OE2 A:GLU333 5.0 42.8 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Dbbq-Bound 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 Crystal Structure of Dbbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:41.6 occ:1.00 O C:HOH727 3.0 40.3 1.0 O A:HOH565 3.1 45.3 1.0 N A:ASN338 3.2 39.3 1.0 N C:GLU354 3.3 39.9 1.0 CD2 A:PHE339 3.7 40.9 1.0 N A:PHE339 3.8 46.2 1.0 CA A:HIS337 3.8 43.9 1.0 CA C:GLY353 3.8 40.2 1.0 C A:HIS337 4.0 43.4 1.0 C C:GLY353 4.1 41.8 1.0 CB C:GLU354 4.1 43.7 1.0 O A:ALA336 4.2 43.2 1.0 CA A:ASN338 4.2 39.1 1.0 CA C:GLU354 4.3 43.8 1.0 O C:HOH699 4.3 38.2 1.0 CB A:ASN338 4.4 40.3 1.0 CB A:HIS337 4.4 37.2 1.0 CB A:PHE339 4.4 44.0 1.0 O C:HOH770 4.4 44.2 1.0 CG A:PHE339 4.4 43.3 1.0 C A:ASN338 4.4 44.6 1.0 CE2 A:PHE339 4.5 40.8 1.0 CA A:PHE339 4.6 44.2 1.0 CG C:GLU354 4.6 43.9 1.0 O A:PHE339 4.7 44.8 1.0 N C:THR355 4.8 38.2 1.0 N A:HIS337 4.9 40.8 1.0 O C:GLY352 4.9 43.7 1.0 C A:ALA336 5.0 42.8 1.0 O C:HOH617 5.0 42.5 1.0 CD2 A:HIS337 5.0 40.6 1.0 NE2 C:GLN313 5.0 38.9 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Dbbq-Bound 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 Crystal Structure of Dbbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ a:Cl2106 b:47.7 occ:1.00 O d:HOH553 3.2 48.7 1.0 O a:HOH2243 3.2 47.3 1.0 NZ d:LYS317 3.3 47.0 1.0 ND2 a:ASN181 3.3 40.1 1.0 N a:GLU333 3.4 38.9 1.0 CB a:HIS332 3.6 39.4 1.0 CA a:HIS332 3.7 39.9 1.0 CG a:GLU333 4.0 43.9 1.0 C a:HIS332 4.0 39.1 1.0 CE d:LYS317 4.1 41.5 1.0 OD1 a:ASN181 4.1 43.9 1.0 CG a:ASN181 4.2 45.3 1.0 CG2 a:VAL185 4.2 35.0 1.0 CD2 d:LEU321 4.2 37.3 1.0 O a:HOH2232 4.4 47.4 1.0 CA a:GLU333 4.4 44.5 1.0 CB d:LYS317 4.5 39.2 1.0 CD1 d:LEU321 4.5 36.4 1.0 O a:HOH2277 4.5 44.8 1.0 CG a:HIS332 4.6 42.1 1.0 CG d:LEU321 4.6 46.2 1.0 CG d:LYS317 4.8 42.1 1.0 CB a:GLU333 4.8 38.9 1.0 OE2 a:GLU333 4.8 47.1 1.0 CD a:GLU333 4.9 47.9 1.0 CD2 a:HIS332 4.9 37.8 1.0 O d:LYS317 4.9 43.1 1.0 O d:HOH545 5.0 56.8 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Dbbq-Bound 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 Crystal Structure of Dbbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ a:Cl2107 b:46.0 occ:1.00 O a:HOH2287 3.0 51.4 1.0 O c:HOH663 3.1 45.5 1.0 N a:ASN338 3.1 45.1 1.0 N c:GLU354 3.4 48.0 1.0 CA a:HIS337 3.6 43.2 1.0 N a:PHE339 3.7 43.1 1.0 CD2 a:PHE339 3.8 48.1 1.0 CA c:GLY353 3.8 42.9 1.0 C a:HIS337 3.9 49.2 1.0 CA a:ASN338 4.1 41.5 1.0 C c:GLY353 4.1 48.7 1.0 O a:ALA336 4.1 43.1 1.0 CB a:HIS337 4.2 36.2 1.0 CB c:GLU354 4.2 45.8 1.0 CB a:ASN338 4.3 40.2 1.0 CB a:PHE339 4.4 43.5 1.0 CG a:PHE339 4.4 48.6 1.0 CA c:GLU354 4.4 50.0 1.0 C a:ASN338 4.4 48.3 1.0 O c:HOH657 4.4 42.4 1.0 CE2 a:PHE339 4.5 50.5 1.0 O a:HOH2308 4.5 41.9 1.0 CA a:PHE339 4.6 50.0 1.0 O a:PHE339 4.6 47.8 1.0 CG c:GLU354 4.7 47.4 1.0 N a:HIS337 4.7 37.1 1.0 C a:ALA336 4.9 46.1 1.0 CD2 a:HIS337 4.9 39.2 1.0 CG a:HIS337 4.9 41.2 1.0 CG a:ASN338 4.9 52.1 1.0 N c:THR355 4.9 39.3 1.0 O c:HOH620 5.0 44.6 1.0

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