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

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

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
Sodium	(Na)	3 atoms

The binding sites of Manganese 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 Manganese atom.
In total 3 binding sites of Manganese 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 Manganese binding site number: 1; 2; 3;

Manganese 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 Manganese with other atoms in the Mn 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:Mn205 b:38.6 occ:0.50 O A:HOH373 2.8 26.1 1.0 O4 A:U3 4.4 18.2 1.0 K A:K203 4.5 23.8 0.6 O A:HOH316 4.5 14.6 1.0 O6 A:G4 4.5 12.8 1.0 C5 A:U3 4.9 18.1 1.0 C4 A:U3 5.0 18.0 1.0

Manganese 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 Manganese with other atoms in the Mn 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 B:Mn204 b:27.2 occ:1.00 OP1 B:A9 2.0 26.9 1.0 OP1 B:G10 2.3 20.1 1.0 N7 B:G10 2.4 20.2 1.0 O B:HOH240 2.4 17.6 1.0 C8 B:G10 3.1 18.9 1.0 P B:A9 3.3 23.7 1.0 C5 B:G10 3.6 20.2 1.0 P B:G10 3.7 20.3 1.0 O5' B:A9 3.8 24.1 1.0 OP2 B:A9 4.0 23.6 1.0 C5' B:A9 4.0 21.3 1.0 O6 B:G10 4.1 20.9 1.0 O5' B:G10 4.1 20.7 1.0 C6 B:G10 4.2 21.1 1.0 O B:HOH219 4.3 14.8 1.0 N9 B:G10 4.4 19.4 1.0 O3' B:A8 4.5 25.9 1.0 O B:HOH216 4.5 19.4 1.0 OP2 B:G10 4.5 19.5 1.0 O B:HOH225 4.6 19.6 1.0 C4 B:G10 4.6 19.6 1.0 O3' B:A9 4.8 19.4 1.0 NA B:NA209 4.8 18.1 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn206 b:23.7 occ:0.50 O6 B:G14 2.2 17.5 1.0 O B:HOH244 2.9 26.2 1.0 O B:HOH220 3.2 27.3 1.0 C6 B:G14 3.4 17.0 1.0 N4 A:C11 3.7 14.4 1.0 O6 A:G10 4.0 13.1 1.0 N4 B:C15 4.1 6.5 1.0 C5 B:G14 4.2 16.6 1.0 N7 B:G14 4.3 17.4 1.0 N1 B:G14 4.4 15.9 1.0 O A:HOH336 4.6 32.7 1.0 C4 A:C11 4.8 17.2 1.0

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