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Sodium in PDB 3ov9: Structure of the Nucleoprotein From Rift Valley Fever Virus

Protein crystallography data

The structure of Structure of the Nucleoprotein From Rift Valley Fever Virus, PDB code: 3ov9 was solved by F.Ferron, E.I.Danek, Z.Li, D.Luo, Y.H.Wong, B.Coutard, V.Lantez, R.Charrel, B.Canard, T.Walz, J.Lescar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.43 / 1.60
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 180.878, 180.878, 47.743, 90.00, 90.00, 120.00
R / Rfree (%) 22.2 / 25.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Nucleoprotein From Rift Valley Fever Virus (pdb code 3ov9). 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 Nucleoprotein From Rift Valley Fever Virus, PDB code: 3ov9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3ov9

Go back to Sodium Binding Sites List in 3ov9
Sodium binding site 1 out of 2 in the Structure of the Nucleoprotein From Rift Valley Fever Virus


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 Nucleoprotein From Rift Valley Fever Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na247

b:31.6
occ:1.00
O A:HOH564 2.5 54.0 1.0
O A:ILE209 2.8 16.0 1.0
O A:SER206 3.0 16.4 1.0
O A:HOH269 3.3 17.5 1.0
CD2 A:HIS211 3.7 18.1 1.0
C A:ILE209 3.7 16.1 1.0
C A:ASN207 3.7 16.8 1.0
CA A:ASN207 3.8 17.0 1.0
C A:SER206 4.0 16.4 1.0
N A:PHE208 4.0 16.6 1.0
CA A:SER210 4.0 16.2 1.0
NE A:ARG214 4.0 15.2 1.0
NE2 A:HIS211 4.1 18.2 1.0
O A:ASN207 4.1 17.0 1.0
O A:HOH327 4.1 23.2 1.0
O A:HOH290 4.1 25.5 1.0
N A:HIS211 4.1 16.3 1.0
C A:SER210 4.2 16.4 1.0
N A:SER210 4.3 16.2 1.0
C A:PHE208 4.4 16.2 1.0
N A:ASN207 4.4 16.7 1.0
O A:PHE208 4.4 16.0 1.0
NH2 A:ARG214 4.5 13.5 1.0
CZ A:ARG214 4.5 14.1 1.0
N A:ILE209 4.7 15.9 1.0
CD A:ARG214 4.7 15.7 1.0
CA A:PHE208 4.8 16.1 1.0
CG A:HIS211 4.8 16.9 1.0
CA A:ILE209 4.8 16.1 1.0
O A:SER210 4.9 16.1 1.0

Sodium binding site 2 out of 2 in 3ov9

Go back to Sodium Binding Sites List in 3ov9
Sodium binding site 2 out of 2 in the Structure of the Nucleoprotein From Rift Valley Fever Virus


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 Nucleoprotein From Rift Valley Fever Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na247

b:24.0
occ:1.00
O B:HOH356 2.8 24.9 1.0
O A:HOH960 2.9 23.4 1.0
O B:SER148 3.0 10.4 1.0
O B:ALA109 3.0 9.8 1.0
CA B:GLY151 3.5 11.7 1.0
N B:GLY151 3.5 11.5 1.0
C B:ALA109 3.8 9.9 1.0
C B:SER148 3.8 10.7 1.0
CZ B:PHE33 3.8 15.8 1.0
CB B:ALA112 3.9 11.2 1.0
CA B:SER148 3.9 10.8 1.0
CA B:ALA109 4.0 9.7 1.0
CB B:ALA109 4.1 9.4 1.0
NH2 A:ARG8 4.1 26.8 1.0
CE2 B:PHE33 4.2 16.2 1.0
CB B:ALA203 4.3 13.4 1.0
C B:GLY151 4.5 12.0 1.0
CB B:SER148 4.6 11.3 1.0
O B:HOH294 4.7 18.0 1.0
C B:ALA150 4.7 11.1 1.0
O B:HOH579 5.0 28.1 1.0
CE1 B:PHE33 5.0 15.9 1.0
O B:PRO147 5.0 11.6 1.0

Reference:

F.Ferron, Z.Li, E.I.Danek, D.Luo, Y.Wong, B.Coutard, V.Lantez, R.Charrel, B.Canard, T.Walz, J.Lescar. The Hexamer Structure of Rift Valley Fever Virus Nucleoprotein Suggests A Mechanism For Its Assembly Into Ribonucleoprotein Complexes Plos Pathog. V. 7 02030 2011.
ISSN: ISSN 1553-7366
PubMed: 21589902
DOI: 10.1371/JOURNAL.PPAT.1002030
Page generated: Tue Dec 15 06:20:31 2020

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