Magnesium in PDB 462d: Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site

The structure of Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site, PDB code: 462d was solved by E.Ennifar, M.Yusupov, P.Walter, R.Marquet, C.Ehresmann, B.Ehresmann, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.100, 59.100, 64.000, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 21.2

The binding sites of Magnesium atom in the Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site (pdb code 462d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site, PDB code: 462d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of the Hiv-1 Genomic 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 Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:68.2 occ:1.00 O A:HOH606 2.0 58.2 0.9 O A:HOH621 2.1 84.7 1.0 O A:HOH618 2.2 65.9 1.0 O A:HOH622 2.5 95.5 1.0 O A:HOH591 3.6 47.8 0.9 N7 A:G7 4.2 35.7 1.0 O4 A:U6 4.2 32.2 1.0 O6 A:G7 4.2 37.7 1.0 O A:HOH636 4.3 39.0 0.7 C5 A:U6 4.5 37.6 1.0 O A:HOH552 4.5 43.6 0.9 C4 A:U6 4.6 37.6 1.0 C5 A:G7 5.0 36.7 1.0 C6 A:G7 5.0 37.9 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of the Hiv-1 Genomic 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 Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:45.3 occ:1.00 O A:HOH587 2.6 59.7 1.0 O A:HOH607 2.7 54.7 0.8 O6 A:G4 2.8 43.9 1.0 O B:HOH517 2.8 49.8 1.0 O4 A:U3 2.9 44.8 1.0 O B:HOH586 3.2 81.6 1.0 C4 A:U3 3.8 45.5 1.0 C6 A:G4 3.8 46.2 1.0 N7 A:G4 4.1 46.1 1.0 C5 A:U3 4.2 45.1 1.0 N4 B:C20 4.3 39.9 1.0 C5 A:G4 4.3 46.4 1.0 O A:HOH599 4.6 64.9 0.6 O6 B:G19 4.6 35.2 1.0 N6 B:A21 4.7 45.0 1.0 O B:HOH519 4.7 53.1 1.0 N4 A:C5 4.7 37.0 1.0 N3 A:U3 4.8 46.0 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of the Hiv-1 Genomic 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 Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:48.6 occ:1.00 O A:HOH623 2.2 71.7 1.0 N7 A:G9 2.3 35.9 1.0 O A:HOH509 2.3 60.9 1.0 OP2 A:A8 2.4 37.7 1.0 O A:HOH583 2.5 58.3 1.0 O A:HOH608 2.5 52.6 0.6 C8 A:G9 3.2 34.9 1.0 C5 A:G9 3.3 35.6 1.0 O6 A:G9 3.5 29.4 1.0 C6 A:G9 3.7 35.2 1.0 P A:A8 3.9 39.8 1.0 O A:HOH582 4.1 47.8 1.0 N9 A:G9 4.4 36.0 1.0 C4 A:G9 4.4 36.1 1.0 N7 A:G10 4.4 46.1 1.0 OP2 A:G9 4.5 47.8 1.0 OP1 A:A8 4.6 38.1 1.0 C2' A:G7 4.6 34.8 1.0 O3' A:G7 4.7 36.8 1.0 C3' A:G7 4.8 34.9 1.0 O5' A:A8 4.8 41.7 1.0 O A:HOH553 4.9 74.3 0.9 O6 A:G10 4.9 41.5 1.0 C5' A:A8 4.9 42.3 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of the Hiv-1 Genomic 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 Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:66.7 occ:1.00 O B:HOH513 1.9 70.8 0.5 O B:HOH515 3.0 49.1 1.0 O6 B:G12 3.1 40.6 1.0 O A:HOH581 3.1 97.3 1.0 O6 A:G12 3.1 51.2 1.0 O A:HOH582 3.5 47.8 1.0 N4 B:C13 3.7 42.1 1.0 O A:HOH553 3.7 74.3 0.9 O B:HOH531 3.8 34.3 1.0 N4 A:C13 3.9 43.9 1.0 C6 B:G12 4.2 37.9 1.0 C6 A:G12 4.3 50.2 1.0 O4 B:U11 4.4 33.9 1.0 O B:HOH584 4.5 42.0 0.7 O A:HOH594 4.6 61.4 0.7 O A:HOH558 4.8 58.0 0.9 C4 B:C13 4.8 45.3 1.0 O B:HOH592 4.9 48.7 0.9 N7 B:G12 4.9 37.3 1.0 C5 B:G12 5.0 37.2 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:85.7 occ:1.00 O A:HOH565 2.0 72.3 1.0 OP1 B:G9 2.1 39.6 0.5 OP1 B:G9 2.1 35.1 0.5 O A:HOH597 2.1 66.4 1.0 OP1 A:G9 2.1 46.8 1.0 O B:HOH571 2.4 71.5 1.0 O B:HOH594 2.5 45.5 0.9 P B:G9 3.3 35.0 0.5 P A:G9 3.4 47.3 1.0 P B:G9 3.5 38.5 0.5 O3' A:A8 3.7 45.2 1.0 OP2 B:G9 3.8 35.3 0.5 O B:HOH524 4.0 66.6 1.0 OP2 A:G9 4.2 47.8 1.0 OP2 B:G9 4.2 40.3 0.5 OP2 B:G10 4.2 32.5 1.0 O3' B:A8 4.2 36.5 0.5 O3' B:A8 4.3 40.4 0.5 O5' B:G9 4.4 34.9 0.5 O5' B:G9 4.4 37.7 0.5 O5' A:G9 4.5 44.6 1.0 C5' B:G9 4.6 33.2 0.5 OP2 A:G10 4.6 45.8 1.0 O B:HOH552 4.7 61.0 0.9 O A:HOH521 4.8 49.1 1.0 C5' B:G9 4.9 32.0 0.5 C5' A:G9 4.9 41.5 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:54.0 occ:1.00 O B:HOH605 2.0 64.2 0.8 O B:HOH606 2.3 52.0 1.0 O B:HOH582 2.3 82.5 0.9 O B:HOH572 2.3 47.8 0.9 O B:HOH607 2.4 91.4 1.0 O B:HOH537 3.9 61.6 0.9 O A:HOH542 4.0 58.4 1.0 O B:HOH539 4.0 51.7 1.0 O B:HOH549 4.2 81.7 1.0 O4 B:U3 4.3 40.7 1.0 O6 B:G4 4.4 33.4 1.0 O A:HOH625 4.6 49.7 1.0 O B:HOH533 4.6 48.5 0.9 O A:HOH563 4.7 31.3 0.5 O A:HOH585 4.7 45.9 0.7 N7 B:G4 4.7 33.7 1.0 C4 B:U3 4.8 42.0 1.0 C5 B:U3 4.8 39.8 1.0 O A:HOH516 5.0 40.8 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:41.2 occ:1.00 O B:HOH589 2.0 29.5 0.8 O B:HOH565 2.0 45.8 1.0 O B:HOH523 2.2 51.0 1.0 O B:HOH580 2.3 54.3 1.0 O B:HOH573 2.4 51.3 1.0 O B:HOH564 2.5 21.5 1.0 O B:HOH613 3.7 25.4 0.9 O6 B:G7 3.9 28.6 0.5 O6 B:G7 4.0 29.2 0.5 O B:HOH612 4.1 40.5 0.8 O A:HOH570 4.2 56.0 1.0 O4 B:U6 4.3 28.5 1.0 O B:HOH535 4.3 59.6 1.0 N7 B:G7 4.6 31.9 0.5 C5 B:U6 4.7 26.6 1.0 C4 B:U6 4.7 29.3 1.0 N7 B:G7 4.7 31.6 0.5 O B:HOH510 4.8 37.9 1.0 C6 B:G7 4.8 31.0 0.5 C6 B:G7 5.0 31.1 0.5

Magnesium binding site 8 out of 8 in the Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Hiv-1 Genomic Rna Dimerization Initiation Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:35.8 occ:1.00 O B:HOH566 1.9 42.5 1.0 O B:HOH509 2.0 37.9 0.8 OP2 B:A8 2.0 29.8 0.5 O B:HOH507 2.1 45.7 0.9 N7 B:G9 2.3 29.5 0.5 N7 B:G9 2.4 32.2 0.5 OP2 B:A8 2.5 33.2 0.5 O B:HOH511 2.6 34.1 0.8 C8 B:G9 3.2 31.4 0.5 C5 B:G9 3.3 29.3 0.5 C8 B:G9 3.3 33.6 0.5 C5 B:G9 3.4 31.9 0.5 P B:A8 3.5 31.3 0.5 O6 B:G9 3.6 26.8 0.5 O6 B:G9 3.6 29.2 0.5 P B:A8 3.8 33.6 0.5 C6 B:G9 3.8 29.9 0.5 C6 B:G9 3.9 32.4 0.5 O B:HOH581 4.0 58.4 1.0 O B:HOH592 4.1 48.7 0.9 O B:HOH528 4.1 49.7 1.0 O B:HOH584 4.2 42.0 0.7 O5' B:A8 4.2 34.2 0.5 OP1 B:A8 4.2 31.0 0.5 OP1 B:A8 4.2 35.5 0.5 N9 B:G9 4.4 31.4 0.5 OP2 B:G9 4.4 40.3 0.5 O3' B:G7 4.4 28.8 0.5 C4 B:G9 4.4 30.4 0.5 C2' B:G7 4.5 29.0 0.5 C5' B:A8 4.5 38.5 0.5 N9 B:G9 4.5 33.1 0.5 OP2 B:G9 4.6 35.3 0.5 C3' B:G7 4.6 29.2 0.5 C4 B:G9 4.6 32.7 0.5 O3' B:G7 4.7 32.4 0.5 N7 B:G10 4.7 32.2 1.0 O5' B:A8 4.8 35.2 0.5 C3' B:G7 4.8 31.5 0.5 C2' B:G7 4.8 31.1 0.5

E.Ennifar, M.Yusupov, P.Walter, R.Marquet, B.Ehresmann, C.Ehresmann, P.Dumas. The Crystal Structure of the Dimerization Initiation Site of Genomic Hiv-1 Rna Reveals An Extended Duplex with Two Adenine Bulges. Structure Fold.Des. V. 7 1439 1999.
ISSN: ISSN 0969-2126
PubMed: 10574792
DOI: 10.1016/S0969-2126(00)80033-7