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Sodium in PDB 3sce: Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb)

Protein crystallography data

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb), PDB code: 3sce was solved by A.A.Trofimov, K.M.Polyakov, K.M.Boyko, T.V.Tikhonova, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 1.45
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 193.000, 193.000, 193.000, 90.00, 90.00, 90.00
R / Rfree (%) 12.4 / 14

Other elements in 3sce:

The structure of Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb) 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 with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb) (pdb code 3sce). 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 with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb), PDB code: 3sce:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3sce

Go back to Sodium Binding Sites List in 3sce
Sodium binding site 1 out of 2 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb)


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 with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na534

b:25.1
occ:0.50
O A:HOH1047 1.8 22.6 0.5
O A:HOH1130 2.4 17.6 1.0
O A:GLU390 2.5 15.5 1.0
O A:HOH1135 3.2 25.1 1.0
O A:HOH882 3.6 32.1 1.0
C A:GLU390 3.6 14.6 1.0
O B:HOH671 4.1 17.6 1.0
O A:LEU389 4.3 18.1 1.0
CA A:GLU390 4.4 15.2 1.0
OD1 A:ASN391 4.4 12.6 1.0
O B:HOH906 4.4 28.2 1.0
N A:ASN391 4.5 13.6 1.0
O A:HOH639 4.5 22.8 1.0
OD1 B:ASP147 4.5 14.6 1.0
CA A:ASN391 4.6 14.2 1.0
CG A:ASN391 4.9 12.4 1.0

Sodium binding site 2 out of 2 in 3sce

Go back to Sodium Binding Sites List in 3sce
Sodium binding site 2 out of 2 in the Structure of the Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb)


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 with A Covalent Bond Between the CE1 Atom of TYR303 and the Cg Atom of GLN360 (Tvnirb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na535

b:31.1
occ:1.00
O A:HOH897 2.4 42.2 1.0
O A:GLU265 2.4 20.0 1.0
O A:HOH1077 2.5 33.1 1.0
OD2 A:ASP288 2.5 18.8 1.0
O A:HOH1108 2.8 32.0 0.5
C A:GLU265 3.5 18.1 1.0
CG A:ASP288 3.5 19.0 1.0
OD1 A:ASP288 3.9 21.0 1.0
OE2 A:GLU265 4.1 53.8 1.0
N A:GLY268 4.1 16.1 1.0
CA A:GLY268 4.1 14.9 1.0
CA A:GLU265 4.2 19.1 1.0
O A:HOH880 4.4 25.5 0.5
CD A:GLU265 4.5 42.4 1.0
CG A:GLU265 4.6 29.0 1.0
N A:GLN266 4.6 16.9 1.0
O A:SER264 4.6 17.8 1.0
CB A:ASP288 4.8 15.6 1.0
C A:GLN266 4.8 14.9 1.0
C A:GLY268 4.9 14.0 1.0
CA A:GLN266 4.9 17.5 1.0

Reference:

A.A.Trofimov, K.M.Polyakov, T.V.Tikhonova, A.V.Tikhonov, T.N.Safonova, K.M.Boyko, P.V.Dorovatovskii, V.O.Popov. Covalent Modifications of the Catalytic Tyrosine in Octahaem Cytochrome C Nitrite Reductase and Their Effect on the Enzyme Activity. Acta Crystallogr.,Sect.D V. 68 144 2012.
ISSN: ISSN 0907-4449
PubMed: 22281743
DOI: 10.1107/S0907444911052632
Page generated: Tue Dec 15 06:24:32 2020

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