Sodium in PDB 2b8s: Structure of Hiv-1(Mal) Genomic Rna Dis

The structure of Structure of Hiv-1(Mal) Genomic Rna Dis, PDB code: 2b8s was solved by E.Ennifar, P.Walter, B.Ehresmann, C.Ehresmann, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.76
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	27.076, 114.822, 94.399, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.3

The structure of Structure of Hiv-1(Mal) Genomic Rna Dis also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Sodium atom in the Structure of Hiv-1(Mal) Genomic Rna Dis (pdb code 2b8s). 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 Hiv-1(Mal) Genomic Rna Dis, PDB code: 2b8s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Hiv-1(Mal) Genomic Rna Dis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Hiv-1(Mal) Genomic Rna Dis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:43.6 occ:1.00 C5 A:G7 3.8 21.3 1.0 O A:HOH309 3.8 47.6 1.0 N6 A:A16 4.0 24.3 1.0 C6 A:G7 4.0 20.3 1.0 N7 A:G7 4.1 21.7 1.0 C4 A:G7 4.1 22.7 1.0 O6 A:G7 4.4 20.1 1.0 O A:HOH253 4.4 29.6 1.0 C8 A:G7 4.4 25.3 1.0 O2' A:G7 4.5 32.6 1.0 N9 A:G7 4.5 26.1 1.0 O A:HOH203 4.5 35.8 1.0 N1 A:G7 4.5 21.8 1.0 N3 A:G7 4.6 20.1 1.0 C2 A:G7 4.7 20.1 1.0 O A:HOH300 4.8 39.7 1.0 C6 A:A16 5.0 26.5 1.0

Sodium binding site 2 out of 2 in the Structure of Hiv-1(Mal) Genomic Rna Dis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Hiv-1(Mal) Genomic Rna Dis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na111 b:38.8 occ:1.00 O2' B:A8 3.7 23.3 1.0 N3 B:A8 3.8 9.9 1.0 O4' B:G9 3.8 21.8 1.0 OP1 B:U11 3.9 29.6 1.0 O3' B:G10 4.1 25.0 1.0 C4' B:G9 4.2 22.7 1.0 C2 B:A8 4.3 7.4 1.0 C2' B:A8 4.4 19.9 1.0 P B:U11 4.5 27.1 1.0 O B:HOH286 4.6 39.4 1.0 C5' B:G10 4.7 21.6 1.0 C5' B:G9 4.7 21.2 1.0 C1' B:G9 4.8 22.7 1.0 C4' B:G10 4.9 24.0 1.0 C4 B:A8 5.0 10.7 1.0

E.Ennifar, P.Walter, B.Ehresmann, C.Ehresmann, P.Dumas. Crystal Structures of Coaxially Stacked Kissing Complexes of the Hiv-1 Rna Dimerization Initiation Site Nat.Struct.Biol. V. 8 1064 2001.
ISSN: ISSN 1072-8368
PubMed: 11702070
DOI: 10.1038/NSB727