Sodium in PDB 2zo5: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Azide

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Azide, PDB code: 2zo5 was solved by K.M.Polyakov, K.M.Boyko, A.Slutsky, T.V.Tikhonova, A.N.Antipov, R.A.Zvyagilskaya, A.N.Popov, V.S.Lamzin, G.P.Bourenkov, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	11.99 / 1.70
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	193.027, 193.027, 193.027, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 16.8

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Azide also contains other interesting chemical elements:

Iron	(Fe)	16 atoms
Calcium	(Ca)	4 atoms

The binding sites of Sodium atom in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Azide (pdb code 2zo5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Azide, PDB code: 2zo5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Azide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Azide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na529 b:25.7 occ:0.33 O A:HOH1416 2.2 35.1 1.0 O A:HOH1415 2.5 35.8 1.0 OD2 A:ASP450 4.0 23.6 1.0 O A:HOH1373 4.1 34.7 1.0 C2 A:TRS1012 4.2 28.9 0.3 HZ2 A:LYS102 4.3 20.4 0.0 O3 A:TRS1012 4.5 27.5 0.3 O A:HOH1372 4.6 33.6 1.0 HZ3 A:LYS102 4.6 20.4 0.0 O A:HOH1300 4.7 34.3 1.0 O1 A:TRS1012 4.7 27.6 0.3 NZ A:LYS102 4.9 20.0 0.5 CG A:ASP450 5.0 21.0 1.0

Sodium binding site 2 out of 2 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Azide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Azide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na529 b:18.8 occ:0.33 O B:HOH1476 2.5 31.1 1.0 O B:HOH1475 2.7 13.9 0.5 C3 B:TRS1012 3.9 26.1 0.3 OD2 B:ASP450 4.2 20.4 1.0 O B:HOH1433 4.4 31.2 1.0 HZ2 B:LYS102 4.4 15.7 0.0 O2 B:TRS1012 4.5 24.1 0.3 O B:HOH1612 4.6 18.3 0.5 O B:HOH1432 4.7 30.6 1.0 O1 B:TRS1012 4.8 22.5 0.3 HZ3 B:LYS102 4.8 15.7 0.0 O B:HOH1361 4.8 16.9 0.5 O3 B:TRS1012 4.8 25.5 0.3 C B:TRS1012 4.9 25.4 0.3

K.M.Polyakov, K.M.Boyko, T.V.Tikhonova, A.Slutsky, A.N.Antipov, R.A.Zvyagilskaya, A.N.Popov, G.P.Bourenkov, V.S.Lamzin, V.O.Popov. High-Resolution Structural Analysis of A Novel Octaheme Cytochrome C Nitrite Reductase From the Haloalkaliphilic Bacterium Thioalkalivibrio Nitratireducens J.Mol.Biol. V. 389 846 2009.
ISSN: ISSN 0022-2836
PubMed: 19393666
DOI: 10.1016/J.JMB.2009.04.037