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Sodium in PDB 3d1i: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite

Protein crystallography data

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite, PDB code: 3d1i 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 / 1.80
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 193.412, 193.412, 193.412, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 16.5

Other elements in 3d1i:

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite 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 Nitrite (pdb code 3d1i). 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 Nitrite, PDB code: 3d1i:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3d1i

Go back to Sodium Binding Sites List in 3d1i
Sodium binding site 1 out of 2 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite


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 Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na529

b:24.5
occ:0.33
O A:HOH1404 2.3 33.6 1.0
O A:HOH1405 2.4 32.0 1.0
O A:HOH1365 3.7 31.3 1.0
OD2 A:ASP450 4.1 22.1 1.0
HZ2 A:LYS102 4.2 20.0 0.0
O A:HOH1363 4.6 29.6 1.0
HZ3 A:LYS102 4.7 20.0 0.0
NZ A:LYS102 4.7 19.9 0.5
O A:HOH1448 4.7 25.6 1.0
HZ1 A:LYS102 4.8 20.0 0.0
O A:HOH1321 4.9 32.0 1.0
CG A:ASP450 5.0 22.1 1.0

Sodium binding site 2 out of 2 in 3d1i

Go back to Sodium Binding Sites List in 3d1i
Sodium binding site 2 out of 2 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase in A Complex with Nitrite


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 Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na529

b:26.4
occ:0.33
O B:HOH1863 2.1 10.8 0.5
O B:HOH1864 2.3 28.3 1.0
O B:HOH1994 2.5 21.7 0.5
OD2 B:ASP450 3.7 19.3 1.0
O B:HOH1824 3.8 26.5 1.0
HZ2 B:LYS102 3.9 18.1 0.0
HZ3 B:LYS102 4.4 18.1 0.0
NZ B:LYS102 4.5 18.0 0.5
O B:HOH1907 4.6 22.5 1.0
O B:HOH1822 4.7 31.8 1.0
CG B:ASP450 4.7 16.7 1.0
O B:HOH1783 4.8 29.7 1.0
HZ1 B:LYS102 4.8 18.1 0.0
O B:HOH1908 4.8 31.6 0.3
HZ2 B:LYS102 4.9 11.2 0.0

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: Tue Dec 15 06:08:16 2020

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