Sodium 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
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 with Hydrogen Peroxide (pdb code 4kvj). 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 with Hydrogen Peroxide, PDB code: 4kvj:
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 with Hydrogen Peroxide


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 with Hydrogen Peroxide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na720 b:64.2 occ:1.00 O A:HOH1083 2.4 52.8 1.0 O A:HOH969 2.6 57.1 1.0 O A:ASP505 2.7 41.6 1.0 O7 A:P33705 2.8 62.4 1.0 O10 A:P33705 2.9 60.7 1.0 C12 A:P33705 3.5 57.0 1.0 C6 A:P33705 3.6 64.4 1.0 C A:ASP505 3.7 43.2 1.0 C11 A:P33705 3.7 56.3 1.0 O13 A:P33705 3.7 58.2 1.0 C8 A:P33705 3.8 57.1 1.0 C9 A:P33705 3.9 55.4 1.0 C5 A:P33705 3.9 65.0 1.0 CA A:ASP505 4.0 44.3 1.0 CB A:ASP505 4.2 46.0 1.0 C14 A:P33705 4.4 57.0 1.0 C3 A:P33705 4.5 64.8 1.0 O4 A:P33705 4.8 66.2 1.0 N A:LEU506 4.9 43.2 1.0 OD1 A:ASP505 4.9 49.6 1.0 CG A:ASP505 5.0 47.6 1.0

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


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 with Hydrogen Peroxide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na721 b:61.3 occ:1.00 O1 A:PG4707 2.9 69.2 1.0 O5 A:PG4707 2.9 60.9 1.0 O A:HOH1004 2.9 60.1 1.0 O2 A:PG4707 3.0 58.2 1.0 O3 A:PG4707 3.0 55.2 1.0 OG A:SER608 3.0 41.7 1.0 O4 A:PG4707 3.1 56.0 1.0 C5 A:PG4707 3.8 55.2 1.0 C4 A:PG4707 3.9 57.2 1.0 C1 A:PG4707 3.9 65.4 1.0 C3 A:PG4707 3.9 56.3 1.0 C2 A:PG4707 3.9 62.2 1.0 C6 A:PG4707 4.0 54.6 1.0 C8 A:PG4707 4.1 58.9 1.0 CB A:SER608 4.1 37.1 1.0 C7 A:PG4707 4.1 57.5 1.0 CA A:SER608 4.6 34.9 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