Sodium 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
Chlorine	(Cl)	4 atoms
Calcium	(Ca)	1 atom

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase, PDB code: 4kvk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na717 b:51.3 occ:1.00 O A:HOH981 2.4 43.0 1.0 O A:HOH980 2.4 62.3 1.0 O A:HOH1117 2.6 49.9 1.0 O A:ASP505 2.7 35.0 1.0 OH3 A:1PE705 3.1 47.0 1.0 OH4 A:1PE705 3.3 46.3 1.0 OH2 A:1PE705 3.3 48.5 1.0 C A:ASP505 3.6 34.6 1.0 O A:HOH1029 3.6 40.9 1.0 C13 A:1PE705 3.9 44.5 1.0 CA A:ASP505 3.9 35.0 1.0 C12 A:1PE705 3.9 49.5 1.0 C23 A:1PE705 3.9 44.6 1.0 C22 A:1PE705 4.1 47.8 1.0 C14 A:1PE705 4.2 45.0 1.0 CB A:ASP505 4.2 35.1 1.0 C24 A:1PE705 4.3 47.5 1.0 N A:LEU506 4.9 34.5 1.0 OD1 A:ASP505 4.9 37.6 1.0 CG A:ASP505 4.9 37.2 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na718 b:54.1 occ:1.00 O A:HOH1228 2.7 45.0 1.0 O4 A:PG4707 3.0 45.9 1.0 O2 A:PG4707 3.1 51.3 1.0 OG A:SER608 3.1 28.3 0.5 O3 A:PG4707 3.3 48.2 1.0 O1 A:PG4707 3.4 61.7 1.0 O5 A:PG4707 3.4 57.4 1.0 CB A:SER608 3.8 23.9 0.5 C5 A:PG4707 3.8 45.7 1.0 C4 A:PG4707 3.9 50.0 1.0 C1 A:PG4707 3.9 58.1 1.0 C7 A:PG4707 3.9 52.7 1.0 CB A:SER608 4.0 25.0 0.5 C8 A:PG4707 4.0 54.0 1.0 C3 A:PG4707 4.0 49.2 1.0 C6 A:PG4707 4.0 45.3 1.0 C2 A:PG4707 4.1 54.7 1.0 CA A:SER608 4.7 24.9 0.5 CA A:SER608 4.7 24.0 0.5 OG A:SER608 4.7 21.8 0.5

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