Magnesium in PDB 1k9w: Hiv-1(Mal) Rna Dimerization Initiation Site

The structure of Hiv-1(Mal) Rna Dimerization Initiation Site, PDB code: 1k9w 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 / 3.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.070, 27.320, 92.100, 90.00, 93.47, 90.00
R / Rfree (%)	22.7 / 26.5

The binding sites of Magnesium atom in the Hiv-1(Mal) Rna Dimerization Initiation Site (pdb code 1k9w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Hiv-1(Mal) Rna Dimerization Initiation Site, PDB code: 1k9w:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Hiv-1(Mal) Rna Dimerization Initiation Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hiv-1(Mal) Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:85.7 occ:1.00 N3 B:G9 4.3 22.2 1.0 N2 B:G9 4.5 50.5 1.0 C5' B:G10 4.6 42.0 1.0 O3' B:G9 4.8 34.9 1.0 C2 B:G9 4.9 30.6 1.0 C1' B:G9 5.0 9.5 1.0

Magnesium binding site 2 out of 4 in the Hiv-1(Mal) Rna Dimerization Initiation Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hiv-1(Mal) Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg102 b:70.5 occ:1.00 N7 D:G9 3.0 33.1 1.0 O6 D:G9 3.3 36.7 1.0 N7 D:A8 3.6 26.7 1.0 C5 D:G9 3.7 20.6 1.0 C8 D:A8 3.8 27.5 1.0 C6 D:G9 3.9 22.0 1.0 C8 D:G9 4.1 33.0 1.0 OP1 D:A8 4.3 83.9 1.0 C5 D:A8 4.4 13.1 1.0 N9 D:A8 4.8 17.8 1.0

Magnesium binding site 3 out of 4 in the Hiv-1(Mal) Rna Dimerization Initiation Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hiv-1(Mal) Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:71.9 occ:1.00 OP1 B:U11 3.1 24.1 1.0 O2' B:A8 3.3 24.4 1.0 OP2 B:G12 4.2 46.4 1.0 O3' B:A8 4.2 22.7 1.0 P B:U11 4.2 43.0 1.0 OP2 B:U11 4.5 32.3 1.0 C2' B:A8 4.6 19.5 1.0 C5' B:G9 4.8 24.3 1.0 C3' B:A8 4.8 20.5 1.0 O5' B:U11 4.9 33.2 1.0 OP1 B:G12 5.0 49.7 1.0 C4' B:A8 5.0 13.2 1.0 P B:G12 5.0 39.9 1.0

Magnesium binding site 4 out of 4 in the Hiv-1(Mal) Rna Dimerization Initiation Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hiv-1(Mal) Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:41.5 occ:1.00 OP1 B:C15 3.4 39.1 1.0 C5' B:C15 4.2 15.8 1.0 P B:C15 4.5 32.8 1.0 O5' B:C15 4.9 3.5 1.0 OP2 B:C15 4.9 17.6 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