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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: Tue Dec 15 05:52:26 2020

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