Mercury in PDB 1wqs: Crystal Structure of Norovirus 3C-Like Protease
Protein crystallography data
The structure of Crystal Structure of Norovirus 3C-Like Protease, PDB code: 1wqs
was solved by
K.Nakamura,
Y.Someya,
T.Kumasaka,
N.Tanaka,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
2.80
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
128.890,
128.890,
118.080,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20.6 /
24
|
Mercury Binding Sites:
The binding sites of Mercury atom in the Crystal Structure of Norovirus 3C-Like Protease
(pdb code 1wqs). This binding sites where shown within
5.0 Angstroms radius around Mercury atom.
In total 8 binding sites of Mercury where determined in the
Crystal Structure of Norovirus 3C-Like Protease, PDB code: 1wqs:
Jump to Mercury binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Mercury binding site 1 out
of 8 in 1wqs
Go back to
Mercury Binding Sites List in 1wqs
Mercury binding site 1 out
of 8 in the Crystal Structure of Norovirus 3C-Like Protease
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 1 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1001
b:81.4
occ:0.47
|
SG
|
A:CYS169
|
2.8
|
55.5
|
1.0
|
CB
|
A:CYS154
|
2.9
|
41.2
|
1.0
|
CB
|
A:CYS77
|
3.5
|
78.7
|
1.0
|
N
|
A:CYS77
|
3.6
|
52.7
|
1.0
|
HG
|
A:HG1002
|
3.6
|
65.2
|
0.3
|
SG
|
A:CYS154
|
3.9
|
65.3
|
1.0
|
OE1
|
A:GLN117
|
3.9
|
35.7
|
1.0
|
CB
|
A:CYS169
|
3.9
|
34.1
|
1.0
|
CB
|
A:TYR143
|
4.0
|
32.5
|
1.0
|
CA
|
A:CYS77
|
4.1
|
59.6
|
1.0
|
CE
|
A:MET101
|
4.1
|
19.7
|
1.0
|
N
|
A:GLY155
|
4.2
|
39.5
|
1.0
|
CA
|
A:CYS154
|
4.2
|
38.0
|
1.0
|
C
|
A:CYS154
|
4.2
|
44.7
|
1.0
|
CD1
|
A:TYR143
|
4.2
|
35.2
|
1.0
|
CG
|
A:MET101
|
4.3
|
30.1
|
1.0
|
CG
|
A:TYR143
|
4.3
|
36.5
|
1.0
|
CD
|
A:GLN117
|
4.5
|
40.2
|
1.0
|
SD
|
A:MET101
|
4.6
|
54.4
|
1.0
|
C
|
A:GLY76
|
4.6
|
48.0
|
1.0
|
O
|
A:CYS154
|
4.8
|
41.8
|
1.0
|
CA
|
A:GLY155
|
4.8
|
42.4
|
1.0
|
CG1
|
A:VAL171
|
4.8
|
33.2
|
1.0
|
CA
|
A:GLY76
|
4.8
|
40.9
|
1.0
|
SG
|
A:CYS83
|
4.9
|
48.3
|
1.0
|
CB
|
A:GLN117
|
4.9
|
41.0
|
1.0
|
|
Mercury binding site 2 out
of 8 in 1wqs
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Mercury Binding Sites List in 1wqs
Mercury binding site 2 out
of 8 in the Crystal Structure of Norovirus 3C-Like Protease
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 2 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg1002
b:65.2
occ:0.35
|
SG
|
A:CYS83
|
2.1
|
48.3
|
1.0
|
SG
|
A:CYS154
|
2.2
|
65.3
|
1.0
|
CB
|
A:CYS77
|
2.9
|
78.7
|
1.0
|
CD2
|
A:TYR145
|
3.1
|
42.8
|
1.0
|
CB
|
A:CYS154
|
3.4
|
41.2
|
1.0
|
CB
|
A:CYS83
|
3.5
|
33.5
|
1.0
|
CE2
|
A:TYR145
|
3.5
|
49.6
|
1.0
|
SG
|
A:CYS77
|
3.6
|
0.9
|
1.0
|
HG
|
A:HG1001
|
3.6
|
81.4
|
0.5
|
CA
|
A:CYS77
|
4.0
|
59.6
|
1.0
|
O
|
A:TYR143
|
4.0
|
42.6
|
1.0
|
CG
|
A:TYR145
|
4.2
|
47.8
|
1.0
|
CG
|
A:MET101
|
4.4
|
30.1
|
1.0
|
CB
|
A:TYR143
|
4.5
|
32.5
|
1.0
|
N
|
A:CYS77
|
4.5
|
52.7
|
1.0
|
C
|
A:TYR143
|
4.5
|
34.3
|
1.0
|
CB
|
A:TYR145
|
4.6
|
43.0
|
1.0
|
CA
|
A:CYS83
|
4.6
|
34.5
|
1.0
|
CA
|
A:CYS154
|
4.7
|
38.0
|
1.0
|
N
|
A:CYS154
|
4.8
|
36.0
|
1.0
|
N
|
A:TYR145
|
4.8
|
38.6
|
1.0
|
CG2
|
A:VAL81
|
4.8
|
26.6
|
1.0
|
CZ
|
A:TYR145
|
4.9
|
43.8
|
1.0
|
C
|
A:VAL144
|
4.9
|
32.5
|
1.0
|
|
Mercury binding site 3 out
of 8 in 1wqs
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Mercury Binding Sites List in 1wqs
Mercury binding site 3 out
of 8 in the Crystal Structure of Norovirus 3C-Like Protease
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 3 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg1003
b:69.3
occ:0.44
|
SG
|
B:CYS169
|
2.3
|
58.3
|
1.0
|
SG
|
B:CYS154
|
2.6
|
98.6
|
1.0
|
HG
|
B:HG1004
|
3.2
|
0.2
|
0.5
|
O
|
B:CYS154
|
3.4
|
77.9
|
1.0
|
CB
|
B:TYR143
|
3.4
|
39.6
|
1.0
|
C
|
B:CYS154
|
3.5
|
67.6
|
1.0
|
CD1
|
B:TYR143
|
3.6
|
49.7
|
1.0
|
CB
|
B:CYS154
|
3.6
|
70.8
|
1.0
|
CG
|
B:TYR143
|
3.6
|
39.2
|
1.0
|
N
|
B:GLY155
|
3.9
|
61.2
|
1.0
|
CB
|
B:CYS169
|
4.0
|
58.9
|
1.0
|
CA
|
B:GLY155
|
4.0
|
53.6
|
1.0
|
CE
|
B:MET101
|
4.1
|
43.3
|
1.0
|
SG
|
B:CYS77
|
4.1
|
81.8
|
1.0
|
CA
|
B:CYS154
|
4.1
|
69.4
|
1.0
|
CG
|
B:GLN117
|
4.2
|
56.5
|
1.0
|
SD
|
B:MET101
|
4.6
|
61.1
|
1.0
|
CG1
|
B:VAL171
|
4.6
|
55.4
|
1.0
|
CE1
|
B:TYR143
|
4.6
|
56.2
|
1.0
|
O
|
B:TYR143
|
4.6
|
49.8
|
1.0
|
CD2
|
B:TYR143
|
4.6
|
40.2
|
1.0
|
CG
|
B:MET101
|
4.7
|
43.4
|
1.0
|
C
|
B:GLY155
|
4.8
|
53.4
|
1.0
|
CB
|
B:GLN117
|
4.9
|
60.9
|
1.0
|
CA
|
B:TYR143
|
4.9
|
40.8
|
1.0
|
|
Mercury binding site 4 out
of 8 in 1wqs
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Mercury Binding Sites List in 1wqs
Mercury binding site 4 out
of 8 in the Crystal Structure of Norovirus 3C-Like Protease
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 4 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg1004
b:0.2
occ:0.48
|
SG
|
B:CYS77
|
2.2
|
81.8
|
1.0
|
SG
|
B:CYS83
|
2.4
|
82.4
|
1.0
|
SG
|
B:CYS154
|
2.5
|
98.6
|
1.0
|
CB
|
B:CYS83
|
2.5
|
50.5
|
1.0
|
HG
|
B:HG1003
|
3.2
|
69.3
|
0.4
|
CB
|
B:CYS154
|
3.3
|
70.8
|
1.0
|
CB
|
B:TYR143
|
3.4
|
39.6
|
1.0
|
O
|
B:TYR143
|
3.6
|
49.8
|
1.0
|
CG
|
B:MET101
|
3.6
|
43.4
|
1.0
|
SD
|
B:MET101
|
4.0
|
61.1
|
1.0
|
CB
|
B:CYS77
|
4.0
|
66.1
|
1.0
|
CD1
|
B:TYR143
|
4.0
|
49.7
|
1.0
|
C
|
B:TYR143
|
4.1
|
50.3
|
1.0
|
CG
|
B:TYR143
|
4.2
|
39.2
|
1.0
|
CA
|
B:CYS83
|
4.2
|
49.0
|
1.0
|
CA
|
B:TYR143
|
4.3
|
40.8
|
1.0
|
O
|
B:VAL144
|
4.5
|
67.0
|
1.0
|
CA
|
B:CYS154
|
4.7
|
69.4
|
1.0
|
CD2
|
B:TYR145
|
4.7
|
79.9
|
1.0
|
CE
|
B:MET101
|
4.8
|
43.3
|
1.0
|
N
|
B:CYS83
|
4.9
|
53.2
|
1.0
|
N
|
B:VAL144
|
4.9
|
55.2
|
1.0
|
|
Mercury binding site 5 out
of 8 in 1wqs
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Mercury Binding Sites List in 1wqs
Mercury binding site 5 out
of 8 in the Crystal Structure of Norovirus 3C-Like Protease
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 5 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Hg1005
b:60.3
occ:0.36
|
SG
|
C:CYS169
|
2.5
|
37.6
|
1.0
|
SG
|
C:CYS154
|
2.6
|
75.0
|
1.0
|
CE
|
C:MET101
|
3.0
|
26.4
|
1.0
|
CB
|
C:CYS169
|
3.6
|
19.7
|
1.0
|
C
|
C:CYS154
|
3.7
|
36.4
|
1.0
|
O
|
C:CYS154
|
3.8
|
38.1
|
1.0
|
CB
|
C:TYR143
|
3.9
|
37.2
|
1.0
|
CD1
|
C:TYR143
|
3.9
|
44.2
|
1.0
|
N
|
C:CYS77
|
4.0
|
76.1
|
1.0
|
CB
|
C:CYS154
|
4.0
|
32.5
|
1.0
|
OE1
|
C:GLN117
|
4.0
|
63.8
|
1.0
|
N
|
C:GLY155
|
4.0
|
30.0
|
1.0
|
CG
|
C:TYR143
|
4.1
|
48.4
|
1.0
|
CA
|
C:GLY155
|
4.2
|
32.5
|
1.0
|
CG1
|
C:VAL171
|
4.3
|
28.6
|
1.0
|
CA
|
C:CYS154
|
4.4
|
38.8
|
1.0
|
HG
|
C:HG1006
|
4.5
|
75.2
|
0.4
|
CA
|
C:GLY76
|
4.6
|
72.3
|
1.0
|
C
|
C:GLY76
|
4.6
|
72.9
|
1.0
|
SG
|
C:CYS77
|
4.6
|
0.8
|
1.0
|
CD
|
C:GLN117
|
4.7
|
57.2
|
1.0
|
CE1
|
C:TYR143
|
4.7
|
41.2
|
1.0
|
CB
|
C:GLN117
|
4.7
|
30.4
|
1.0
|
SD
|
C:MET101
|
4.8
|
45.8
|
1.0
|
C
|
C:GLY155
|
4.9
|
25.8
|
1.0
|
CG
|
C:GLN117
|
4.9
|
38.6
|
1.0
|
O
|
C:TYR143
|
5.0
|
38.9
|
1.0
|
|
Mercury binding site 6 out
of 8 in 1wqs
Go back to
Mercury Binding Sites List in 1wqs
Mercury binding site 6 out
of 8 in the Crystal Structure of Norovirus 3C-Like Protease
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 6 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Hg1006
b:75.2
occ:0.41
|
SG
|
C:CYS154
|
2.1
|
75.0
|
1.0
|
SG
|
C:CYS83
|
2.2
|
58.2
|
1.0
|
CB
|
C:CYS154
|
2.9
|
32.5
|
1.0
|
CD2
|
C:TYR145
|
3.0
|
73.1
|
1.0
|
CB
|
C:CYS77
|
3.4
|
88.2
|
1.0
|
CE2
|
C:TYR145
|
3.5
|
77.8
|
1.0
|
CB
|
C:CYS83
|
3.6
|
43.1
|
1.0
|
CG
|
C:TYR145
|
3.6
|
52.1
|
1.0
|
O
|
C:TYR143
|
3.7
|
38.9
|
1.0
|
SG
|
C:CYS77
|
3.9
|
0.8
|
1.0
|
CB
|
C:TYR145
|
3.9
|
49.2
|
1.0
|
O
|
C:VAL144
|
4.0
|
46.2
|
1.0
|
C
|
C:VAL144
|
4.1
|
45.2
|
1.0
|
C
|
C:TYR143
|
4.3
|
34.0
|
1.0
|
CA
|
C:CYS154
|
4.3
|
38.8
|
1.0
|
N
|
C:TYR145
|
4.4
|
46.8
|
1.0
|
CA
|
C:CYS77
|
4.4
|
80.4
|
1.0
|
N
|
C:CYS154
|
4.4
|
37.8
|
1.0
|
HG
|
C:HG1005
|
4.5
|
60.3
|
0.4
|
CZ
|
C:TYR145
|
4.5
|
65.0
|
1.0
|
N
|
C:CYS77
|
4.6
|
76.1
|
1.0
|
CA
|
C:VAL144
|
4.6
|
42.8
|
1.0
|
CB
|
C:TYR143
|
4.6
|
37.2
|
1.0
|
CD1
|
C:TYR145
|
4.6
|
49.3
|
1.0
|
CA
|
C:CYS83
|
4.6
|
39.7
|
1.0
|
N
|
C:VAL144
|
4.6
|
36.9
|
1.0
|
CA
|
C:TYR145
|
4.7
|
48.5
|
1.0
|
|
Mercury binding site 7 out
of 8 in 1wqs
Go back to
Mercury Binding Sites List in 1wqs
Mercury binding site 7 out
of 8 in the Crystal Structure of Norovirus 3C-Like Protease
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 7 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Hg1007
b:64.7
occ:0.48
|
SG
|
D:CYS169
|
2.5
|
59.1
|
1.0
|
HG
|
D:HG1008
|
2.9
|
96.2
|
0.3
|
SG
|
D:CYS154
|
3.0
|
77.6
|
1.0
|
CE
|
D:MET101
|
3.4
|
37.6
|
1.0
|
CB
|
D:CYS169
|
3.5
|
51.2
|
1.0
|
CB
|
D:CYS154
|
3.6
|
58.6
|
1.0
|
O
|
D:CYS154
|
3.7
|
58.6
|
1.0
|
C
|
D:CYS154
|
3.7
|
51.7
|
1.0
|
CD1
|
D:TYR143
|
3.9
|
26.6
|
1.0
|
CB
|
D:TYR143
|
3.9
|
40.5
|
1.0
|
CG
|
D:TYR143
|
4.0
|
29.1
|
1.0
|
N
|
D:GLY155
|
4.1
|
42.6
|
1.0
|
CA
|
D:CYS154
|
4.2
|
57.0
|
1.0
|
CA
|
D:GLY155
|
4.4
|
33.1
|
1.0
|
NE2
|
D:GLN117
|
4.4
|
61.6
|
1.0
|
SG
|
D:CYS83
|
4.6
|
76.6
|
1.0
|
CE1
|
D:TYR143
|
4.8
|
20.2
|
1.0
|
CG
|
D:GLN117
|
4.8
|
62.4
|
1.0
|
SD
|
D:MET101
|
4.8
|
54.2
|
1.0
|
SG
|
D:CYS77
|
4.9
|
79.5
|
1.0
|
CG1
|
D:VAL171
|
4.9
|
46.6
|
1.0
|
CA
|
D:GLY76
|
4.9
|
89.2
|
1.0
|
CD
|
D:GLN117
|
4.9
|
66.3
|
1.0
|
CA
|
D:CYS169
|
4.9
|
54.4
|
1.0
|
CG
|
D:MET101
|
4.9
|
50.5
|
1.0
|
N
|
D:CYS77
|
4.9
|
77.2
|
1.0
|
|
Mercury binding site 8 out
of 8 in 1wqs
Go back to
Mercury Binding Sites List in 1wqs
Mercury binding site 8 out
of 8 in the Crystal Structure of Norovirus 3C-Like Protease
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 8 of Crystal Structure of Norovirus 3C-Like Protease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Hg1008
b:96.2
occ:0.34
|
SG
|
D:CYS154
|
1.8
|
77.6
|
1.0
|
SG
|
D:CYS83
|
1.9
|
76.6
|
1.0
|
SG
|
D:CYS77
|
2.7
|
79.5
|
1.0
|
HG
|
D:HG1007
|
2.9
|
64.7
|
0.5
|
CB
|
D:CYS83
|
3.1
|
60.7
|
1.0
|
CG
|
D:MET101
|
3.2
|
50.5
|
1.0
|
CB
|
D:CYS77
|
3.5
|
72.2
|
1.0
|
CB
|
D:CYS154
|
3.5
|
58.6
|
1.0
|
CE
|
D:MET101
|
3.6
|
37.6
|
1.0
|
SD
|
D:MET101
|
4.0
|
54.2
|
1.0
|
CB
|
D:MET101
|
4.3
|
47.3
|
1.0
|
CB
|
D:TYR143
|
4.3
|
40.5
|
1.0
|
CD1
|
D:TYR143
|
4.4
|
26.6
|
1.0
|
CA
|
D:CYS83
|
4.7
|
50.3
|
1.0
|
CA
|
D:CYS77
|
4.7
|
72.9
|
1.0
|
N
|
D:CYS77
|
4.7
|
77.2
|
1.0
|
CG
|
D:TYR143
|
4.8
|
29.1
|
1.0
|
N
|
D:CYS83
|
4.9
|
49.7
|
1.0
|
|
Reference:
K.Nakamura,
Y.Someya,
T.Kumasaka,
G.Ueno,
M.Yamamoto,
T.Sato,
N.Takeda,
T.Miyamura,
N.Tanaka.
A Norovirus Protease Structure Provides Insights Into Active and Substrate Binding Site Integrity J.Virol. V. 79 13685 2005.
ISSN: ISSN 0022-538X
PubMed: 16227288
DOI: 10.1128/JVI.79.21.13685-13693.2005
Page generated: Sun Aug 11 01:43:04 2024
|