Bromine in PDB 3a0b: Crystal Structure of Br-Substituted Photosystem II Complex

The structure of Crystal Structure of Br-Substituted Photosystem II Complex, PDB code: 3a0b was solved by K.Kawakami, Y.Umena, N.Kamiya, J.-R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.70 / 3.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	130.589, 226.394, 307.514, 90.00, 90.00, 90.00
R / Rfree (%)	30.2 / 35.8

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

Magnesium	(Mg)	70 atoms
Manganese	(Mn)	8 atoms
Iron	(Fe)	6 atoms
Calcium	(Ca)	2 atoms

The binding sites of Bromine atom in the Crystal Structure of Br-Substituted Photosystem II Complex (pdb code 3a0b). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of Br-Substituted Photosystem II Complex, PDB code: 3a0b:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of Br-Substituted Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Br-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1064 b:0.3 occ:1.00 NZ D:LYS317 3.4 0.9 1.0 OD1 A:ASN181 3.4 0.4 1.0 N A:GLU333 3.5 0.2 1.0 ND2 A:ASN181 3.8 0.4 1.0 CA A:HIS332 3.9 0.5 1.0 CG A:ASN181 4.0 0.8 1.0 CB A:HIS332 4.1 0.6 1.0 C A:HIS332 4.2 0.5 1.0 CB D:LYS317 4.3 99.3 1.0 CA A:GLU333 4.5 0.3 1.0 CG2 A:VAL185 4.5 0.1 1.0 CE D:LYS317 4.6 0.1 1.0 CG A:GLU333 4.7 0.6 1.0 CG D:LYS317 4.7 0.2 1.0 CD D:LYS317 4.7 0.8 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of Br-Substituted Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Br-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1065 b:0.5 occ:1.00 CB A:HIS337 3.1 0.0 1.0 CD2 A:PHE339 3.2 0.8 1.0 N A:ASN338 3.5 0.3 1.0 CA A:HIS337 3.6 0.3 1.0 N C:GLU354 3.7 0.6 1.0 N A:PHE339 3.8 0.9 1.0 C A:HIS337 3.9 0.8 1.0 CB C:GLU354 4.0 0.3 1.0 CB A:PHE339 4.0 0.8 1.0 CG A:PHE339 4.0 0.7 1.0 CE2 A:PHE339 4.1 0.9 1.0 CA C:GLU354 4.4 0.8 1.0 CA C:GLY353 4.4 0.5 1.0 CA A:PHE339 4.4 0.3 1.0 CG A:HIS337 4.5 0.2 1.0 C A:ASN338 4.5 0.4 1.0 C C:GLY353 4.5 0.3 1.0 OG1 C:THR355 4.5 0.1 1.0 CA A:ASN338 4.5 0.6 1.0 N C:THR355 4.6 0.8 1.0 O A:HIS337 4.8 0.6 1.0 O A:PHE339 5.0 0.7 1.0 N A:HIS337 5.0 0.1 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of Br-Substituted Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Br-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ d:Br6064 b:0.9 occ:1.00 NZ d:LYS5317 3.0 98.0 1.0 N a:GLU5333 3.5 0.2 1.0 CB d:LYS5317 3.8 0.5 1.0 OD1 a:ASN5181 3.9 0.6 1.0 ND2 a:ASN5181 4.0 1.0 1.0 CG a:GLU5333 4.1 0.5 1.0 CA a:GLU5333 4.1 0.9 1.0 CE d:LYS5317 4.2 0.3 1.0 CG a:ASN5181 4.3 0.5 1.0 CG d:LYS5317 4.4 0.4 1.0 CD d:LYS5317 4.5 0.8 1.0 C a:HIS5332 4.5 0.9 1.0 CA a:HIS5332 4.5 0.1 1.0 CB a:GLU5333 4.7 1.0 1.0 CA d:LYS5317 4.8 0.9 1.0 CG2 a:VAL5185 4.9 0.6 1.0 CB a:HIS5332 4.9 0.9 1.0 CD2 d:LEU5321 5.0 98.4 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of Br-Substituted Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Br-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ a:Br6065 b:0.1 occ:1.00 CB a:HIS5337 3.2 0.6 1.0 CA a:HIS5337 3.4 0.7 1.0 N c:GLU5354 3.5 0.9 1.0 N a:ASN5338 3.5 0.8 1.0 CD2 a:PHE5339 3.6 0.3 1.0 N a:PHE5339 3.7 0.5 1.0 CB c:GLU5354 3.8 0.8 1.0 C a:HIS5337 3.8 0.8 1.0 CB a:PHE5339 4.0 0.6 1.0 CA c:GLY5353 4.0 0.7 1.0 C c:GLY5353 4.1 0.2 1.0 CG a:PHE5339 4.2 0.2 1.0 CA c:GLU5354 4.3 0.4 1.0 CA a:PHE5339 4.4 0.1 1.0 CE2 a:PHE5339 4.5 0.4 1.0 CA a:ASN5338 4.5 0.6 1.0 C a:ASN5338 4.6 0.4 1.0 OG1 c:THR5355 4.6 0.9 1.0 O a:PHE5339 4.6 0.4 1.0 CG a:HIS5337 4.6 0.7 1.0 N c:THR5355 4.7 0.0 1.0 C a:PHE5339 4.8 0.6 1.0 N a:HIS5337 4.8 0.1 1.0 O a:HIS5337 4.9 0.7 1.0

K.Kawakami, Y.Umena, N.Kamiya, J.-R.Shen. Location of Chloride and Its Possible Functions in Oxygen-Evolving Photosystem II Revealed By X-Ray Crystallography Proc.Natl.Acad.Sci.Usa V. 106 8567 2009.
ISSN: ISSN 0027-8424
PubMed: 19433803
DOI: 10.1073/PNAS.0812797106