Magnesium 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:

Sodium

(Na)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Hiv-1(Mal) Genomic Rna Dis, PDB code: 2b8s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Structure of Hiv-1(Mal) Genomic Rna Dis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg103 b:47.0 occ:1.00 O A:HOH269 2.1 60.8 1.0 O B:HOH262 2.1 76.5 1.0 O A:HOH254 2.2 44.0 1.0 O B:HOH315 2.2 55.4 1.0 O A:HOH229 2.5 30.0 1.0 O B:HOH215 2.5 42.1 1.0 O3 B:SO4102 3.7 88.3 0.7 O4 A:U11 4.1 27.2 1.0 O6 B:G12 4.1 25.3 1.0 O6 A:G12 4.2 24.6 1.0 O B:HOH266 4.3 41.8 1.0 O B:HOH277 4.4 29.4 1.0 O4 B:U11 4.5 28.5 1.0 N4 B:C13 4.7 24.2 1.0 C4 A:U11 4.9 28.5 1.0 N4 A:C13 4.9 21.1 1.0

Magnesium binding site 2 out of 6 in the Structure of Hiv-1(Mal) Genomic Rna Dis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Hiv-1(Mal) Genomic Rna Dis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:38.4 occ:1.00 O A:HOH300 2.1 39.7 1.0 O A:HOH244 2.3 55.6 1.0 O A:HOH272 2.4 29.6 1.0 O A:HOH310 2.5 32.8 1.0 O A:HOH238 4.4 24.4 1.0 O4 A:U6 4.7 31.5 1.0 O A:HOH203 4.8 35.8 1.0 O6 A:G7 4.9 20.1 1.0

Magnesium binding site 3 out of 6 in the Structure of Hiv-1(Mal) Genomic Rna Dis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Hiv-1(Mal) Genomic Rna Dis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:60.3 occ:1.00 O6 A:G23 3.3 12.1 1.0 N7 A:G23 4.1 15.5 1.0 N6 A:A22 4.1 27.8 1.0 N7 A:A22 4.2 26.7 1.0 C6 A:G23 4.3 13.2 1.0 O3 A:SO4106 4.5 78.5 1.0 C5 A:G23 4.6 14.6 1.0 C5 A:A22 4.8 27.1 1.0 C6 A:A22 4.8 27.6 1.0 O A:HOH248 4.9 47.2 1.0 N4 A:C1 5.0 17.1 1.0

Magnesium binding site 4 out of 6 in the Structure of Hiv-1(Mal) Genomic Rna Dis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Hiv-1(Mal) Genomic Rna Dis within 5.0Å range:

Magnesium binding site 5 out of 6 in the Structure of Hiv-1(Mal) Genomic Rna Dis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Hiv-1(Mal) Genomic Rna Dis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg110 b:28.1 occ:0.45 O B:HOH274 3.4 55.3 1.0 OP1 B:C15 3.8 29.1 1.0 OP2 B:A16 3.9 32.0 1.0 O5' B:C15 4.4 27.5 1.0 OP2 B:U3 4.4 27.3 1.0 O B:HOH288 4.4 50.6 1.0 O B:HOH241 4.5 50.6 1.0 P B:C15 4.6 27.9 1.0 C5' B:C15 4.6 26.5 1.0 P B:A16 4.8 32.8 1.0

Magnesium binding site 6 out of 6 in the Structure of Hiv-1(Mal) Genomic Rna Dis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Hiv-1(Mal) Genomic Rna Dis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg112 b:42.3 occ:1.00 O A:HOH268 3.6 43.2 1.0 O B:HOH306 3.8 54.1 1.0 N2 B:G10 3.8 31.5 1.0 O B:HOH297 4.1 52.0 1.0 O4' A:A16 4.4 29.3 1.0 O2' A:A16 4.4 27.4 1.0 C1' A:A16 4.6 27.1 1.0 C1' B:U11 4.7 26.1 1.0 C2 B:G10 4.9 28.5 1.0 O4' B:U11 4.9 24.6 1.0 N3 B:G10 4.9 26.5 1.0 C4' A:A16 5.0 28.0 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