Chlorine in PDB 8gn2: 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;

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

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
Manganese	(Mn)	8 atoms
Magnesium	(Mg)	72 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Ppbq-Bound Photosystem II Complex, PDB code: 8gn2:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Ppbq-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 Ppbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:38.9 occ:1.00 O D:HOH564 3.0 37.5 1.0 NZ D:LYS317 3.3 44.0 1.0 ND2 A:ASN181 3.3 32.3 1.0 N A:GLU333 3.4 35.7 1.0 O A:HOH580 3.4 44.3 1.0 CB A:HIS332 3.7 33.2 1.0 CA A:HIS332 3.7 36.8 1.0 CG A:GLU333 4.0 35.1 1.0 CE D:LYS317 4.0 39.2 1.0 C A:HIS332 4.0 39.6 1.0 OD1 A:ASN181 4.1 39.1 1.0 CG A:ASN181 4.2 35.8 1.0 CG2 A:VAL185 4.2 32.7 1.0 CD2 D:LEU321 4.3 34.1 1.0 CA A:GLU333 4.4 35.3 1.0 CD1 D:LEU321 4.4 28.5 1.0 O D:HOH509 4.4 41.1 1.0 CB D:LYS317 4.4 32.7 1.0 O A:HOH556 4.6 36.8 1.0 CG D:LEU321 4.6 34.1 1.0 CG A:HIS332 4.7 35.1 1.0 CG D:LYS317 4.8 34.4 1.0 CB A:GLU333 4.8 33.4 1.0 O D:LYS317 4.8 33.6 1.0 OE2 A:GLU333 4.9 39.9 1.0 CD A:GLU333 4.9 39.8 1.0 CD2 A:HIS332 5.0 35.6 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Ppbq-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 Ppbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:38.0 occ:1.00 O C:HOH765 2.9 37.1 1.0 O A:HOH589 3.2 41.2 1.0 N A:ASN338 3.3 38.5 1.0 N C:GLU354 3.4 37.8 1.0 CD2 A:PHE339 3.7 37.6 1.0 CA A:HIS337 3.7 36.2 1.0 N A:PHE339 3.8 37.6 1.0 CA C:GLY353 3.9 32.9 1.0 C A:HIS337 4.0 37.4 1.0 C C:GLY353 4.1 39.3 1.0 O A:ALA336 4.1 34.7 1.0 CB C:GLU354 4.2 35.0 1.0 CA A:ASN338 4.2 40.2 1.0 CB A:HIS337 4.3 29.6 1.0 CA C:GLU354 4.3 35.6 1.0 O C:HOH747 4.4 36.5 1.0 CB A:PHE339 4.4 38.5 1.0 CB A:ASN338 4.4 38.5 1.0 CG A:PHE339 4.4 41.7 1.0 C A:ASN338 4.5 41.3 1.0 CE2 A:PHE339 4.5 36.2 1.0 O C:HOH807 4.5 40.4 1.0 CG C:GLU354 4.6 38.5 1.0 CA A:PHE339 4.6 36.6 1.0 O A:PHE339 4.7 38.5 1.0 N A:HIS337 4.8 34.3 1.0 N C:THR355 4.9 31.3 1.0 CD2 A:HIS337 4.9 33.6 1.0 O C:GLY352 4.9 38.7 1.0 C A:ALA336 4.9 40.9 1.0 CG A:HIS337 5.0 33.9 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Ppbq-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 Ppbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ a:Cl405 b:44.2 occ:1.00 O d:HOH538 3.1 44.6 1.0 NZ d:LYS317 3.3 44.2 1.0 ND2 a:ASN181 3.4 34.0 1.0 O a:HOH592 3.4 46.0 1.0 N a:GLU333 3.4 34.7 1.0 CB a:HIS332 3.7 36.3 1.0 CA a:HIS332 3.7 35.6 1.0 CG a:GLU333 4.0 40.8 1.0 CE d:LYS317 4.0 38.0 1.0 C a:HIS332 4.1 34.9 1.0 OD1 a:ASN181 4.1 39.9 1.0 CG2 a:VAL185 4.2 33.9 1.0 CG a:ASN181 4.2 40.0 1.0 CD2 d:LEU321 4.2 39.3 1.0 CA a:GLU333 4.4 37.1 1.0 CB d:LYS317 4.4 36.4 1.0 CD1 d:LEU321 4.5 33.1 1.0 O a:HOH584 4.5 38.3 1.0 O a:HOH508 4.6 44.3 1.0 CG d:LEU321 4.6 36.2 1.0 CG a:HIS332 4.7 39.6 1.0 CG d:LYS317 4.8 36.5 1.0 O d:LYS317 4.8 36.4 1.0 CB a:GLU333 4.8 38.9 1.0 OE2 a:GLU333 4.9 39.8 1.0 CD a:GLU333 4.9 42.5 1.0 CD2 a:HIS332 4.9 36.7 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Ppbq-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 Ppbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ a:Cl406 b:41.7 occ:1.00 O a:HOH620 3.0 45.5 1.0 O c:HOH760 3.1 38.9 1.0 N a:ASN338 3.2 38.9 1.0 N c:GLU354 3.4 39.9 1.0 CA a:HIS337 3.7 38.8 1.0 CD2 a:PHE339 3.7 45.1 1.0 N a:PHE339 3.8 42.4 1.0 CA c:GLY353 3.8 39.9 1.0 C a:HIS337 3.9 41.0 1.0 C c:GLY353 4.1 40.9 1.0 O a:ALA336 4.1 40.9 1.0 CA a:ASN338 4.2 39.7 1.0 CB a:HIS337 4.2 34.2 1.0 CB c:GLU354 4.2 45.3 1.0 CB a:PHE339 4.3 40.8 1.0 CB a:ASN338 4.4 41.4 1.0 CG a:PHE339 4.4 46.5 1.0 O c:HOH750 4.4 42.1 1.0 CA c:GLU354 4.4 44.4 1.0 C a:ASN338 4.5 45.1 1.0 CE2 a:PHE339 4.5 43.3 1.0 O c:HOH791 4.6 43.8 1.0 CA a:PHE339 4.6 46.0 1.0 CG c:GLU354 4.6 39.1 1.0 O a:PHE339 4.6 43.5 1.0 N a:HIS337 4.8 38.3 1.0 CD2 a:HIS337 4.8 38.2 1.0 CG a:HIS337 4.9 37.7 1.0 N c:THR355 4.9 37.9 1.0 C a:ALA336 4.9 41.6 1.0 CG a:ASN338 5.0 47.5 1.0 O c:GLY352 5.0 40.1 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