Zinc in PDB 2g9t: Crystal Structure of the Sars Coronavirus NSP10 at 2.1A
Protein crystallography data
The structure of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A, PDB code: 2g9t
was solved by
D.Su,
Z.Lou,
H.Yang,
F.Sun,
Z.Rao,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.10
|
Space group
|
C 2 2 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
159.111,
321.829,
161.957,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.7 /
24.7
|
Zinc Binding Sites:
Zinc binding site 1 out
of 48 in 2g9t
Go back to
Zinc Binding Sites List in 2g9t
Zinc binding site 1 out
of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn998
b:27.1
occ:1.00
|
NE2
|
A:HIS83
|
2.0
|
34.0
|
1.0
|
SG
|
A:CYS74
|
2.2
|
24.1
|
1.0
|
SG
|
A:CYS77
|
2.3
|
29.1
|
1.0
|
SG
|
A:CYS90
|
2.4
|
35.2
|
1.0
|
CD2
|
A:HIS83
|
3.0
|
32.8
|
1.0
|
CB
|
A:CYS74
|
3.0
|
23.5
|
1.0
|
CE1
|
A:HIS83
|
3.1
|
33.2
|
1.0
|
CB
|
A:CYS90
|
3.3
|
39.2
|
1.0
|
CB
|
A:CYS77
|
3.5
|
28.2
|
1.0
|
N
|
A:CYS77
|
3.6
|
24.9
|
1.0
|
CA
|
A:CYS77
|
4.0
|
26.0
|
1.0
|
CG
|
A:HIS83
|
4.1
|
34.6
|
1.0
|
ND1
|
A:HIS83
|
4.2
|
32.8
|
1.0
|
O
|
A:HOH1040
|
4.2
|
44.6
|
1.0
|
CA
|
A:CYS90
|
4.4
|
41.5
|
1.0
|
CB
|
A:TYR76
|
4.5
|
23.3
|
1.0
|
CA
|
A:CYS74
|
4.5
|
22.4
|
1.0
|
C
|
A:TYR76
|
4.5
|
23.0
|
1.0
|
CB
|
A:LYS93
|
4.8
|
33.6
|
1.0
|
N
|
A:LYS93
|
4.8
|
32.5
|
1.0
|
CA
|
A:TYR76
|
4.8
|
23.8
|
1.0
|
C
|
A:CYS74
|
4.9
|
20.4
|
1.0
|
N
|
A:TYR76
|
4.9
|
21.9
|
1.0
|
O
|
A:CYS74
|
5.0
|
20.0
|
1.0
|
|
Zinc binding site 2 out
of 48 in 2g9t
Go back to
Zinc Binding Sites List in 2g9t
Zinc binding site 2 out
of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn999
b:36.6
occ:1.00
|
SG
|
A:CYS120
|
2.3
|
28.5
|
1.0
|
SG
|
A:CYS128
|
2.3
|
34.7
|
1.0
|
SG
|
A:CYS117
|
2.4
|
33.9
|
1.0
|
O
|
A:HOH1068
|
2.5
|
24.5
|
1.0
|
CB
|
A:CYS117
|
3.1
|
30.5
|
1.0
|
CB
|
A:CYS128
|
3.3
|
37.6
|
1.0
|
CB
|
A:CYS120
|
3.4
|
31.9
|
1.0
|
N
|
A:CYS120
|
3.7
|
32.4
|
1.0
|
N
|
A:SER129
|
3.8
|
45.6
|
1.0
|
CA
|
A:CYS128
|
3.9
|
39.9
|
1.0
|
OG
|
A:SER129
|
3.9
|
50.5
|
1.0
|
C
|
A:CYS128
|
4.1
|
42.3
|
1.0
|
CA
|
A:CYS120
|
4.2
|
31.7
|
1.0
|
CB
|
A:VAL119
|
4.4
|
32.6
|
1.0
|
NZ
|
A:LYS124
|
4.6
|
43.7
|
1.0
|
CA
|
A:CYS117
|
4.6
|
31.4
|
1.0
|
CA
|
A:SER129
|
4.6
|
47.9
|
1.0
|
CB
|
A:SER129
|
4.6
|
48.5
|
1.0
|
C
|
A:VAL119
|
4.8
|
33.6
|
1.0
|
C
|
A:CYS120
|
5.0
|
30.4
|
1.0
|
|
Zinc binding site 3 out
of 48 in 2g9t
Go back to
Zinc Binding Sites List in 2g9t
Zinc binding site 3 out
of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn998
b:27.3
occ:1.00
|
NE2
|
B:HIS83
|
2.1
|
30.3
|
1.0
|
SG
|
B:CYS74
|
2.2
|
24.5
|
1.0
|
SG
|
B:CYS77
|
2.3
|
24.7
|
1.0
|
SG
|
B:CYS90
|
2.4
|
30.8
|
1.0
|
CD2
|
B:HIS83
|
2.8
|
32.5
|
1.0
|
CB
|
B:CYS74
|
3.1
|
22.3
|
1.0
|
CB
|
B:CYS90
|
3.2
|
39.7
|
1.0
|
CE1
|
B:HIS83
|
3.2
|
32.6
|
1.0
|
CB
|
B:CYS77
|
3.5
|
24.5
|
1.0
|
N
|
B:CYS77
|
3.6
|
24.0
|
1.0
|
CA
|
B:CYS77
|
4.0
|
23.2
|
1.0
|
O
|
B:HOH1024
|
4.0
|
39.5
|
1.0
|
CG
|
B:HIS83
|
4.1
|
33.4
|
1.0
|
ND1
|
B:HIS83
|
4.2
|
31.3
|
1.0
|
CA
|
B:CYS90
|
4.5
|
42.5
|
1.0
|
C
|
B:TYR76
|
4.5
|
23.6
|
1.0
|
CB
|
B:TYR76
|
4.5
|
25.3
|
1.0
|
CA
|
B:CYS74
|
4.6
|
22.6
|
1.0
|
CB
|
B:LYS93
|
4.8
|
32.3
|
1.0
|
CA
|
B:TYR76
|
4.9
|
23.2
|
1.0
|
N
|
B:LYS93
|
4.9
|
31.7
|
1.0
|
N
|
B:TYR76
|
5.0
|
21.6
|
1.0
|
C
|
B:CYS74
|
5.0
|
22.1
|
1.0
|
|
Zinc binding site 4 out
of 48 in 2g9t
Go back to
Zinc Binding Sites List in 2g9t
Zinc binding site 4 out
of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn999
b:41.2
occ:1.00
|
SG
|
B:CYS117
|
2.4
|
32.5
|
1.0
|
SG
|
B:CYS128
|
2.5
|
40.9
|
1.0
|
SG
|
B:CYS120
|
2.5
|
38.4
|
1.0
|
O
|
B:HOH1058
|
2.5
|
22.4
|
1.0
|
CB
|
B:CYS117
|
3.1
|
30.4
|
1.0
|
CB
|
B:CYS120
|
3.4
|
35.6
|
1.0
|
CB
|
B:CYS128
|
3.4
|
43.5
|
1.0
|
N
|
B:CYS120
|
3.7
|
34.2
|
1.0
|
OG
|
B:SER129
|
3.8
|
53.5
|
1.0
|
N
|
B:SER129
|
3.8
|
49.8
|
1.0
|
CA
|
B:CYS128
|
3.9
|
44.6
|
1.0
|
CA
|
B:CYS120
|
4.1
|
34.2
|
1.0
|
C
|
B:CYS128
|
4.3
|
47.2
|
1.0
|
CB
|
B:VAL119
|
4.5
|
36.5
|
1.0
|
CA
|
B:CYS117
|
4.5
|
31.9
|
1.0
|
CB
|
B:SER129
|
4.6
|
52.4
|
1.0
|
CA
|
B:SER129
|
4.7
|
51.6
|
1.0
|
C
|
B:VAL119
|
4.8
|
35.8
|
1.0
|
CG1
|
B:VAL119
|
4.9
|
36.1
|
1.0
|
C
|
B:CYS120
|
5.0
|
32.5
|
1.0
|
NZ
|
B:LYS124
|
5.0
|
36.6
|
1.0
|
|
Zinc binding site 5 out
of 48 in 2g9t
Go back to
Zinc Binding Sites List in 2g9t
Zinc binding site 5 out
of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn998
b:27.4
occ:1.00
|
SG
|
C:CYS77
|
2.2
|
27.0
|
1.0
|
NE2
|
C:HIS83
|
2.2
|
33.6
|
1.0
|
SG
|
C:CYS74
|
2.3
|
26.1
|
1.0
|
SG
|
C:CYS90
|
2.3
|
32.0
|
1.0
|
CD2
|
C:HIS83
|
2.9
|
33.7
|
1.0
|
CB
|
C:CYS74
|
3.2
|
27.0
|
1.0
|
CB
|
C:CYS90
|
3.3
|
38.8
|
1.0
|
CB
|
C:CYS77
|
3.3
|
25.0
|
1.0
|
CE1
|
C:HIS83
|
3.3
|
32.4
|
1.0
|
N
|
C:CYS77
|
3.6
|
25.5
|
1.0
|
CA
|
C:CYS77
|
3.9
|
26.0
|
1.0
|
CG
|
C:HIS83
|
4.2
|
35.6
|
1.0
|
ND1
|
C:HIS83
|
4.3
|
33.3
|
1.0
|
O
|
C:HOH1054
|
4.5
|
46.5
|
1.0
|
C
|
C:TYR76
|
4.5
|
25.5
|
1.0
|
CA
|
C:CYS90
|
4.5
|
41.1
|
1.0
|
CB
|
C:TYR76
|
4.6
|
26.3
|
1.0
|
CA
|
C:CYS74
|
4.6
|
25.4
|
1.0
|
CB
|
C:LYS93
|
4.8
|
30.9
|
1.0
|
N
|
C:LYS93
|
4.9
|
29.3
|
1.0
|
CA
|
C:TYR76
|
4.9
|
25.3
|
1.0
|
C
|
C:CYS74
|
4.9
|
25.2
|
1.0
|
N
|
C:TYR76
|
5.0
|
23.0
|
1.0
|
O
|
C:CYS74
|
5.0
|
24.0
|
1.0
|
|
Zinc binding site 6 out
of 48 in 2g9t
Go back to
Zinc Binding Sites List in 2g9t
Zinc binding site 6 out
of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn999
b:36.0
occ:1.00
|
SG
|
C:CYS120
|
2.4
|
28.1
|
1.0
|
O
|
C:HOH1065
|
2.4
|
19.6
|
1.0
|
SG
|
C:CYS128
|
2.4
|
36.0
|
1.0
|
SG
|
C:CYS117
|
2.4
|
31.9
|
1.0
|
CB
|
C:CYS117
|
3.1
|
30.8
|
1.0
|
CB
|
C:CYS120
|
3.3
|
30.8
|
1.0
|
CB
|
C:CYS128
|
3.6
|
37.0
|
1.0
|
N
|
C:CYS120
|
3.7
|
33.7
|
1.0
|
N
|
C:SER129
|
3.8
|
45.1
|
1.0
|
O
|
C:HOH1060
|
3.8
|
59.8
|
1.0
|
OG
|
C:SER129
|
4.0
|
46.4
|
1.0
|
CA
|
C:CYS128
|
4.0
|
39.5
|
1.0
|
CA
|
C:CYS120
|
4.1
|
31.4
|
1.0
|
C
|
C:CYS128
|
4.3
|
42.0
|
1.0
|
NZ
|
C:LYS124
|
4.5
|
43.6
|
1.0
|
CA
|
C:CYS117
|
4.6
|
32.4
|
1.0
|
CB
|
C:VAL119
|
4.6
|
35.2
|
1.0
|
CA
|
C:SER129
|
4.7
|
47.5
|
1.0
|
CB
|
C:SER129
|
4.8
|
47.5
|
1.0
|
C
|
C:VAL119
|
4.8
|
35.6
|
1.0
|
C
|
C:CYS120
|
4.9
|
30.8
|
1.0
|
|
Zinc binding site 7 out
of 48 in 2g9t
Go back to
Zinc Binding Sites List in 2g9t
Zinc binding site 7 out
of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn998
b:27.5
occ:1.00
|
NE2
|
D:HIS83
|
2.0
|
34.6
|
1.0
|
SG
|
D:CYS77
|
2.3
|
26.7
|
1.0
|
SG
|
D:CYS90
|
2.3
|
30.6
|
1.0
|
SG
|
D:CYS74
|
2.4
|
25.6
|
1.0
|
CE1
|
D:HIS83
|
2.9
|
34.1
|
1.0
|
CD2
|
D:HIS83
|
3.0
|
33.0
|
1.0
|
CB
|
D:CYS74
|
3.2
|
23.6
|
1.0
|
CB
|
D:CYS90
|
3.3
|
39.1
|
1.0
|
CB
|
D:CYS77
|
3.5
|
23.9
|
1.0
|
N
|
D:CYS77
|
3.6
|
21.8
|
1.0
|
CA
|
D:CYS77
|
4.0
|
22.9
|
1.0
|
ND1
|
D:HIS83
|
4.0
|
32.8
|
1.0
|
CG
|
D:HIS83
|
4.1
|
35.3
|
1.0
|
CB
|
D:TYR76
|
4.4
|
24.8
|
1.0
|
CA
|
D:CYS90
|
4.5
|
39.8
|
1.0
|
C
|
D:TYR76
|
4.5
|
22.2
|
1.0
|
CA
|
D:CYS74
|
4.6
|
24.0
|
1.0
|
CA
|
D:TYR76
|
4.9
|
23.0
|
1.0
|
CB
|
D:LYS93
|
4.9
|
31.5
|
1.0
|
|
Zinc binding site 8 out
of 48 in 2g9t
Go back to
Zinc Binding Sites List in 2g9t
Zinc binding site 8 out
of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn999
b:37.0
occ:1.00
|
SG
|
D:CYS128
|
1.8
|
61.4
|
1.0
|
SG
|
D:CYS120
|
2.2
|
53.2
|
1.0
|
SG
|
D:CYS117
|
2.2
|
33.3
|
1.0
|
O
|
D:HOH1062
|
2.4
|
22.3
|
1.0
|
CB
|
D:CYS120
|
2.8
|
43.7
|
1.0
|
CB
|
D:CYS117
|
3.0
|
33.5
|
1.0
|
N
|
D:CYS120
|
3.3
|
39.6
|
1.0
|
CB
|
D:CYS128
|
3.6
|
56.1
|
1.0
|
CA
|
D:CYS120
|
3.7
|
40.0
|
1.0
|
OG
|
D:SER129
|
3.9
|
55.4
|
1.0
|
N
|
D:SER129
|
4.1
|
57.7
|
1.0
|
O
|
D:HOH1044
|
4.3
|
40.3
|
1.0
|
CB
|
D:VAL119
|
4.4
|
36.9
|
1.0
|
CA
|
D:CYS128
|
4.4
|
56.3
|
1.0
|
C
|
D:CYS128
|
4.5
|
57.0
|
1.0
|
CA
|
D:CYS117
|
4.5
|
33.1
|
1.0
|
C
|
D:VAL119
|
4.5
|
38.8
|
1.0
|
NZ
|
D:LYS124
|
4.5
|
46.1
|
1.0
|
CB
|
D:SER129
|
4.6
|
57.4
|
1.0
|
CA
|
D:SER129
|
4.7
|
58.3
|
1.0
|
C
|
D:CYS120
|
4.7
|
38.1
|
1.0
|
CA
|
D:VAL119
|
4.8
|
36.7
|
1.0
|
N
|
D:GLY121
|
4.8
|
36.2
|
1.0
|
N
|
D:VAL119
|
4.9
|
36.2
|
1.0
|
C
|
D:CYS117
|
5.0
|
33.8
|
1.0
|
|
Zinc binding site 9 out
of 48 in 2g9t
Go back to
Zinc Binding Sites List in 2g9t
Zinc binding site 9 out
of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn998
b:27.6
occ:1.00
|
NE2
|
E:HIS83
|
2.1
|
33.3
|
1.0
|
SG
|
E:CYS77
|
2.2
|
26.3
|
1.0
|
SG
|
E:CYS74
|
2.3
|
24.1
|
1.0
|
SG
|
E:CYS90
|
2.3
|
32.9
|
1.0
|
CD2
|
E:HIS83
|
2.9
|
34.0
|
1.0
|
CE1
|
E:HIS83
|
3.2
|
35.9
|
1.0
|
CB
|
E:CYS74
|
3.2
|
23.9
|
1.0
|
CB
|
E:CYS90
|
3.2
|
39.0
|
1.0
|
CB
|
E:CYS77
|
3.4
|
27.2
|
1.0
|
N
|
E:CYS77
|
3.5
|
24.7
|
1.0
|
CA
|
E:CYS77
|
3.9
|
24.7
|
1.0
|
O
|
E:HOH1029
|
4.0
|
47.9
|
1.0
|
CG
|
E:HIS83
|
4.1
|
35.7
|
1.0
|
ND1
|
E:HIS83
|
4.2
|
33.9
|
1.0
|
CB
|
E:TYR76
|
4.3
|
24.8
|
1.0
|
CA
|
E:CYS90
|
4.4
|
41.3
|
1.0
|
C
|
E:TYR76
|
4.5
|
24.6
|
1.0
|
CA
|
E:CYS74
|
4.6
|
22.5
|
1.0
|
CA
|
E:TYR76
|
4.8
|
25.6
|
1.0
|
N
|
E:LYS93
|
4.9
|
31.4
|
1.0
|
CB
|
E:LYS93
|
4.9
|
33.7
|
1.0
|
N
|
E:TYR76
|
4.9
|
25.2
|
1.0
|
C
|
E:CYS74
|
5.0
|
22.1
|
1.0
|
|
Zinc binding site 10 out
of 48 in 2g9t
Go back to
Zinc Binding Sites List in 2g9t
Zinc binding site 10 out
of 48 in the Crystal Structure of the Sars Coronavirus NSP10 at 2.1A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of Crystal Structure of the Sars Coronavirus NSP10 at 2.1A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn999
b:36.0
occ:1.00
|
SG
|
E:CYS120
|
2.3
|
32.3
|
1.0
|
SG
|
E:CYS128
|
2.4
|
39.9
|
1.0
|
SG
|
E:CYS117
|
2.4
|
34.5
|
1.0
|
O
|
E:HOH1062
|
2.5
|
24.5
|
1.0
|
CB
|
E:CYS117
|
3.0
|
33.2
|
1.0
|
CB
|
E:CYS120
|
3.3
|
33.3
|
1.0
|
CB
|
E:CYS128
|
3.4
|
41.6
|
1.0
|
N
|
E:CYS120
|
3.8
|
33.0
|
1.0
|
CA
|
E:CYS128
|
3.9
|
43.0
|
1.0
|
OG
|
E:SER129
|
4.0
|
50.4
|
1.0
|
N
|
E:SER129
|
4.1
|
47.0
|
1.0
|
CA
|
E:CYS120
|
4.1
|
32.4
|
1.0
|
C
|
E:CYS128
|
4.3
|
45.3
|
1.0
|
O
|
E:HOH1037
|
4.4
|
68.1
|
1.0
|
NZ
|
E:LYS124
|
4.5
|
47.7
|
1.0
|
CA
|
E:CYS117
|
4.5
|
33.5
|
1.0
|
CB
|
E:VAL119
|
4.7
|
36.6
|
1.0
|
CB
|
E:SER129
|
4.8
|
49.3
|
1.0
|
C
|
E:VAL119
|
4.9
|
35.4
|
1.0
|
C
|
E:CYS120
|
4.9
|
32.0
|
1.0
|
CA
|
E:SER129
|
5.0
|
49.7
|
1.0
|
|
Reference:
D.Su,
Z.Lou,
F.Sun,
Y.Zhai,
H.Yang,
R.Zhang,
A.Joachimiak,
X.C.Zhang,
M.Bartlam,
Z.Rao.
Dodecamer Structure of Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein NSP10 J.Virol. V. 80 7902 2006.
ISSN: ISSN 0022-538X
PubMed: 16873247
DOI: 10.1128/JVI.00483-06
Page generated: Thu Oct 17 00:05:39 2024
|