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Magnesium in PDB 1y95: Hiv-1 Dis(Mal) Duplex Pb-Soaked

Protein crystallography data

The structure of Hiv-1 Dis(Mal) Duplex Pb-Soaked, PDB code: 1y95 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) 7.97 / 2.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 59.200, 59.200, 65.800, 90.00, 90.00, 120.00
R / Rfree (%) 22.6 / 25.3

Other elements in 1y95:

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

Lead (Pb) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hiv-1 Dis(Mal) Duplex Pb-Soaked (pdb code 1y95). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Hiv-1 Dis(Mal) Duplex Pb-Soaked, PDB code: 1y95:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 1y95

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Magnesium binding site 1 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-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 Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg30

b:56.9
occ:1.00
 O6 A:G7 3.8 53.4 1.0
N7 A:G7 3.9 54.2 1.0
O4 A:U6 4.0 51.5 1.0
O B:HOH126 4.0 77.0 0.8
C5 A:U6 4.5 49.4 1.0
C4 A:U6 4.5 49.8 1.0
C6 A:G7 4.5 53.9 1.0
C5 A:G7 4.6 54.1 1.0

Magnesium binding site 2 out of 10 in 1y95

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Magnesium binding site 2 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-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 Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg32

b:46.0
occ:1.00
 MG B:MG41 2.1 63.4 0.8
O6 A:G4 2.9 53.8 1.0
O4 A:U3 3.1 54.7 1.0
MG A:MG40 3.6 67.1 1.0
C4 A:U3 3.9 54.6 1.0
C6 A:G4 4.0 54.7 1.0
C5 A:U3 4.3 55.4 1.0
N7 A:G4 4.5 56.5 1.0
C5 A:G4 4.6 55.7 1.0
N6 B:A21 4.7 49.9 1.0
N4 A:C5 4.7 54.0 1.0
N4 B:C20 4.8 55.6 1.0
O6 B:G19 4.9 44.4 1.0
N3 A:U3 5.0 54.1 1.0

Magnesium binding site 3 out of 10 in 1y95

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Magnesium binding site 3 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-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 Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg37

b:50.0
occ:0.98
 O B:HOH143 3.4 68.0 0.8
O6 A:G12 3.7 51.9 1.0
O4 A:U11 3.9 52.6 1.0
C4 A:U11 4.5 52.9 1.0
C6 A:G12 4.7 52.1 1.0
O6 B:G12 4.7 55.5 1.0
N7 A:G12 4.7 53.0 1.0
C5 A:U11 4.8 52.7 1.0
N4 A:C13 4.9 58.8 1.0
N4 B:C13 5.0 56.6 1.0

Magnesium binding site 4 out of 10 in 1y95

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Magnesium binding site 4 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-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 Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg38

b:57.4
occ:0.98
 N7 A:G23 3.7 40.6 1.0
O6 A:G23 3.8 41.5 1.0
N7 A:A22 4.4 41.2 1.0
C5 A:G23 4.5 39.9 1.0
C6 A:G23 4.5 39.9 1.0
C8 A:G23 4.8 39.8 1.0

Magnesium binding site 5 out of 10 in 1y95

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Magnesium binding site 5 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-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 Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg40

b:67.1
occ:1.00
 N7 A:G4 3.4 56.5 1.0
MG A:MG32 3.6 46.0 1.0
OP2 A:G4 3.8 62.5 1.0
C5 A:U3 3.8 55.4 1.0
C8 A:G4 4.2 57.5 1.0
C6 A:U3 4.3 55.7 1.0
C4 A:U3 4.4 54.6 1.0
C5 A:G4 4.6 55.7 1.0
OP2 A:U3 4.6 58.9 1.0
O4 A:U3 4.6 54.7 1.0
O6 A:G4 4.7 53.8 1.0

Magnesium binding site 6 out of 10 in 1y95

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Magnesium binding site 6 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-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 Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg43

b:39.5
occ:1.00
 N7 A:G19 3.7 37.4 1.0
N7 A:A18 4.1 48.8 1.0
N4 A:C20 4.2 42.2 1.0
MG B:MG33 4.2 34.9 1.0
O6 A:G19 4.3 38.5 1.0
C8 A:A18 4.6 47.6 1.0
C8 A:G19 4.6 37.9 1.0
C5 A:G19 4.6 37.2 1.0
C5 A:A18 4.7 47.0 1.0
C6 A:G19 4.9 38.2 1.0
OP2 A:A18 4.9 50.7 1.0
N6 A:A18 5.0 43.7 1.0

Magnesium binding site 7 out of 10 in 1y95

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Magnesium binding site 7 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-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 Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg33

b:34.9
occ:1.00
 O B:HOH127 3.3 47.9 1.0
O6 B:G4 3.4 42.9 1.0
O4 B:U3 3.4 50.5 1.0
C4 B:U3 4.2 48.3 1.0
MG A:MG43 4.2 39.5 1.0
C6 B:G4 4.4 41.6 1.0
C5 B:U3 4.5 47.3 1.0
N7 B:G4 4.5 41.8 1.0
N4 A:C20 4.9 42.2 1.0
C5 B:G4 4.9 41.0 1.0

Magnesium binding site 8 out of 10 in 1y95

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Magnesium binding site 8 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-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 Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg34

b:67.1
occ:1.00
 O B:HOH116 2.5 41.2 1.0
O6 B:G7 3.2 50.8 0.5
O6 B:G7 3.5 47.7 0.5
O4 B:U6 3.6 39.8 1.0
N4 A:C17 4.3 44.4 1.0
C6 B:G7 4.3 49.2 0.5
C4 B:U6 4.4 36.4 1.0
N7 B:G7 4.4 46.7 0.5
C6 B:G7 4.5 47.0 0.5
N6 A:A16 4.6 48.4 1.0
N7 B:G7 4.7 47.9 0.5
C5 B:G7 4.8 46.9 0.5
C5 B:G7 4.9 48.5 0.5
C5 B:U6 4.9 36.4 1.0
O B:HOH123 4.9 44.7 0.8
N6 A:A18 4.9 43.7 1.0

Magnesium binding site 9 out of 10 in 1y95

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Magnesium binding site 9 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Hiv-1 Dis(Mal) Duplex Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg41

b:63.4
occ:0.79
 MG A:MG32 2.1 46.0 1.0
O6 A:G4 3.7 53.8 1.0
O6 B:G19 3.9 44.4 1.0
N4 B:C20 4.1 55.6 1.0
N6 B:A18 4.5 51.0 1.0
N7 B:A18 4.6 53.3 1.0
N7 B:G19 4.7 47.6 1.0
N4 A:C5 4.8 54.0 1.0
O4 A:U3 4.8 54.7 1.0
C6 B:G19 4.9 44.9 1.0
C6 A:G4 4.9 54.7 1.0

Magnesium binding site 10 out of 10 in 1y95

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Magnesium binding site 10 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Hiv-1 Dis(Mal) Duplex Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg42

b:56.5
occ:0.88
 O B:HOH119 4.0 35.0 0.9
O5' B:C1 4.8 52.0 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: Tue Aug 13 18:33:05 2024

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