Atomistry » Sodium » PDB 2mat-2oj0 » 2oj0
Atomistry »
  Sodium »
    PDB 2mat-2oj0 »
      2oj0 »

Sodium in PDB 2oj0: Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked

Protein crystallography data

The structure of Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked, PDB code: 2oj0 was solved by E.Ennifar, P.Walter, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.97 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.538, 47.834, 58.681, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 23

Other elements in 2oj0:

The structure of Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked also contains other interesting chemical elements:

Potassium (K) 5 atoms
Manganese (Mn) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked (pdb code 2oj0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked, PDB code: 2oj0:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2oj0

Go back to Sodium Binding Sites List in 2oj0
Sodium binding site 1 out of 3 in the Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na262

b:40.3
occ:0.80
O A:HOH391 3.7 25.8 1.0
O4' B:G10 4.8 21.4 1.0
O2' A:C17 4.8 22.9 1.0
O4' A:C17 4.9 21.8 1.0

Sodium binding site 2 out of 3 in 2oj0

Go back to Sodium Binding Sites List in 2oj0
Sodium binding site 2 out of 3 in the Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na315

b:40.8
occ:0.90
OP1 A:C13 2.5 12.7 1.0
P A:C13 3.6 10.8 1.0
O3' A:G12 3.6 12.3 1.0
C5' A:C13 4.0 12.5 1.0
O5' A:C13 4.2 9.1 1.0
OP2 A:C13 4.9 10.2 1.0
C3' A:G12 5.0 13.0 1.0

Sodium binding site 3 out of 3 in 2oj0

Go back to Sodium Binding Sites List in 2oj0
Sodium binding site 3 out of 3 in the Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Duplex Form of the Hiv-1(Lai) Rna Dimerization Initiation Site Mn Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na209

b:18.1
occ:1.00
O B:HOH219 2.7 14.8 1.0
N4 B:C11 3.1 18.4 1.0
O B:HOH260 3.2 43.5 1.0
O B:HOH240 3.3 17.6 1.0
O B:HOH245 3.5 22.2 1.0
O B:HOH263 3.6 37.4 1.0
O A:HOH320 4.2 18.8 1.0
C4 B:C11 4.2 17.6 1.0
C5 B:C11 4.4 16.8 1.0
O6 B:G12 4.4 15.2 1.0
OP1 B:A9 4.4 26.9 1.0
O6 A:G14 4.6 10.6 1.0
O6 B:G10 4.7 20.9 1.0
MN B:MN204 4.8 27.2 1.0

Reference:

E.Ennifar, P.Walter, P.Dumas. Cation-Dependent Cleavage of the Duplex Form of the Subtype-B Hiv-1 Rna Dimerization Initiation Site. Nucleic Acids Res. V. 38 5807 2010.
ISSN: ISSN 0305-1048
PubMed: 20460458
DOI: 10.1093/NAR/GKQ344
Page generated: Mon Oct 7 03:12:22 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy