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Magnesium in PDB 1y73: Hiv-1 Dis(Mal) Duplex Pt-Soaked

Protein crystallography data

The structure of Hiv-1 Dis(Mal) Duplex Pt-Soaked, PDB code: 1y73 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) 7.99 / 2.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 58.915, 58.915, 65.194, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 19.4

Other elements in 1y73:

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

Platinum (Pt) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hiv-1 Dis(Mal) Duplex Pt-Soaked (pdb code 1y73). 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 Pt-Soaked, PDB code: 1y73:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1y73

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Magnesium binding site 1 out of 8 in the Hiv-1 Dis(Mal) Duplex Pt-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 Pt-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg24

b:55.8
occ:0.93
 O6 A:G7 4.0 46.2 1.0
N7 A:G7 4.1 48.5 1.0
O4 A:U6 4.2 44.6 1.0
C5 A:U6 4.4 46.1 1.0
C4 A:U6 4.6 45.8 1.0
O B:HOH167 4.7 50.0 0.8
C6 A:G7 4.8 48.3 1.0
C5 A:G7 4.8 48.2 1.0

Magnesium binding site 2 out of 8 in 1y73

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Magnesium binding site 2 out of 8 in the Hiv-1 Dis(Mal) Duplex Pt-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 Pt-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg25

b:44.6
occ:1.00
 O B:HOH123 2.8 55.8 0.8
O6 A:G4 2.9 59.2 1.0
O4 A:U3 3.0 52.6 1.0
O B:HOH171 3.6 74.8 1.0
C4 A:U3 3.8 53.0 1.0
C6 A:G4 4.0 57.4 1.0
N7 A:G4 4.2 54.4 1.0
C5 A:U3 4.3 52.7 1.0
C5 A:G4 4.4 56.3 1.0
N6 B:A21 4.6 55.0 1.0
N4 B:C20 4.8 45.2 1.0
N3 A:U3 4.9 52.5 1.0
O6 B:G19 5.0 42.8 1.0
O4 A:U2 5.0 52.1 1.0

Magnesium binding site 3 out of 8 in 1y73

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Magnesium binding site 3 out of 8 in the Hiv-1 Dis(Mal) Duplex Pt-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 Pt-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg26

b:46.7
occ:0.73
 N7 A:G9 2.3 50.8 1.0
OP2 A:A8 2.8 54.2 1.0
C5 A:G9 3.1 51.5 1.0
O6 A:G9 3.3 52.4 1.0
C8 A:G9 3.3 51.0 1.0
C6 A:G9 3.5 51.7 1.0
P A:A8 4.2 54.1 1.0
C4 A:G9 4.3 51.2 1.0
N7 A:G10 4.4 52.7 1.0
N9 A:G9 4.4 51.3 1.0
C2' A:G7 4.4 48.6 1.0
OP2 A:G9 4.6 56.6 1.0
C3' A:G7 4.7 49.1 1.0
O3' A:G7 4.8 51.4 1.0
N1 A:G9 4.8 52.3 1.0

Magnesium binding site 4 out of 8 in 1y73

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Magnesium binding site 4 out of 8 in the Hiv-1 Dis(Mal) Duplex Pt-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 Pt-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg27

b:52.2
occ:0.97
 O B:HOH122 3.0 56.5 1.0
O6 B:G12 3.2 45.6 1.0
O B:HOH129 3.4 44.9 1.0
O6 A:G12 3.4 58.6 1.0
N4 B:C13 3.9 48.5 1.0
N4 A:C13 4.0 62.7 1.0
C6 B:G12 4.3 46.5 1.0
O4 B:U11 4.3 43.9 1.0
O B:HOH149 4.4 66.4 1.0
C6 A:G12 4.6 59.9 1.0
O4 A:U11 4.7 51.9 1.0
N7 B:G12 4.9 47.7 1.0

Magnesium binding site 5 out of 8 in 1y73

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Magnesium binding site 5 out of 8 in the Hiv-1 Dis(Mal) Duplex Pt-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 Pt-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg24

b:51.6
occ:0.62
 OP1 B:G9 2.4 52.0 0.5
OP1 A:G9 3.1 58.1 1.0
OP1 B:G9 3.1 54.9 0.5
P B:G9 3.5 51.6 0.5
O3' B:A8 3.7 52.6 0.5
O3' B:A8 4.1 55.2 0.5
OP2 B:G9 4.1 51.8 0.5
P B:G9 4.2 53.5 0.5
P A:G9 4.3 57.6 1.0
O3' A:A8 4.3 57.5 1.0
C5' A:G9 4.8 55.4 1.0
O5' B:G9 4.8 49.8 0.5
C5' B:G9 4.8 46.9 0.5
OP2 A:G10 4.9 53.4 1.0
O2' B:A8 5.0 60.7 0.5

Magnesium binding site 6 out of 8 in 1y73

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Magnesium binding site 6 out of 8 in the Hiv-1 Dis(Mal) Duplex Pt-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 Pt-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg25

b:48.7
occ:1.00
 O B:HOH151 4.0 51.2 0.6
O A:HOH228 4.1 76.8 0.6
O4 B:U3 4.2 46.4 1.0
O A:HOH255 4.2 53.6 0.9
O6 B:G4 4.3 37.5 1.0
O A:HOH252 4.3 51.7 1.0
C4 B:U3 4.7 47.1 1.0
O B:HOH140 4.8 48.3 0.6
C5 B:U3 4.8 47.4 1.0

Magnesium binding site 7 out of 8 in 1y73

Go back to Magnesium Binding Sites List in 1y73
Magnesium binding site 7 out of 8 in the Hiv-1 Dis(Mal) Duplex Pt-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 Pt-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg26

b:59.3
occ:0.83
 O A:HOH246 3.5 87.8 0.5
O6 B:G7 4.0 38.4 0.5
O A:HOH235 4.1 42.8 0.7
O4 B:U6 4.1 37.5 1.0
O A:HOH222 4.3 68.4 0.5
O6 B:G7 4.4 40.5 0.5
C5 B:U6 4.5 36.0 1.0
C4 B:U6 4.5 35.5 1.0
N7 B:G7 4.5 39.2 0.5
N7 B:G7 4.6 40.8 0.5
C6 B:G7 4.9 38.0 0.5

Magnesium binding site 8 out of 8 in 1y73

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Magnesium binding site 8 out of 8 in the Hiv-1 Dis(Mal) Duplex Pt-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 Pt-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg27

b:58.9
occ:1.00
 OP2 B:A8 2.9 53.2 0.5
N7 B:G9 3.2 41.5 0.5
N7 B:G9 3.2 38.8 0.5
OP2 B:A8 3.3 49.6 0.5
O5' B:A8 3.6 54.2 0.5
OP2 B:G9 3.7 54.5 0.5
O6 B:G9 3.8 39.1 0.5
O B:HOH159 3.8 57.7 0.9
P B:A8 3.9 53.0 0.5
C5 B:G9 3.9 38.9 0.5
C8 B:G9 3.9 42.5 0.5
C8 B:G9 4.0 40.2 0.5
C5' B:A8 4.1 55.9 0.5
C6 B:G9 4.1 38.5 0.5
OP1 B:A8 4.1 50.2 0.5
P B:A8 4.2 49.6 0.5
C5 B:G9 4.3 41.5 0.5
O6 B:G9 4.5 41.8 0.5
O3' B:G7 4.7 49.5 0.5
O6 B:G10 4.7 40.2 1.0
N7 B:G10 4.7 39.4 1.0
C6 B:G9 4.8 41.3 0.5
OP2 B:G9 4.9 51.8 0.5
O B:HOH122 4.9 56.5 1.0
C3' B:G7 5.0 46.0 0.5
C4 B:G9 5.0 39.8 0.5

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 18:31:36 2024

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