Chlorine in PDB 4kvj: Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase with Hydrogen Peroxide

The structure of Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase with Hydrogen Peroxide, PDB code: 4kvj was solved by G.Zhu, M.Koszelak-Rosenblum, M.G.Malkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.86 / 2.12
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	72.279, 129.650, 187.711, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.8

The structure of Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase with Hydrogen Peroxide also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Calcium	(Ca)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase with Hydrogen Peroxide (pdb code 4kvj). 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 Oryza Sativa Fatty Acid Alpha-Dioxygenase with Hydrogen Peroxide, PDB code: 4kvj:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase with Hydrogen Peroxide


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 Oryza Sativa Fatty Acid Alpha-Dioxygenase with Hydrogen Peroxide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl715 b:38.4 occ:1.00 NZ A:LYS309 3.1 31.4 1.0 NE1 A:TRP333 3.2 29.9 1.0 O A:HOH990 3.2 45.3 1.0 CE A:LYS309 3.7 29.9 1.0 CA A:LYS584 3.7 37.4 1.0 CG A:LYS584 3.8 41.8 1.0 O A:HOH818 3.9 37.2 1.0 CD A:LYS309 3.9 29.7 1.0 CE1 A:TYR334 4.0 30.6 1.0 CE2 A:TRP333 4.1 30.6 1.0 O A:VAL583 4.1 33.9 1.0 CD1 A:TRP333 4.1 31.9 1.0 CG1 A:VAL583 4.2 36.6 1.0 N A:LYS584 4.3 36.6 1.0 CB A:LYS584 4.3 40.2 1.0 OH A:TYR334 4.3 31.4 1.0 C A:VAL583 4.3 35.2 1.0 CZ2 A:TRP333 4.4 30.4 1.0 CZ A:PHE570 4.4 36.3 1.0 CZ A:TYR334 4.5 31.1 1.0 O A:LYS584 4.7 36.4 1.0 C A:LYS584 4.7 36.6 1.0 CE2 A:PHE570 4.8 35.7 1.0 OD1 A:ASP343 4.8 41.3 1.0 CD1 A:TYR334 4.8 30.2 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase with Hydrogen Peroxide


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 Oryza Sativa Fatty Acid Alpha-Dioxygenase with Hydrogen Peroxide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl716 b:40.5 occ:1.00 O A:HOH896 2.8 33.7 1.0 NH2 A:ARG330 3.3 33.6 1.0 O A:HOH805 3.3 25.3 1.0 N A:LYS339 3.3 32.6 1.0 NE A:ARG330 3.3 31.9 1.0 CZ A:ARG330 3.7 32.5 1.0 CA A:GLY338 3.8 30.4 1.0 CB A:LYS339 3.9 34.0 1.0 C A:GLY338 4.0 31.5 1.0 CD2 A:TYR334 4.1 30.7 1.0 CA A:LYS339 4.2 33.3 1.0 CB A:TYR334 4.3 30.6 1.0 CB A:ARG330 4.4 30.4 1.0 CD A:ARG330 4.4 31.3 1.0 CG A:TYR334 4.4 30.2 1.0 O A:HOH879 4.6 41.4 1.0 CE2 A:TYR334 4.9 30.3 1.0 CG A:ARG330 4.9 30.7 1.0 O A:HOH863 5.0 27.3 1.0 N A:GLY338 5.0 29.3 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase with Hydrogen Peroxide


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 Oryza Sativa Fatty Acid Alpha-Dioxygenase with Hydrogen Peroxide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl717 b:51.6 occ:1.00 O A:HOH1013 2.9 59.0 1.0 N A:GLY350 3.1 42.7 1.0 N A:LEU353 3.2 35.0 1.0 CA A:GLY350 3.2 42.5 1.0 N A:ILE352 3.3 38.9 1.0 C A:GLY350 3.3 42.0 1.0 CB A:ILE352 3.6 42.4 1.0 O A:GLY350 3.6 41.4 1.0 CA A:ILE352 3.8 38.8 1.0 N A:PRO351 3.8 40.5 1.0 CG A:LEU353 3.9 39.2 1.0 CB A:LEU353 3.9 37.8 1.0 C A:ILE352 4.0 37.4 1.0 CA A:LEU353 4.2 36.0 1.0 CD1 A:LEU353 4.2 40.3 1.0 C A:GLY349 4.3 43.9 1.0 C A:PRO351 4.3 40.6 1.0 CD A:PRO351 4.3 41.4 1.0 CG1 A:ILE352 4.4 44.8 1.0 CA A:PRO351 4.6 40.3 1.0 CG2 A:ILE352 4.7 42.8 1.0 CA A:GLY349 4.8 41.7 1.0 CD1 A:ILE352 4.8 46.7 1.0 CG A:PRO351 4.9 41.0 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase with Hydrogen Peroxide


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 Oryza Sativa Fatty Acid Alpha-Dioxygenase with Hydrogen Peroxide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl718 b:49.8 occ:1.00 OH A:TYR379 2.8 51.4 1.0 O A:HOH886 3.1 34.2 1.0 NH1 A:ARG559 3.1 43.1 1.0 NE2 A:HIS311 3.1 31.1 1.0 NH2 A:ARG559 3.5 40.7 1.0 CZ A:ARG559 3.7 39.4 1.0 CZ A:TYR379 3.8 45.1 1.0 CB A:ALA556 3.9 33.5 1.0 CE1 A:HIS311 4.0 30.5 1.0 CE2 A:TYR379 4.1 45.2 1.0 CD2 A:PHE552 4.1 51.2 1.0 CD2 A:HIS311 4.1 30.9 1.0 CH2 A:TRP159 4.4 40.2 1.0 CE2 A:PHE552 4.4 51.9 1.0 CG A:PHE552 4.5 46.3 1.0 CA A:ALA556 4.7 33.8 1.0 O A:HOH849 4.9 30.9 1.0 OG1 A:THR316 4.9 31.1 1.0 CB A:PHE552 4.9 42.3 1.0 CE1 A:PHE375 4.9 35.5 1.0

G.Zhu, M.Koszelak-Rosenblum, M.G.Malkowski. Crystal Structures of Alpha-Dioxygenase From Oryza Sativa: Insights Into Substrate Binding and Activation By Hydrogen Peroxide. Protein Sci. V. 22 1432 2013.
ISSN: ISSN 0961-8368
PubMed: 23934749
DOI: 10.1002/PRO.2327