Chlorine in PDB 5b5e: Crystal Structure Analysis of Photosystem II Complex

All present enzymatic activity of Crystal Structure Analysis of Photosystem II Complex:
1.10.3.9;

The structure of Crystal Structure Analysis of Photosystem II Complex, PDB code: 5b5e was solved by A.Tanaka, Y.Fukushima, N.Kamiya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.98 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	121.404, 228.224, 286.429, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.2

The structure of Crystal Structure Analysis of Photosystem II Complex also contains other interesting chemical elements:

Magnesium	(Mg)	72 atoms
Manganese	(Mn)	8 atoms
Iron	(Fe)	6 atoms
Calcium	(Ca)	7 atoms

The binding sites of Chlorine atom in the Crystal Structure Analysis of Photosystem II Complex (pdb code 5b5e). 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 Analysis of Photosystem II Complex, PDB code: 5b5e:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure Analysis 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 Crystal Structure Analysis of Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:19.2 occ:1.00 O D:HOH587 3.1 17.5 1.0 NZ D:LYS317 3.2 16.6 1.0 ND2 A:ASN181 3.3 16.5 1.0 O A:HOH542 3.4 20.9 1.0 N A:GLU333 3.4 17.8 1.0 CA A:HIS332 3.8 18.4 1.0 CB A:HIS332 3.8 17.8 1.0 CG A:GLU333 4.0 16.6 1.0 CE D:LYS317 4.0 16.1 1.0 C A:HIS332 4.0 18.7 1.0 OD1 A:ASN181 4.1 19.9 1.0 CG2 A:VAL185 4.1 20.4 1.0 CG A:ASN181 4.1 16.7 1.0 CD2 D:LEU321 4.2 13.7 1.0 O D:HOH515 4.3 17.1 1.0 CD1 D:LEU321 4.4 15.9 1.0 CB D:LYS317 4.4 17.1 1.0 CA A:GLU333 4.4 16.2 1.0 CG D:LEU321 4.6 15.2 1.0 O A:HOH524 4.6 19.1 1.0 CG D:LYS317 4.8 17.1 1.0 CB A:GLU333 4.8 17.0 1.0 CG A:HIS332 4.8 17.2 1.0 OE2 A:GLU333 4.8 16.4 1.0 O D:LYS317 4.9 16.8 1.0 CD A:GLU333 4.9 16.9 1.0 O D:HOH556 5.0 19.4 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure Analysis 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 Crystal Structure Analysis of Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:20.8 occ:1.00 O C:HOH743 3.0 20.9 1.0 O A:HOH592 3.1 18.1 1.0 N A:ASN338 3.2 16.5 1.0 N C:GLU354 3.3 19.7 1.0 N A:PHE339 3.7 20.1 1.0 CA A:HIS337 3.7 18.2 1.0 CD2 A:PHE339 3.8 20.9 1.0 CA C:GLY353 3.8 20.8 1.0 C A:HIS337 3.9 17.9 1.0 C C:GLY353 4.0 21.4 1.0 CA A:ASN338 4.1 17.8 1.0 O A:ALA336 4.2 18.5 1.0 CB C:GLU354 4.2 21.2 1.0 CB A:HIS337 4.2 17.1 1.0 CA C:GLU354 4.3 21.6 1.0 CB A:PHE339 4.3 21.4 1.0 O C:HOH717 4.3 19.4 1.0 CB A:ASN338 4.4 18.6 1.0 C A:ASN338 4.4 17.9 1.0 CG A:PHE339 4.4 21.7 1.0 CE2 A:PHE339 4.5 21.7 1.0 CA A:PHE339 4.5 21.1 1.0 CG C:GLU354 4.6 23.6 1.0 O A:PHE339 4.6 21.4 1.0 O C:HOH803 4.7 19.3 1.0 N A:HIS337 4.8 16.3 1.0 N C:THR355 4.9 17.9 1.0 NE2 C:GLN313 4.9 19.5 1.0 C A:ALA336 4.9 19.0 1.0 CD2 A:HIS337 4.9 17.2 1.0 CG A:HIS337 5.0 18.5 1.0 O C:GLY352 5.0 21.4 1.0 CG A:ASN338 5.0 19.8 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure Analysis 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 Crystal Structure Analysis of Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ a:Cl404 b:19.7 occ:1.00 O d:HOH516 3.2 22.4 1.0 NZ d:LYS317 3.2 18.6 1.0 O a:HOH579 3.3 22.2 1.0 ND2 a:ASN181 3.4 17.2 1.0 N a:GLU333 3.4 17.7 1.0 CB a:HIS332 3.6 16.8 1.0 CA a:HIS332 3.7 16.8 1.0 CE d:LYS317 4.0 16.3 1.0 C a:HIS332 4.0 19.7 1.0 CG a:GLU333 4.1 18.8 1.0 CG2 a:VAL185 4.1 16.2 1.0 OD1 a:ASN181 4.2 19.4 1.0 CG a:ASN181 4.2 20.1 1.0 CD2 d:LEU321 4.3 15.7 1.0 O d:HOH532 4.3 18.6 1.0 CA a:GLU333 4.4 19.3 1.0 CB d:LYS317 4.4 17.3 1.0 CD1 d:LEU321 4.5 15.6 1.0 O a:HOH571 4.6 21.9 1.0 CG d:LEU321 4.6 16.7 1.0 CG a:HIS332 4.7 18.8 1.0 O d:LYS317 4.8 17.9 1.0 CB a:GLU333 4.8 18.2 1.0 OE2 a:GLU333 4.8 19.8 1.0 CD a:GLU333 4.9 20.2 1.0 CG d:LYS317 4.9 17.9 1.0 O d:HOH583 5.0 19.1 1.0 CD2 a:HIS332 5.0 20.1 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure Analysis 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 Crystal Structure Analysis of Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ a:Cl405 b:21.3 occ:1.00 O c:HOH1178 2.9 21.0 1.0 O a:HOH600 3.1 21.9 1.0 N a:ASN338 3.2 20.3 1.0 N c:GLU354 3.4 21.0 1.0 N a:PHE339 3.6 21.4 1.0 CA a:HIS337 3.6 19.7 1.0 CD2 a:PHE339 3.7 24.7 1.0 CA c:GLY353 3.8 19.8 1.0 C a:HIS337 3.9 21.4 1.0 C c:GLY353 4.1 21.3 1.0 O a:ALA336 4.1 21.7 1.0 CA a:ASN338 4.1 21.6 1.0 CB a:HIS337 4.2 17.3 1.0 CB c:GLU354 4.3 24.6 1.0 CB a:PHE339 4.3 22.0 1.0 CB a:ASN338 4.3 21.1 1.0 CG a:PHE339 4.3 23.6 1.0 C a:ASN338 4.4 23.6 1.0 O c:HOH1112 4.4 21.0 1.0 CA c:GLU354 4.4 23.9 1.0 CA a:PHE339 4.4 20.5 1.0 CE2 a:PHE339 4.5 27.4 1.0 O a:PHE339 4.6 23.6 1.0 CG c:GLU354 4.6 27.2 1.0 O c:HOH1185 4.7 23.4 1.0 N a:HIS337 4.8 18.8 1.0 C a:ALA336 4.9 21.5 1.0 N c:THR355 4.9 22.8 1.0 C a:PHE339 5.0 23.4 1.0 O c:GLY352 5.0 21.9 1.0 CG a:HIS337 5.0 18.3 1.0 CD2 a:HIS337 5.0 19.4 1.0 CG a:ASN338 5.0 21.0 1.0 NE2 c:GLN313 5.0 19.8 1.0

A.Tanaka, Y.Fukushima, N.Kamiya. Two Different Structures of the Oxygen-Evolving Complex in the Same Polypeptide Frameworks of Photosystem II J. Am. Chem. Soc. V. 139 1718 2017.
ISSN: ESSN 1520-5126
PubMed: 28102667
DOI: 10.1021/JACS.6B09666