Chlorine in PDB 4kvk: Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase

The structure of Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase, PDB code: 4kvk 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)	106.27 / 1.98
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	72.460, 128.583, 188.740, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.2

The structure of Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase 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 (pdb code 4kvk). 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, PDB code: 4kvk:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl713 b:30.1 occ:1.00 O A:HOH1132 3.0 31.0 1.0 NZ A:LYS309 3.1 24.1 1.0 NE1 A:TRP333 3.2 23.0 1.0 CA A:LYS584 3.7 28.0 1.0 CE A:LYS309 3.7 22.9 1.0 O A:HOH842 3.9 22.9 1.0 CG A:LYS584 3.9 32.0 1.0 CD A:LYS309 4.0 20.1 1.0 CE1 A:TYR334 4.0 23.7 1.0 O A:VAL583 4.1 24.9 1.0 CD1 A:TRP333 4.1 22.8 1.0 CE2 A:TRP333 4.1 22.9 1.0 N A:LYS584 4.2 25.9 1.0 CG1 A:VAL583 4.2 25.3 1.0 C A:VAL583 4.3 26.3 1.0 CB A:LYS584 4.3 29.4 1.0 CZ A:PHE570 4.4 32.5 1.0 CZ2 A:TRP333 4.4 25.9 1.0 OH A:TYR334 4.4 27.5 1.0 CZ A:TYR334 4.6 27.9 1.0 OD1 A:ASP343 4.6 32.5 1.0 C A:LYS584 4.7 28.6 1.0 O A:LYS584 4.7 28.8 1.0 CE2 A:PHE570 4.7 30.8 1.0 CD1 A:TYR334 4.9 22.6 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl714 b:30.0 occ:1.00 O A:HOH954 3.1 23.1 1.0 O A:HOH804 3.2 18.4 1.0 N A:LYS339 3.3 24.3 1.0 O A:HOH1150 3.3 38.1 1.0 NE A:ARG330 3.3 23.4 1.0 NH2 A:ARG330 3.4 29.4 1.0 CA A:GLY338 3.7 22.1 1.0 CZ A:ARG330 3.8 26.9 1.0 CB A:LYS339 3.9 25.7 1.0 C A:GLY338 4.0 24.5 1.0 CD2 A:TYR334 4.0 27.3 1.0 CA A:LYS339 4.1 25.9 1.0 O A:HOH1005 4.2 51.9 1.0 CB A:TYR334 4.3 23.5 1.0 CB A:ARG330 4.4 21.8 1.0 CD A:ARG330 4.4 22.1 1.0 CG A:TYR334 4.4 22.7 1.0 O A:HOH850 4.5 28.8 1.0 O A:HOH1027 4.6 36.9 1.0 CE2 A:TYR334 4.8 24.5 1.0 CG A:ARG330 4.9 21.6 1.0 N A:GLY338 4.9 23.1 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl715 b:41.8 occ:1.00 O A:HOH922 2.7 46.1 1.0 N A:GLY350 3.3 35.2 1.0 N A:LEU353 3.3 26.3 1.0 N A:ILE352 3.3 30.1 1.0 CA A:GLY350 3.4 34.3 1.0 C A:GLY350 3.5 33.6 1.0 CB A:ILE352 3.6 31.4 1.0 CA A:ILE352 3.8 29.7 1.0 O A:GLY350 3.8 32.6 1.0 CG A:LEU353 3.9 28.9 1.0 N A:PRO351 3.9 33.4 1.0 C A:ILE352 4.0 27.7 1.0 CB A:LEU353 4.0 26.9 1.0 CD1 A:LEU353 4.2 29.8 1.0 CD A:PRO351 4.3 34.0 1.0 CA A:LEU353 4.3 25.4 1.0 CG1 A:ILE352 4.4 34.0 1.0 C A:PRO351 4.4 31.6 1.0 C A:GLY349 4.5 36.9 1.0 CG2 A:ILE352 4.6 32.1 1.0 CA A:PRO351 4.7 32.3 1.0 CD1 A:ILE352 4.7 39.8 1.0 CG A:PRO351 4.9 34.5 1.0 CA A:GLY349 5.0 35.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl716 b:33.9 occ:1.00 OH A:TYR379 2.9 30.9 1.0 NE2 A:HIS311 3.2 21.6 1.0 O A:HOH801 3.2 26.4 1.0 O A:HOH948 3.3 23.5 1.0 CB A:ALA556 3.7 24.5 1.0 CZ A:TYR379 3.8 31.1 1.0 CE2 A:TYR379 3.9 30.1 1.0 CD2 A:HIS311 4.1 22.5 1.0 CE1 A:HIS311 4.2 24.1 1.0 CH2 A:TRP159 4.3 30.9 1.0 CD2 A:PHE552 4.3 42.1 1.0 CZ A:PHE375 4.3 30.6 1.0 CA A:ALA556 4.5 24.3 1.0 CE1 A:PHE375 4.5 27.1 1.0 CZ3 A:TRP159 4.5 31.9 1.0 CE2 A:PHE552 4.6 44.4 1.0 CG A:PHE552 4.7 34.2 1.0 O A:HOH825 4.9 23.7 1.0 N A:ALA556 5.0 23.1 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