Atomistry » Sodium » PDB 2zgx-3a03 » 2zo5
Atomistry »
  Sodium »
    PDB 2zgx-3a03 »
      2zo5 »

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

Protein crystallography data

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

Other elements in 2zo5:

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

Sodium Binding Sites:

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 2zo5

Go back to Sodium Binding Sites List in 2zo5
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 2zo5

Go back to Sodium Binding Sites List in 2zo5
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

Reference:

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
Page generated: Mon Oct 7 05:38:40 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy