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Sodium in PDB 2dvo: Structure of PH1917 Protein with the Complex of Itp From Pyrococcus Horikoshii

Protein crystallography data

The structure of Structure of PH1917 Protein with the Complex of Itp From Pyrococcus Horikoshii, PDB code: 2dvo was solved by N.K.Lokanath, N.Kunishima, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.21
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 78.261, 93.068, 54.051, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 22.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of PH1917 Protein with the Complex of Itp From Pyrococcus Horikoshii (pdb code 2dvo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of PH1917 Protein with the Complex of Itp From Pyrococcus Horikoshii, PDB code: 2dvo:

Sodium binding site 1 out of 1 in 2dvo

Go back to Sodium Binding Sites List in 2dvo
Sodium binding site 1 out of 1 in the Structure of PH1917 Protein with the Complex of Itp From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of PH1917 Protein with the Complex of Itp From Pyrococcus Horikoshii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:31.0
occ:1.00
OD1 A:ASP65 2.6 29.6 1.0
O2G A:ITT201 2.7 18.2 1.0
O A:GLU64 2.7 17.2 1.0
OE1 A:GLU36 3.0 24.7 1.0
O2A A:ITT201 3.1 29.5 1.0
O1A A:ITT201 3.3 30.9 1.0
CD A:GLU36 3.4 24.2 1.0
OH A:TYR34 3.5 23.1 1.0
O1G A:ITT201 3.5 22.0 1.0
OE2 A:GLU36 3.5 22.3 1.0
PA A:ITT201 3.6 34.1 1.0
NZ A:LYS12 3.6 24.0 1.0
CG A:ASP65 3.6 27.8 1.0
PG A:ITT201 3.6 22.5 1.0
O3A A:ITT201 3.7 33.6 1.0
CA A:ASP65 3.7 18.5 1.0
C A:GLU64 3.8 18.2 1.0
CB A:ASP65 3.9 22.0 1.0
O A:HOH325 4.0 18.4 1.0
N A:ASP65 4.2 18.0 1.0
O3B A:ITT201 4.5 27.3 1.0
CZ A:TYR34 4.6 23.4 1.0
CG A:GLU36 4.6 22.9 1.0
OD2 A:ASP65 4.7 30.3 1.0
O3G A:ITT201 4.7 22.8 1.0
PB A:ITT201 4.8 28.1 1.0
C A:ASP65 5.0 18.5 1.0
CE A:LYS12 5.0 24.4 1.0

Reference:

N.K.Lokanath, K.J.Pampa, K.Takio, N.Kunishima. Structures of Dimeric Nonstandard Nucleotide Triphosphate Pyrophosphatase From Pyrococcus Horikoshii OT3: Functional Significance of Interprotomer Conformational Changes J.Mol.Biol. V. 375 1013 2008.
ISSN: ISSN 0022-2836
PubMed: 18062990
DOI: 10.1016/J.JMB.2007.11.018
Page generated: Tue Dec 15 05:47:40 2020

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