Magnesium in PDB 1svm: Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp
Protein crystallography data
The structure of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp, PDB code: 1svm
was solved by
D.Gai,
R.Zhao,
C.V.Finkielstein,
X.S.Chen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
1.94
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
125.021,
89.377,
148.506,
90.00,
91.31,
90.00
|
R / Rfree (%)
|
21.8 /
24.1
|
Other elements in 1svm:
The structure of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp
(pdb code 1svm). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp, PDB code: 1svm:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 1svm
Go back to
Magnesium Binding Sites List in 1svm
Magnesium binding site 1 out
of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg750
b:31.6
occ:1.00
|
O1G
|
A:ATP800
|
1.9
|
39.6
|
1.0
|
OG1
|
A:THR433
|
2.0
|
27.6
|
1.0
|
O
|
A:HOH936
|
2.1
|
29.6
|
1.0
|
O
|
A:HOH935
|
2.2
|
29.9
|
1.0
|
O
|
A:HOH802
|
2.2
|
21.3
|
1.0
|
O2B
|
A:ATP800
|
2.3
|
30.7
|
1.0
|
CB
|
A:THR433
|
3.1
|
24.9
|
1.0
|
PG
|
A:ATP800
|
3.3
|
48.3
|
1.0
|
PB
|
A:ATP800
|
3.5
|
35.5
|
1.0
|
OE1
|
A:GLU473
|
3.6
|
38.5
|
1.0
|
O3B
|
A:ATP800
|
3.7
|
36.1
|
1.0
|
OD2
|
F:ASP502
|
3.9
|
28.5
|
1.0
|
N
|
A:THR433
|
3.9
|
23.6
|
1.0
|
O3A
|
A:ATP800
|
4.0
|
33.7
|
1.0
|
PA
|
A:ATP800
|
4.0
|
39.6
|
1.0
|
CA
|
A:THR433
|
4.0
|
25.0
|
1.0
|
OD1
|
A:ASP474
|
4.1
|
47.1
|
1.0
|
O3G
|
A:ATP800
|
4.1
|
41.8
|
1.0
|
CG2
|
A:THR433
|
4.1
|
24.9
|
1.0
|
O1A
|
A:ATP800
|
4.2
|
41.6
|
1.0
|
O
|
A:HOH818
|
4.3
|
28.9
|
1.0
|
OE2
|
A:GLU473
|
4.4
|
40.4
|
1.0
|
O
|
A:HOH910
|
4.4
|
37.3
|
1.0
|
O2G
|
A:ATP800
|
4.4
|
37.9
|
1.0
|
CD
|
A:GLU473
|
4.4
|
36.9
|
1.0
|
NZ
|
F:LYS418
|
4.5
|
23.6
|
1.0
|
NH1
|
F:ARG540
|
4.5
|
39.8
|
1.0
|
CG
|
A:ASP474
|
4.6
|
45.9
|
1.0
|
O1B
|
A:ATP800
|
4.8
|
40.4
|
1.0
|
CB
|
A:LYS432
|
4.9
|
25.8
|
1.0
|
CE
|
A:LYS432
|
4.9
|
22.6
|
1.0
|
O2A
|
A:ATP800
|
4.9
|
36.6
|
1.0
|
NZ
|
A:LYS432
|
5.0
|
26.3
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 1svm
Go back to
Magnesium Binding Sites List in 1svm
Magnesium binding site 2 out
of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg750
b:28.6
occ:1.00
|
O1G
|
B:ATP800
|
1.8
|
35.6
|
1.0
|
OG1
|
B:THR433
|
2.0
|
24.3
|
1.0
|
O
|
B:HOH938
|
2.1
|
20.2
|
1.0
|
O
|
B:HOH937
|
2.2
|
16.5
|
1.0
|
O
|
B:HOH939
|
2.2
|
24.0
|
1.0
|
O2B
|
B:ATP800
|
2.3
|
24.8
|
1.0
|
CB
|
B:THR433
|
3.1
|
21.8
|
1.0
|
PG
|
B:ATP800
|
3.2
|
46.4
|
1.0
|
PB
|
B:ATP800
|
3.4
|
30.4
|
1.0
|
O3B
|
B:ATP800
|
3.6
|
32.4
|
1.0
|
OE1
|
B:GLU473
|
3.7
|
41.4
|
1.0
|
OD2
|
B:ASP474
|
3.7
|
63.6
|
1.0
|
O3A
|
B:ATP800
|
3.9
|
29.7
|
1.0
|
N
|
B:THR433
|
4.0
|
19.9
|
1.0
|
O3G
|
B:ATP800
|
4.0
|
36.4
|
1.0
|
PA
|
B:ATP800
|
4.0
|
33.6
|
1.0
|
CA
|
B:THR433
|
4.1
|
21.8
|
1.0
|
CG2
|
B:THR433
|
4.1
|
20.9
|
1.0
|
O1A
|
B:ATP800
|
4.1
|
32.3
|
1.0
|
NH2
|
A:ARG540
|
4.1
|
45.5
|
1.0
|
OD2
|
A:ASP502
|
4.1
|
57.1
|
1.0
|
OE2
|
B:GLU473
|
4.3
|
41.0
|
1.0
|
O2G
|
B:ATP800
|
4.3
|
37.6
|
1.0
|
O
|
B:HOH804
|
4.3
|
39.1
|
1.0
|
O
|
B:HOH817
|
4.4
|
23.5
|
1.0
|
CD
|
B:GLU473
|
4.4
|
38.4
|
1.0
|
NZ
|
A:LYS418
|
4.5
|
25.5
|
1.0
|
CG
|
B:ASP474
|
4.6
|
57.2
|
1.0
|
O1B
|
B:ATP800
|
4.7
|
35.0
|
1.0
|
CE
|
B:LYS432
|
4.8
|
22.6
|
1.0
|
CB
|
B:LYS432
|
4.9
|
24.2
|
1.0
|
NZ
|
B:LYS432
|
5.0
|
21.6
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 1svm
Go back to
Magnesium Binding Sites List in 1svm
Magnesium binding site 3 out
of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg750
b:28.8
occ:1.00
|
O1G
|
C:ATP800
|
1.9
|
43.1
|
1.0
|
OG1
|
C:THR433
|
2.0
|
22.6
|
1.0
|
O
|
C:HOH926
|
2.1
|
15.6
|
1.0
|
O2B
|
C:ATP800
|
2.2
|
33.2
|
1.0
|
O
|
C:HOH803
|
2.3
|
21.8
|
1.0
|
O
|
C:HOH811
|
2.4
|
23.9
|
1.0
|
CB
|
C:THR433
|
3.1
|
23.7
|
1.0
|
PG
|
C:ATP800
|
3.2
|
51.3
|
1.0
|
PB
|
C:ATP800
|
3.2
|
32.6
|
1.0
|
O3B
|
C:ATP800
|
3.6
|
36.2
|
1.0
|
OD2
|
C:ASP474
|
3.7
|
41.9
|
1.0
|
O2A
|
C:ATP800
|
3.8
|
24.5
|
1.0
|
N
|
C:THR433
|
3.9
|
25.3
|
1.0
|
O3G
|
C:ATP800
|
3.9
|
41.2
|
1.0
|
NH2
|
B:ARG540
|
4.0
|
24.4
|
1.0
|
O3A
|
C:ATP800
|
4.0
|
29.6
|
1.0
|
CA
|
C:THR433
|
4.0
|
24.1
|
1.0
|
OD2
|
B:ASP502
|
4.1
|
28.6
|
1.0
|
CG2
|
C:THR433
|
4.2
|
24.1
|
1.0
|
OE2
|
C:GLU473
|
4.2
|
42.8
|
1.0
|
O
|
C:HOH862
|
4.3
|
39.5
|
1.0
|
O2G
|
C:ATP800
|
4.3
|
39.3
|
1.0
|
NZ
|
B:LYS418
|
4.4
|
23.4
|
1.0
|
PA
|
C:ATP800
|
4.4
|
27.1
|
1.0
|
OE1
|
C:GLU473
|
4.4
|
42.0
|
1.0
|
CD
|
C:GLU473
|
4.4
|
39.8
|
1.0
|
O
|
C:HOH824
|
4.5
|
26.4
|
1.0
|
CG
|
C:ASP474
|
4.6
|
41.0
|
1.0
|
O1B
|
C:ATP800
|
4.6
|
35.0
|
1.0
|
CE
|
C:LYS432
|
4.8
|
22.7
|
1.0
|
O1A
|
C:ATP800
|
4.8
|
26.0
|
1.0
|
NZ
|
C:LYS432
|
4.8
|
24.7
|
1.0
|
CB
|
C:LYS432
|
4.8
|
25.1
|
1.0
|
C
|
C:LYS432
|
5.0
|
25.1
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 1svm
Go back to
Magnesium Binding Sites List in 1svm
Magnesium binding site 4 out
of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg750
b:32.2
occ:1.00
|
O1G
|
D:ATP800
|
1.9
|
37.4
|
1.0
|
OG1
|
D:THR433
|
2.1
|
25.0
|
1.0
|
O
|
D:HOH801
|
2.2
|
23.5
|
1.0
|
O
|
D:HOH922
|
2.2
|
24.7
|
1.0
|
O
|
D:HOH921
|
2.2
|
18.7
|
1.0
|
O2B
|
D:ATP800
|
2.3
|
30.2
|
1.0
|
CB
|
D:THR433
|
3.1
|
24.5
|
1.0
|
PG
|
D:ATP800
|
3.2
|
47.9
|
1.0
|
PB
|
D:ATP800
|
3.3
|
32.2
|
1.0
|
O3B
|
D:ATP800
|
3.6
|
33.1
|
1.0
|
O2A
|
D:ATP800
|
3.8
|
26.9
|
1.0
|
OE1
|
D:GLU473
|
3.8
|
38.0
|
1.0
|
O3G
|
D:ATP800
|
3.9
|
37.3
|
1.0
|
OD1
|
D:ASP474
|
3.9
|
53.0
|
1.0
|
OD2
|
C:ASP502
|
3.9
|
28.4
|
1.0
|
N
|
D:THR433
|
4.0
|
26.3
|
1.0
|
O3A
|
D:ATP800
|
4.0
|
27.6
|
1.0
|
CA
|
D:THR433
|
4.1
|
24.8
|
1.0
|
CG2
|
D:THR433
|
4.2
|
23.9
|
1.0
|
OE2
|
D:GLU473
|
4.2
|
36.8
|
1.0
|
O2G
|
D:ATP800
|
4.4
|
36.7
|
1.0
|
NH1
|
C:ARG540
|
4.4
|
42.0
|
1.0
|
PA
|
D:ATP800
|
4.4
|
27.4
|
1.0
|
CG
|
D:ASP474
|
4.4
|
48.7
|
1.0
|
NZ
|
C:LYS418
|
4.4
|
26.3
|
1.0
|
CD
|
D:GLU473
|
4.5
|
34.5
|
1.0
|
O
|
D:HOH808
|
4.5
|
28.9
|
1.0
|
O1B
|
D:ATP800
|
4.7
|
34.6
|
1.0
|
OD2
|
D:ASP474
|
4.7
|
53.6
|
1.0
|
O1A
|
D:ATP800
|
4.8
|
24.2
|
1.0
|
CE
|
D:LYS432
|
4.8
|
29.1
|
1.0
|
CB
|
D:LYS432
|
4.9
|
29.2
|
1.0
|
NZ
|
D:LYS432
|
4.9
|
25.1
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 1svm
Go back to
Magnesium Binding Sites List in 1svm
Magnesium binding site 5 out
of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg750
b:72.7
occ:1.00
|
O1G
|
E:ATP800
|
2.0
|
52.9
|
1.0
|
OG1
|
E:THR433
|
2.0
|
24.2
|
1.0
|
O
|
E:HOH958
|
2.1
|
62.3
|
1.0
|
O
|
E:HOH957
|
2.3
|
24.9
|
1.0
|
O
|
D:HOH823
|
2.3
|
58.6
|
1.0
|
O2B
|
E:ATP800
|
2.6
|
24.3
|
1.0
|
CB
|
E:THR433
|
3.2
|
21.5
|
1.0
|
PG
|
E:ATP800
|
3.3
|
57.4
|
1.0
|
OD2
|
E:ASP474
|
3.6
|
47.9
|
1.0
|
PB
|
E:ATP800
|
3.6
|
24.4
|
1.0
|
OE1
|
E:GLU473
|
3.6
|
40.1
|
1.0
|
O3B
|
E:ATP800
|
3.9
|
21.6
|
1.0
|
O3G
|
E:ATP800
|
3.9
|
49.8
|
1.0
|
OE2
|
E:GLU473
|
3.9
|
40.4
|
1.0
|
O2A
|
E:ATP800
|
4.1
|
25.9
|
1.0
|
N
|
E:THR433
|
4.1
|
20.8
|
1.0
|
CA
|
E:THR433
|
4.2
|
21.8
|
1.0
|
CG2
|
E:THR433
|
4.2
|
22.6
|
1.0
|
CD
|
E:GLU473
|
4.2
|
36.9
|
1.0
|
O
|
E:HOH950
|
4.3
|
39.2
|
1.0
|
OD1
|
D:ASP502
|
4.3
|
55.7
|
1.0
|
CG
|
E:ASP474
|
4.3
|
42.1
|
1.0
|
O3A
|
E:ATP800
|
4.4
|
26.5
|
1.0
|
NH1
|
D:ARG540
|
4.5
|
36.9
|
1.0
|
O2G
|
E:ATP800
|
4.5
|
50.1
|
1.0
|
NZ
|
D:LYS418
|
4.7
|
20.6
|
1.0
|
PA
|
E:ATP800
|
4.7
|
25.1
|
1.0
|
CB
|
E:ASP474
|
4.9
|
36.5
|
1.0
|
OG1
|
E:THR527
|
4.9
|
25.6
|
1.0
|
CE
|
E:LYS432
|
5.0
|
23.2
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 1svm
Go back to
Magnesium Binding Sites List in 1svm
Magnesium binding site 6 out
of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg750
b:50.2
occ:1.00
|
O1G
|
F:ATP800
|
1.9
|
55.9
|
1.0
|
OG1
|
F:THR433
|
2.0
|
25.2
|
1.0
|
O
|
F:HOH922
|
2.2
|
27.2
|
1.0
|
O2B
|
F:ATP800
|
2.2
|
21.9
|
1.0
|
O
|
F:HOH805
|
2.3
|
21.1
|
1.0
|
O
|
F:HOH808
|
2.4
|
25.3
|
1.0
|
CB
|
F:THR433
|
3.1
|
23.6
|
1.0
|
PG
|
F:ATP800
|
3.2
|
60.1
|
1.0
|
PB
|
F:ATP800
|
3.2
|
23.4
|
1.0
|
O3B
|
F:ATP800
|
3.6
|
23.1
|
1.0
|
O3G
|
F:ATP800
|
3.8
|
53.6
|
1.0
|
OE2
|
F:GLU473
|
3.8
|
42.3
|
1.0
|
OD1
|
F:ASP474
|
3.9
|
41.9
|
1.0
|
O2A
|
F:ATP800
|
3.9
|
23.3
|
1.0
|
N
|
F:THR433
|
3.9
|
23.3
|
1.0
|
OD2
|
E:ASP502
|
4.0
|
30.2
|
1.0
|
CA
|
F:THR433
|
4.0
|
22.4
|
1.0
|
O3A
|
F:ATP800
|
4.0
|
24.0
|
1.0
|
CG2
|
F:THR433
|
4.1
|
24.3
|
1.0
|
CD
|
F:GLU473
|
4.2
|
37.7
|
1.0
|
O
|
F:HOH818
|
4.2
|
32.3
|
1.0
|
NH1
|
E:ARG540
|
4.3
|
44.7
|
1.0
|
OE1
|
F:GLU473
|
4.3
|
39.2
|
1.0
|
O2G
|
F:ATP800
|
4.4
|
53.4
|
1.0
|
NZ
|
E:LYS418
|
4.5
|
25.6
|
1.0
|
PA
|
F:ATP800
|
4.5
|
26.1
|
1.0
|
O
|
F:HOH812
|
4.5
|
24.3
|
1.0
|
CG
|
F:ASP474
|
4.6
|
40.2
|
1.0
|
O1B
|
F:ATP800
|
4.6
|
22.4
|
1.0
|
O1A
|
F:ATP800
|
4.9
|
22.4
|
1.0
|
CB
|
F:LYS432
|
4.9
|
24.3
|
1.0
|
CE
|
F:LYS432
|
4.9
|
25.4
|
1.0
|
|
Reference:
D.Gai,
R.Zhao,
D.Li,
C.V.Finkielstein,
X.S.Chen.
Mechanisms of Conformational Change For A Replicative Hexameric Helicase of SV40 Large Tumor Antigen. Cell(Cambridge,Mass.) V. 119 47 2004.
ISSN: ISSN 0092-8674
PubMed: 15454080
DOI: 10.1016/J.CELL.2004.09.017
Page generated: Tue Aug 13 14:19:44 2024
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