Zinc 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:
Zinc Binding Sites:
The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc where determined in the
Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp, PDB code: 1svm:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 1svm
Go back to
Zinc Binding Sites List in 1svm
Zinc 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 Zinc with other atoms in the Zn 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:Zn700
b:25.9
occ:1.00
|
ND1
|
A:HIS317
|
2.0
|
23.4
|
1.0
|
SG
|
A:CYS305
|
2.2
|
28.0
|
1.0
|
NE2
|
A:HIS313
|
2.2
|
24.4
|
1.0
|
SG
|
A:CYS302
|
2.3
|
28.9
|
1.0
|
CE1
|
A:HIS317
|
2.9
|
24.8
|
1.0
|
CG
|
A:HIS317
|
3.0
|
23.5
|
1.0
|
CE1
|
A:HIS313
|
3.2
|
25.3
|
1.0
|
CB
|
A:CYS302
|
3.2
|
30.0
|
1.0
|
CD2
|
A:HIS313
|
3.2
|
24.5
|
1.0
|
CB
|
A:CYS305
|
3.3
|
31.6
|
1.0
|
CB
|
A:HIS317
|
3.4
|
24.1
|
1.0
|
N
|
A:CYS305
|
3.7
|
29.4
|
1.0
|
CA
|
A:CYS305
|
3.9
|
32.0
|
1.0
|
NE2
|
A:HIS317
|
4.0
|
24.1
|
1.0
|
CD2
|
A:HIS317
|
4.1
|
24.3
|
1.0
|
ND1
|
A:HIS313
|
4.3
|
24.3
|
1.0
|
CG
|
A:HIS313
|
4.3
|
24.4
|
1.0
|
CB
|
A:LYS304
|
4.5
|
31.4
|
1.0
|
C
|
A:LYS304
|
4.5
|
30.1
|
1.0
|
CA
|
A:CYS302
|
4.6
|
29.7
|
1.0
|
O
|
A:HOH904
|
4.8
|
42.9
|
1.0
|
CA
|
A:PHE299
|
4.9
|
36.7
|
1.0
|
CA
|
A:HIS317
|
4.9
|
24.7
|
1.0
|
C
|
A:CYS302
|
4.9
|
29.5
|
1.0
|
CA
|
A:LYS304
|
5.0
|
31.1
|
1.0
|
O
|
A:CYS302
|
5.0
|
30.0
|
1.0
|
|
Zinc binding site 2 out
of 6 in 1svm
Go back to
Zinc Binding Sites List in 1svm
Zinc 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 Zinc with other atoms in the Zn 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:Zn700
b:23.9
occ:1.00
|
ND1
|
B:HIS317
|
2.1
|
18.4
|
1.0
|
SG
|
B:CYS302
|
2.2
|
20.5
|
1.0
|
NE2
|
B:HIS313
|
2.3
|
21.7
|
1.0
|
SG
|
B:CYS305
|
2.3
|
32.6
|
1.0
|
CE1
|
B:HIS317
|
3.0
|
19.7
|
1.0
|
CB
|
B:CYS302
|
3.1
|
24.9
|
1.0
|
CG
|
B:HIS317
|
3.1
|
19.3
|
1.0
|
CD2
|
B:HIS313
|
3.2
|
24.1
|
1.0
|
CE1
|
B:HIS313
|
3.3
|
24.1
|
1.0
|
CB
|
B:CYS305
|
3.3
|
22.7
|
1.0
|
CB
|
B:HIS317
|
3.5
|
18.9
|
1.0
|
N
|
B:CYS305
|
3.7
|
26.4
|
1.0
|
CA
|
B:CYS305
|
4.0
|
26.8
|
1.0
|
NE2
|
B:HIS317
|
4.2
|
18.8
|
1.0
|
CD2
|
B:HIS317
|
4.2
|
19.0
|
1.0
|
CB
|
B:LYS304
|
4.3
|
29.3
|
1.0
|
CG
|
B:HIS313
|
4.3
|
24.1
|
1.0
|
ND1
|
B:HIS313
|
4.4
|
24.4
|
1.0
|
CA
|
B:CYS302
|
4.5
|
26.9
|
1.0
|
C
|
B:LYS304
|
4.6
|
28.6
|
1.0
|
CB
|
B:PHE299
|
4.8
|
30.5
|
1.0
|
C
|
B:CYS302
|
4.8
|
27.0
|
1.0
|
O
|
B:CYS302
|
4.8
|
25.9
|
1.0
|
CA
|
B:LYS304
|
4.9
|
30.6
|
1.0
|
CA
|
B:PHE299
|
4.9
|
30.7
|
1.0
|
N
|
B:LYS304
|
5.0
|
29.6
|
1.0
|
CA
|
B:HIS317
|
5.0
|
22.6
|
1.0
|
|
Zinc binding site 3 out
of 6 in 1svm
Go back to
Zinc Binding Sites List in 1svm
Zinc 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 Zinc with other atoms in the Zn 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:Zn700
b:36.4
occ:1.00
|
ND1
|
C:HIS317
|
2.0
|
31.9
|
1.0
|
NE2
|
C:HIS313
|
2.3
|
36.1
|
1.0
|
SG
|
C:CYS302
|
2.3
|
60.1
|
1.0
|
SG
|
C:CYS305
|
2.3
|
42.1
|
1.0
|
CE1
|
C:HIS317
|
2.9
|
32.9
|
1.0
|
CG
|
C:HIS317
|
3.0
|
32.9
|
1.0
|
CD2
|
C:HIS313
|
3.2
|
35.8
|
1.0
|
CE1
|
C:HIS313
|
3.2
|
34.8
|
1.0
|
CB
|
C:CYS302
|
3.3
|
66.8
|
1.0
|
CB
|
C:HIS317
|
3.4
|
36.1
|
1.0
|
CB
|
C:CYS305
|
3.5
|
48.4
|
1.0
|
N
|
C:CYS305
|
3.7
|
50.1
|
1.0
|
NE2
|
C:HIS317
|
4.0
|
33.4
|
1.0
|
CB
|
C:LYS304
|
4.1
|
51.0
|
1.0
|
CA
|
C:CYS305
|
4.1
|
50.3
|
1.0
|
CD2
|
C:HIS317
|
4.1
|
32.6
|
1.0
|
ND1
|
C:HIS313
|
4.3
|
36.1
|
1.0
|
CG
|
C:HIS313
|
4.3
|
35.0
|
1.0
|
C
|
C:LYS304
|
4.6
|
51.0
|
1.0
|
CD1
|
C:PHE299
|
4.6
|
69.9
|
1.0
|
CA
|
C:CYS302
|
4.7
|
68.0
|
1.0
|
CA
|
C:LYS304
|
4.8
|
52.6
|
1.0
|
O
|
C:CYS302
|
4.9
|
65.4
|
1.0
|
CA
|
C:HIS317
|
4.9
|
38.4
|
1.0
|
C
|
C:CYS302
|
5.0
|
66.5
|
1.0
|
|
Zinc binding site 4 out
of 6 in 1svm
Go back to
Zinc Binding Sites List in 1svm
Zinc 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 Zinc with other atoms in the Zn 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:Zn700
b:35.0
occ:1.00
|
ND1
|
D:HIS317
|
1.9
|
23.8
|
1.0
|
NE2
|
D:HIS313
|
2.2
|
30.4
|
1.0
|
SG
|
D:CYS302
|
2.3
|
30.9
|
1.0
|
SG
|
D:CYS305
|
2.4
|
34.0
|
1.0
|
CE1
|
D:HIS317
|
2.9
|
23.6
|
1.0
|
CG
|
D:HIS317
|
3.0
|
24.8
|
1.0
|
CE1
|
D:HIS313
|
3.1
|
28.4
|
1.0
|
CB
|
D:CYS302
|
3.2
|
35.7
|
1.0
|
CD2
|
D:HIS313
|
3.2
|
28.9
|
1.0
|
CB
|
D:HIS317
|
3.4
|
26.3
|
1.0
|
CB
|
D:CYS305
|
3.4
|
34.9
|
1.0
|
N
|
D:CYS305
|
3.7
|
35.2
|
1.0
|
NE2
|
D:HIS317
|
4.0
|
24.3
|
1.0
|
CA
|
D:CYS305
|
4.0
|
36.9
|
1.0
|
CD2
|
D:HIS317
|
4.0
|
22.9
|
1.0
|
ND1
|
D:HIS313
|
4.2
|
29.1
|
1.0
|
CG
|
D:HIS313
|
4.3
|
29.4
|
1.0
|
CB
|
D:LYS304
|
4.3
|
35.2
|
1.0
|
C
|
D:LYS304
|
4.5
|
35.8
|
1.0
|
CA
|
D:CYS302
|
4.6
|
36.1
|
1.0
|
CA
|
D:LYS304
|
4.9
|
36.2
|
1.0
|
CA
|
D:HIS317
|
4.9
|
25.7
|
1.0
|
O
|
D:CYS302
|
4.9
|
35.1
|
1.0
|
C
|
D:CYS302
|
4.9
|
36.2
|
1.0
|
CA
|
D:PHE299
|
4.9
|
37.7
|
1.0
|
N
|
D:LYS304
|
5.0
|
36.6
|
1.0
|
|
Zinc binding site 5 out
of 6 in 1svm
Go back to
Zinc Binding Sites List in 1svm
Zinc 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 Zinc with other atoms in the Zn 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:Zn700
b:27.8
occ:1.00
|
CD2
|
E:HIS317
|
2.0
|
15.6
|
1.0
|
SG
|
E:CYS302
|
2.3
|
24.0
|
1.0
|
NE2
|
E:HIS313
|
2.3
|
24.0
|
1.0
|
SG
|
E:CYS305
|
2.3
|
23.6
|
1.0
|
CG
|
E:HIS317
|
3.0
|
17.5
|
1.0
|
NE2
|
E:HIS317
|
3.1
|
19.9
|
1.0
|
CB
|
E:CYS302
|
3.2
|
26.6
|
1.0
|
CD2
|
E:HIS313
|
3.2
|
24.4
|
1.0
|
CB
|
E:CYS305
|
3.3
|
24.5
|
1.0
|
CE1
|
E:HIS313
|
3.3
|
24.1
|
1.0
|
CB
|
E:HIS317
|
3.4
|
19.1
|
1.0
|
N
|
E:CYS305
|
3.7
|
23.9
|
1.0
|
CA
|
E:CYS305
|
4.0
|
24.3
|
1.0
|
ND1
|
E:HIS317
|
4.1
|
20.5
|
1.0
|
CE1
|
E:HIS317
|
4.2
|
14.9
|
1.0
|
CB
|
E:LYS304
|
4.3
|
27.6
|
1.0
|
CG
|
E:HIS313
|
4.3
|
23.4
|
1.0
|
ND1
|
E:HIS313
|
4.4
|
24.5
|
1.0
|
C
|
E:LYS304
|
4.5
|
25.0
|
1.0
|
CA
|
E:CYS302
|
4.6
|
25.0
|
1.0
|
O
|
E:CYS302
|
4.8
|
23.5
|
1.0
|
CB
|
E:PHE299
|
4.8
|
30.1
|
1.0
|
C
|
E:CYS302
|
4.9
|
24.0
|
1.0
|
CA
|
E:LYS304
|
4.9
|
26.5
|
1.0
|
CA
|
E:HIS317
|
4.9
|
22.2
|
1.0
|
CA
|
E:PHE299
|
4.9
|
30.8
|
1.0
|
N
|
E:LYS304
|
5.0
|
26.0
|
1.0
|
|
Zinc binding site 6 out
of 6 in 1svm
Go back to
Zinc Binding Sites List in 1svm
Zinc 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 Zinc with other atoms in the Zn 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:Zn700
b:38.2
occ:1.00
|
ND1
|
F:HIS317
|
1.9
|
36.2
|
1.0
|
NE2
|
F:HIS313
|
2.2
|
31.9
|
1.0
|
SG
|
F:CYS302
|
2.2
|
55.0
|
1.0
|
SG
|
F:CYS305
|
2.3
|
44.7
|
1.0
|
CE1
|
F:HIS317
|
2.8
|
36.1
|
1.0
|
CG
|
F:HIS317
|
3.0
|
34.8
|
1.0
|
CE1
|
F:HIS313
|
3.1
|
32.0
|
1.0
|
CD2
|
F:HIS313
|
3.2
|
33.3
|
1.0
|
CB
|
F:CYS302
|
3.2
|
62.0
|
1.0
|
CB
|
F:HIS317
|
3.4
|
36.1
|
1.0
|
CB
|
F:CYS305
|
3.4
|
51.3
|
1.0
|
N
|
F:CYS305
|
3.7
|
53.1
|
1.0
|
NE2
|
F:HIS317
|
4.0
|
35.8
|
1.0
|
CD2
|
F:HIS317
|
4.1
|
35.1
|
1.0
|
CA
|
F:CYS305
|
4.1
|
53.2
|
1.0
|
ND1
|
F:HIS313
|
4.2
|
32.6
|
1.0
|
CB
|
F:LYS304
|
4.2
|
57.9
|
1.0
|
CG
|
F:HIS313
|
4.3
|
31.4
|
1.0
|
C
|
F:LYS304
|
4.5
|
54.4
|
1.0
|
CD1
|
F:PHE299
|
4.6
|
68.2
|
1.0
|
CA
|
F:CYS302
|
4.6
|
63.9
|
1.0
|
CA
|
F:LYS304
|
4.8
|
56.2
|
1.0
|
C
|
F:CYS302
|
4.9
|
61.7
|
1.0
|
O
|
F:CYS302
|
4.9
|
60.1
|
1.0
|
CA
|
F:HIS317
|
4.9
|
37.9
|
1.0
|
N
|
F:LYS304
|
4.9
|
57.3
|
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: Wed Oct 16 18:56:17 2024
|