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Magnesium in PDB 1o3z: Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked

Protein crystallography data

The structure of Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked, PDB code: 1o3z 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) 8.00 / 2.65
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 59.100, 59.100, 64.100, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 22.8

Other elements in 1o3z:

The structure of Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked also contains other interesting chemical elements:

Ruthenium (Ru) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked (pdb code 1o3z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked, PDB code: 1o3z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1o3z

Go back to Magnesium Binding Sites List in 1o3z
Magnesium binding site 1 out of 8 in the Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:58.2
occ:1.00
 O A:HOH613 2.1 78.1 1.0
O A:HOH598 2.2 73.8 0.9
O A:HOH610 2.2 60.2 1.0
O A:HOH584 3.6 47.2 0.9
N7 A:G7 4.1 34.8 1.0
O6 A:G7 4.1 30.0 1.0
O4 A:U6 4.2 35.5 1.0
O A:HOH627 4.3 35.9 0.7
C5 A:U6 4.3 38.8 1.0
O A:HOH546 4.5 44.3 0.9
C4 A:U6 4.5 38.2 1.0
C5 A:G7 4.8 33.2 1.0
C6 A:G7 4.8 31.6 1.0

Magnesium binding site 2 out of 8 in 1o3z

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Magnesium binding site 2 out of 8 in the Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:34.1
occ:1.00
 O A:HOH581 2.7 59.2 1.0
O6 A:G4 2.8 41.9 1.0
O B:HOH513 2.8 42.7 1.0
O4 A:U3 3.0 42.9 1.0
O B:HOH582 3.2 79.4 1.0
C4 A:U3 3.8 41.3 1.0
C6 A:G4 3.8 42.5 1.0
N7 A:G4 4.1 41.3 1.0
C5 A:U3 4.2 41.2 1.0
C5 A:G4 4.3 42.2 1.0
N4 B:C20 4.4 36.0 1.0
N6 B:A21 4.5 44.5 1.0
O B:HOH515 4.7 46.5 1.0
O6 B:G19 4.8 34.5 1.0
N4 A:C5 4.8 34.2 1.0
N3 A:U3 4.8 40.5 1.0

Magnesium binding site 3 out of 8 in 1o3z

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Magnesium binding site 3 out of 8 in the Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg307

b:46.7
occ:1.00
 O A:HOH614 2.2 69.3 1.0
O A:HOH501 2.3 54.6 1.0
N7 A:G9 2.4 34.8 1.0
OP2 A:A8 2.5 33.3 1.0
O A:HOH577 2.5 55.2 1.0
O A:HOH600 2.5 47.6 0.6
C5 A:G9 3.2 34.2 1.0
C8 A:G9 3.3 34.8 1.0
O6 A:G9 3.4 32.8 1.0
C6 A:G9 3.6 33.8 1.0
P A:A8 3.9 33.8 1.0
O A:HOH576 4.1 51.0 1.0
OP2 A:G9 4.3 39.0 1.0
C4 A:G9 4.4 34.7 1.0
N9 A:G9 4.4 35.3 1.0
C2' A:G7 4.4 32.8 1.0
N7 A:G10 4.4 41.6 1.0
O3' A:G7 4.6 33.8 1.0
C3' A:G7 4.6 33.8 1.0
OP1 A:A8 4.7 34.8 1.0
O A:HOH547 4.9 71.9 0.9
O5' A:A8 4.9 36.1 1.0
N1 A:G9 5.0 34.0 1.0

Magnesium binding site 4 out of 8 in 1o3z

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Magnesium binding site 4 out of 8 in the Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg308

b:63.3
occ:1.00
 O B:HOH509 1.9 67.5 0.5
O6 B:G12 3.0 34.1 1.0
O B:HOH511 3.0 38.5 1.0
O A:HOH575 3.1 93.8 1.0
O6 A:G12 3.4 43.7 1.0
O A:HOH576 3.5 51.0 1.0
O A:HOH547 3.7 71.9 0.9
N4 B:C13 3.7 40.9 1.0
O B:HOH527 3.8 30.1 1.0
N4 A:C13 3.9 40.8 1.0
C6 B:G12 4.1 33.3 1.0
O4 B:U11 4.3 37.0 1.0
O B:HOH580 4.5 40.9 0.7
C6 A:G12 4.5 43.1 1.0
O A:HOH587 4.6 57.8 0.7
O A:HOH552 4.8 50.4 0.9
C4 B:C13 4.9 39.9 1.0
O B:HOH588 4.9 45.5 0.9
C5 B:G12 4.9 33.7 1.0
N7 B:G12 4.9 33.9 1.0

Magnesium binding site 5 out of 8 in 1o3z

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Magnesium binding site 5 out of 8 in the Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:39.2
occ:0.54
 O A:HOH559 2.0 70.0 1.0
O A:HOH590 2.1 60.6 1.0
OP1 A:G9 2.4 39.8 1.0
O B:HOH565 2.4 64.2 1.0
O B:HOH590 2.5 43.1 0.9
OP1 B:G9 2.5 35.5 0.5
OP1 B:G9 2.6 35.5 0.5
OP2 B:G9 3.0 34.2 0.5
P B:G9 3.2 33.4 0.5
P A:G9 3.6 39.8 1.0
O3' A:A8 3.8 39.6 1.0
O3' B:A8 3.9 34.7 0.5
P B:G9 3.9 34.4 0.5
O B:HOH520 4.0 62.1 1.0
OP2 B:G10 4.3 28.8 1.0
OP2 A:G9 4.5 39.0 1.0
OP2 A:G10 4.6 40.9 1.0
O3' B:A8 4.6 36.1 0.5
O5' B:G9 4.6 32.5 0.5
O5' B:G9 4.7 33.2 0.5
C5' B:G9 4.7 29.8 0.5
O B:HOH546 4.7 55.2 0.9
O5' A:G9 4.7 39.6 1.0
O A:HOH513 4.8 45.1 1.0
OP2 B:G9 4.9 36.5 0.5
C5' A:G9 5.0 39.0 1.0
P B:G10 5.0 29.1 1.0

Magnesium binding site 6 out of 8 in 1o3z

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Magnesium binding site 6 out of 8 in the Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:47.1
occ:1.00
 O B:HOH599 2.0 58.6 0.8
O B:HOH600 2.3 44.9 1.0
O B:HOH577 2.3 73.9 0.9
O B:HOH566 2.3 44.9 0.9
O B:HOH601 2.4 86.9 1.0
O B:HOH532 3.9 53.8 0.9
O A:HOH535 4.0 54.9 1.0
O B:HOH534 4.0 45.1 1.0
O4 B:U3 4.3 36.7 1.0
O6 B:G4 4.4 30.7 1.0
O B:HOH529 4.6 43.6 0.9
O A:HOH557 4.7 27.4 0.5
O A:HOH579 4.7 39.2 0.7
C5 B:U3 4.8 37.0 1.0
N7 B:G4 4.8 29.5 1.0
C4 B:U3 4.8 37.8 1.0
O A:HOH508 5.0 35.0 1.0

Magnesium binding site 7 out of 8 in 1o3z

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Magnesium binding site 7 out of 8 in the Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:53.5
occ:1.00
 O B:HOH559 2.1 44.4 1.0
O B:HOH519 2.2 49.8 1.0
O B:HOH586 2.2 48.5 0.8
O B:HOH574 2.3 51.6 1.0
O B:HOH567 2.3 50.5 1.0
O B:HOH558 2.5 34.5 1.0
O6 B:G7 3.4 29.0 0.5
O B:HOH606 4.1 36.5 0.8
O4 B:U6 4.1 22.9 1.0
O6 B:G7 4.1 29.1 0.5
O A:HOH564 4.2 52.0 1.0
C6 B:G7 4.4 28.2 0.5
N7 B:G7 4.6 27.9 0.5
C4 B:U6 4.6 23.6 1.0
C5 B:U6 4.6 22.9 1.0
N7 B:G7 4.7 27.0 0.5
O B:HOH506 4.8 27.0 1.0
C5 B:G7 4.9 27.9 0.5
C6 B:G7 5.0 27.7 0.5

Magnesium binding site 8 out of 8 in 1o3z

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Magnesium binding site 8 out of 8 in the Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Hiv-1 Dis(Mal) Duplex Ru Hexamine-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:43.8
occ:1.00
 O B:HOH560 1.9 40.7 1.0
O B:HOH505 2.0 35.5 0.8
O B:HOH503 2.1 40.3 0.9
OP2 B:A8 2.4 26.0 0.5
N7 B:G9 2.4 25.1 0.5
N7 B:G9 2.5 27.0 0.5
O B:HOH507 2.6 34.8 0.8
OP2 B:A8 2.6 28.8 0.5
C8 B:G9 3.3 25.7 0.5
C8 B:G9 3.3 27.4 0.5
C5 B:G9 3.4 25.7 0.5
OP1 B:A8 3.4 29.7 0.5
P B:A8 3.5 28.6 0.5
C5 B:G9 3.7 28.3 0.5
O6 B:G9 3.7 28.4 0.5
P B:A8 3.8 26.8 0.5
C6 B:G9 3.9 26.9 0.5
O B:HOH576 4.0 49.0 1.0
OP2 B:G9 4.0 36.5 0.5
O6 B:G9 4.1 31.1 0.5
O B:HOH588 4.1 45.5 0.9
O B:HOH524 4.1 46.3 1.0
O B:HOH580 4.2 40.9 0.7
C6 B:G9 4.3 29.6 0.5
N9 B:G9 4.4 26.1 0.5
C2' B:G7 4.4 27.0 0.5
C4 B:G9 4.4 26.0 0.5
OP1 B:A8 4.5 28.0 0.5
O3' B:G7 4.5 25.6 0.5
O3' B:G7 4.5 27.8 0.5
C3' B:G7 4.6 26.8 0.5
N9 B:G9 4.6 27.4 0.5
C2' B:G7 4.6 25.4 0.5
C3' B:G7 4.6 25.2 0.5
O5' B:A8 4.7 31.4 0.5
N7 B:G10 4.7 26.9 1.0
C4 B:G9 4.8 28.3 0.5
O5' B:A8 4.9 29.8 0.5
O5' B:G9 4.9 33.2 0.5
C5' B:A8 4.9 34.1 0.5
C5' B:A8 5.0 33.5 0.5
O6 B:G10 5.0 26.3 1.0

Reference:

E.Ennifar, P.Walter, P.Dumas. A Crystallographic Study of the Binding of 13 Metal Ions to Two Related Rna Duplexes. Nucleic Acids Res. V. 31 2671 2003.
ISSN: ISSN 0305-1048
PubMed: 12736317
DOI: 10.1093/NAR/GKG350
Page generated: Mon Dec 14 06:34:18 2020

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