Magnesium in PDB 1qp5: Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract
Protein crystallography data
The structure of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract, PDB code: 1qp5
was solved by
Y.Timsit,
E.Vilbois,
D.Moras,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
15.00 /
2.60
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.900,
65.900,
47.100,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
n/a /
n/a
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract
(pdb code 1qp5). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract, PDB code: 1qp5:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 1qp5
Go back to
Magnesium Binding Sites List in 1qp5
Magnesium binding site 1 out
of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg68
b:19.0
occ:0.81
|
O
|
A:HOH71
|
2.0
|
17.0
|
0.2
|
O
|
A:HOH74
|
2.0
|
10.5
|
1.0
|
O
|
B:HOH70
|
2.0
|
16.7
|
0.7
|
O
|
A:HOH72
|
2.0
|
11.3
|
0.8
|
O
|
B:HOH73
|
2.0
|
16.9
|
0.3
|
O
|
B:HOH69
|
2.0
|
21.4
|
0.4
|
O6
|
A:DG7
|
3.3
|
54.7
|
1.0
|
O6
|
B:DG17
|
3.6
|
20.5
|
1.0
|
N7
|
B:DG16
|
4.2
|
2.6
|
1.0
|
O
|
B:HOH60
|
4.2
|
69.6
|
0.7
|
O
|
B:HOH47
|
4.3
|
2.0
|
1.0
|
C6
|
A:DG7
|
4.5
|
47.7
|
1.0
|
C6
|
B:DG17
|
4.8
|
21.0
|
1.0
|
C8
|
B:DG16
|
4.9
|
2.0
|
1.0
|
C5
|
B:DG16
|
5.0
|
2.0
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 1qp5
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Magnesium Binding Sites List in 1qp5
Magnesium binding site 2 out
of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg75
b:3.7
occ:0.35
|
O
|
A:HOH77
|
2.0
|
2.0
|
0.3
|
O
|
A:HOH76
|
2.0
|
2.5
|
0.5
|
OP1
|
A:DA12
|
4.4
|
15.0
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 1qp5
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Magnesium Binding Sites List in 1qp5
Magnesium binding site 3 out
of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg80
b:9.9
occ:0.69
|
O
|
A:HOH82
|
2.0
|
8.8
|
0.3
|
O
|
A:HOH81
|
2.0
|
5.9
|
0.5
|
O
|
A:HOH85
|
2.0
|
8.6
|
0.0
|
O
|
A:HOH83
|
2.0
|
10.5
|
0.7
|
O
|
A:HOH84
|
2.0
|
8.7
|
0.0
|
O
|
A:HOH86
|
2.0
|
6.6
|
0.7
|
O
|
B:HOH43
|
4.2
|
30.3
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 1qp5
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Magnesium Binding Sites List in 1qp5
Magnesium binding site 4 out
of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg87
b:4.7
occ:0.59
|
O
|
A:HOH92
|
2.0
|
2.0
|
0.5
|
O
|
A:HOH93
|
2.0
|
4.2
|
0.5
|
O
|
A:HOH88
|
2.0
|
2.9
|
0.1
|
O
|
A:HOH91
|
2.0
|
2.9
|
0.0
|
O
|
A:HOH89
|
2.0
|
2.0
|
0.6
|
O
|
A:HOH90
|
2.0
|
3.9
|
0.8
|
O
|
A:HOH51
|
3.4
|
14.4
|
0.8
|
O
|
A:HOH138
|
3.8
|
2.0
|
0.7
|
O
|
A:HOH126
|
3.8
|
3.0
|
0.7
|
O4'
|
A:DG5
|
4.4
|
20.7
|
1.0
|
C5'
|
A:DG5
|
4.5
|
32.6
|
1.0
|
C4'
|
A:DG5
|
4.6
|
32.6
|
1.0
|
O4'
|
A:DG4
|
4.7
|
34.7
|
1.0
|
O
|
A:HOH95
|
4.7
|
2.0
|
0.8
|
O
|
A:HOH97
|
5.0
|
22.0
|
0.5
|
|
Magnesium binding site 5 out
of 8 in 1qp5
Go back to
Magnesium Binding Sites List in 1qp5
Magnesium binding site 5 out
of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg99
b:24.4
occ:0.67
|
O
|
A:HOH103
|
2.0
|
10.8
|
0.5
|
O
|
A:HOH102
|
2.0
|
17.4
|
0.1
|
O
|
A:HOH100
|
2.0
|
14.9
|
0.4
|
O
|
A:HOH105
|
2.0
|
17.5
|
0.0
|
O
|
A:HOH101
|
2.0
|
16.5
|
0.3
|
O
|
A:HOH104
|
2.0
|
18.3
|
0.8
|
C5
|
A:DC9
|
3.9
|
47.5
|
1.0
|
O
|
A:HOH134
|
3.9
|
2.0
|
0.8
|
O
|
A:HOH25
|
4.4
|
14.1
|
1.0
|
C6
|
A:DC9
|
4.5
|
42.6
|
1.0
|
OP2
|
A:DC9
|
4.7
|
28.1
|
1.0
|
O
|
A:HOH79
|
4.7
|
21.0
|
1.0
|
N4
|
A:DC9
|
4.8
|
41.6
|
1.0
|
C4
|
A:DC9
|
4.9
|
48.5
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 1qp5
Go back to
Magnesium Binding Sites List in 1qp5
Magnesium binding site 6 out
of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg112
b:26.6
occ:0.64
|
O
|
A:HOH117
|
2.0
|
24.6
|
0.4
|
O
|
A:HOH116
|
2.0
|
28.4
|
0.3
|
O
|
A:HOH118
|
2.0
|
27.5
|
0.0
|
O
|
A:HOH114
|
2.0
|
28.5
|
0.2
|
O
|
A:HOH115
|
2.0
|
27.4
|
0.0
|
O
|
A:HOH113
|
2.0
|
30.6
|
0.6
|
O2
|
A:DC2
|
4.0
|
32.6
|
1.0
|
C5'
|
A:DC3
|
4.0
|
39.1
|
1.0
|
O4'
|
A:DC3
|
4.1
|
31.7
|
1.0
|
C4'
|
A:DC3
|
4.2
|
32.2
|
1.0
|
C1'
|
A:DC2
|
4.3
|
18.3
|
1.0
|
O
|
B:HOH98
|
4.4
|
36.1
|
0.9
|
O
|
B:HOH32
|
4.7
|
21.7
|
1.0
|
O4'
|
A:DC2
|
4.9
|
20.8
|
1.0
|
C2'
|
A:DC2
|
4.9
|
18.2
|
1.0
|
O3'
|
A:DC2
|
5.0
|
32.4
|
1.0
|
C2
|
A:DC2
|
5.0
|
29.1
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 1qp5
Go back to
Magnesium Binding Sites List in 1qp5
Magnesium binding site 7 out
of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg61
b:27.5
occ:1.00
|
O
|
B:HOH66
|
2.0
|
28.8
|
0.6
|
O
|
B:HOH63
|
2.0
|
27.9
|
0.6
|
O
|
B:HOH62
|
2.0
|
25.9
|
0.5
|
O
|
B:HOH67
|
2.0
|
25.6
|
0.4
|
O
|
A:HOH65
|
2.0
|
26.0
|
0.4
|
O
|
A:HOH64
|
2.0
|
28.4
|
0.1
|
O6
|
B:DG19
|
3.1
|
34.4
|
1.0
|
O
|
A:HOH132
|
4.2
|
7.8
|
1.0
|
C6
|
B:DG19
|
4.2
|
33.5
|
1.0
|
C5
|
B:DC18
|
4.3
|
18.3
|
1.0
|
O6
|
A:DG5
|
4.6
|
29.7
|
1.0
|
N7
|
B:DG19
|
4.6
|
38.9
|
1.0
|
C5
|
B:DG19
|
4.8
|
37.2
|
1.0
|
C4
|
B:DC18
|
4.8
|
28.3
|
1.0
|
C6
|
B:DC18
|
4.9
|
28.4
|
1.0
|
N7
|
A:DG4
|
4.9
|
16.3
|
1.0
|
N4
|
B:DC18
|
4.9
|
26.0
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 1qp5
Go back to
Magnesium Binding Sites List in 1qp5
Magnesium binding site 8 out
of 8 in the Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Base-Pairing Shift in A Dodecamer Containing A (Ca)N Tract within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg119
b:41.6
occ:0.55
|
O
|
B:HOH121
|
2.0
|
37.6
|
0.4
|
O
|
A:HOH123
|
2.0
|
38.0
|
0.5
|
O
|
B:HOH124
|
2.0
|
40.8
|
0.8
|
O
|
B:HOH125
|
2.0
|
39.0
|
0.0
|
O
|
B:HOH120
|
2.0
|
33.4
|
0.9
|
O
|
B:HOH122
|
2.0
|
43.2
|
1.0
|
O
|
B:HOH44
|
4.0
|
2.0
|
1.0
|
O4'
|
B:DG17
|
4.4
|
14.0
|
1.0
|
O3'
|
B:DG17
|
4.9
|
18.2
|
1.0
|
|
Reference:
Y.Timsit,
E.Vilbois,
D.Moras.
Base-Pairing Shift in the Major Groove of (Ca)N Tracts By B-Dna Crystal Structures. Nature V. 354 167 1991.
ISSN: ISSN 0028-0836
PubMed: 1944598
DOI: 10.1038/354167A0
Page generated: Tue Aug 13 11:54:13 2024
|