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

Protein crystallography data

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

Magnesium Binding Sites:

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 462d

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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 462d

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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 462d

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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 462d

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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 462d

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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 462d

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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 462d

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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 462d

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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

Reference:

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
Page generated: Mon Aug 11 05:29:35 2025

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