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:
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
Go back to
Magnesium Binding Sites List in 1y95
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
Go back to
Magnesium Binding Sites List in 1y95
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
Go back to
Magnesium Binding Sites List in 1y95
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 Sites List in 1y95
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
Go back to
Magnesium Binding Sites List in 1y95
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
Go back to
Magnesium Binding Sites List in 1y95
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
Go back to
Magnesium Binding Sites List in 1y95
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
Go back to
Magnesium Binding Sites List in 1y95
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
Go back to
Magnesium Binding Sites List in 1y95
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
Go back to
Magnesium Binding Sites List in 1y95
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
|