Zinc in PDB 5rmk: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153
Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153
All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153:
3.6.4.12;
3.6.4.13;
Protein crystallography data
The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153, PDB code: 5rmk
was solved by
J.A.Newman,
Y.Yosaatmadja,
A.Douangamath,
A.Aimon,
A.J.Powell,
A.Dias,
D.Fearon,
L.Dunnett,
J.Brandao-Neto,
T.Krojer,
R.Skyner,
T.Gorrie-Stone,
W.Thompson,
F.Von Delft,
C.H.Arrowsmith,
A.Edwards,
C.Bountra,
O.Gileadi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
81.32 /
2.08
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
59.034,
70.039,
85.317,
102.81,
96.07,
112.42
|
R / Rfree (%)
|
22.2 /
27.4
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153
(pdb code 5rmk). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153, PDB code: 5rmk:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 5rmk
Go back to
Zinc Binding Sites List in 5rmk
Zinc binding site 1 out
of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn701
b:59.2
occ:1.00
|
ND1
|
A:HIS75
|
2.3
|
49.0
|
1.0
|
SG
|
A:CYS50
|
2.3
|
55.3
|
1.0
|
SG
|
A:CYS55
|
2.3
|
62.2
|
1.0
|
SG
|
A:CYS72
|
2.6
|
55.1
|
1.0
|
CE1
|
A:HIS75
|
3.2
|
51.8
|
1.0
|
CB
|
A:CYS50
|
3.2
|
61.0
|
1.0
|
CB
|
A:CYS72
|
3.3
|
58.3
|
1.0
|
CG
|
A:HIS75
|
3.3
|
45.8
|
1.0
|
CB
|
A:CYS55
|
3.3
|
55.4
|
1.0
|
CB
|
A:HIS75
|
3.6
|
45.7
|
1.0
|
N
|
A:CYS72
|
3.7
|
53.1
|
1.0
|
CA
|
A:CYS72
|
4.1
|
59.6
|
1.0
|
CB
|
A:ALA52
|
4.2
|
54.2
|
1.0
|
NE2
|
A:HIS75
|
4.4
|
46.7
|
1.0
|
CG2
|
A:VAL57
|
4.4
|
69.2
|
1.0
|
CD2
|
A:HIS75
|
4.4
|
47.5
|
1.0
|
N
|
A:HIS75
|
4.6
|
53.6
|
1.0
|
CB
|
A:VAL57
|
4.6
|
67.2
|
1.0
|
CA
|
A:CYS50
|
4.7
|
59.9
|
1.0
|
CA
|
A:HIS75
|
4.7
|
47.7
|
1.0
|
CA
|
A:CYS55
|
4.7
|
58.1
|
1.0
|
C
|
A:CYS72
|
4.8
|
66.1
|
1.0
|
C
|
A:TYR71
|
4.9
|
47.5
|
1.0
|
O
|
A:CYS72
|
4.9
|
63.9
|
1.0
|
CB
|
A:SER74
|
5.0
|
56.0
|
1.0
|
|
Zinc binding site 2 out
of 6 in 5rmk
Go back to
Zinc Binding Sites List in 5rmk
Zinc binding site 2 out
of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn702
b:53.3
occ:1.00
|
NE2
|
A:HIS33
|
1.9
|
40.2
|
1.0
|
ND1
|
A:HIS39
|
2.2
|
63.0
|
1.0
|
SG
|
A:CYS16
|
2.2
|
67.4
|
1.0
|
SG
|
A:CYS19
|
2.5
|
53.4
|
1.0
|
CD2
|
A:HIS33
|
2.9
|
47.2
|
1.0
|
CE1
|
A:HIS33
|
2.9
|
47.9
|
1.0
|
CG
|
A:HIS39
|
3.1
|
70.9
|
1.0
|
CE1
|
A:HIS39
|
3.2
|
68.5
|
1.0
|
N
|
A:CYS19
|
3.2
|
46.0
|
1.0
|
CB
|
A:CYS16
|
3.3
|
70.2
|
1.0
|
CB
|
A:HIS39
|
3.3
|
64.8
|
1.0
|
CB
|
A:CYS19
|
3.5
|
47.3
|
1.0
|
CA
|
A:CYS19
|
3.7
|
49.4
|
1.0
|
ND1
|
A:HIS33
|
4.0
|
51.3
|
1.0
|
CG
|
A:HIS33
|
4.0
|
50.5
|
1.0
|
C
|
A:ALA18
|
4.1
|
53.9
|
1.0
|
CD2
|
A:HIS39
|
4.2
|
71.1
|
1.0
|
NE2
|
A:HIS39
|
4.2
|
65.9
|
1.0
|
CB
|
A:ALA18
|
4.3
|
60.3
|
1.0
|
CB
|
A:ALA110
|
4.4
|
58.3
|
1.0
|
CA
|
A:ALA18
|
4.6
|
60.3
|
1.0
|
CA
|
A:CYS16
|
4.7
|
69.3
|
1.0
|
N
|
A:ALA18
|
4.7
|
53.6
|
1.0
|
CE2
|
A:PHE106
|
4.8
|
53.4
|
1.0
|
CA
|
A:HIS39
|
4.8
|
62.1
|
1.0
|
CZ
|
A:PHE106
|
4.9
|
51.9
|
1.0
|
O
|
A:ALA18
|
4.9
|
60.2
|
1.0
|
|
Zinc binding site 3 out
of 6 in 5rmk
Go back to
Zinc Binding Sites List in 5rmk
Zinc binding site 3 out
of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn703
b:89.9
occ:1.00
|
SG
|
A:CYS29
|
2.2
|
81.0
|
1.0
|
SG
|
A:CYS8
|
2.2
|
0.8
|
1.0
|
SG
|
A:CYS5
|
2.5
|
64.2
|
1.0
|
SG
|
A:CYS26
|
2.5
|
80.1
|
1.0
|
CB
|
A:CYS29
|
3.2
|
84.5
|
1.0
|
CB
|
A:CYS8
|
3.3
|
0.6
|
1.0
|
CB
|
A:CYS26
|
3.3
|
84.5
|
1.0
|
CB
|
A:CYS5
|
3.8
|
73.3
|
1.0
|
N
|
A:CYS8
|
3.8
|
98.9
|
1.0
|
N
|
A:CYS26
|
4.1
|
81.6
|
1.0
|
CA
|
A:CYS8
|
4.1
|
0.5
|
1.0
|
CA
|
A:CYS26
|
4.2
|
86.6
|
1.0
|
N
|
A:CYS29
|
4.3
|
82.4
|
1.0
|
CA
|
A:CYS29
|
4.3
|
82.7
|
1.0
|
CB
|
A:LEU7
|
4.4
|
97.7
|
1.0
|
CB
|
A:SER10
|
4.8
|
85.6
|
1.0
|
C
|
A:CYS8
|
4.8
|
99.4
|
1.0
|
C
|
A:LEU7
|
4.8
|
96.3
|
1.0
|
C
|
A:CYS26
|
4.8
|
91.6
|
1.0
|
O
|
A:CYS26
|
4.9
|
90.3
|
1.0
|
OG
|
A:SER10
|
4.9
|
80.3
|
1.0
|
|
Zinc binding site 4 out
of 6 in 5rmk
Go back to
Zinc Binding Sites List in 5rmk
Zinc binding site 4 out
of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn702
b:37.7
occ:1.00
|
NE2
|
B:HIS33
|
1.9
|
32.0
|
1.0
|
ND1
|
B:HIS39
|
2.1
|
50.9
|
1.0
|
SG
|
B:CYS16
|
2.2
|
45.7
|
1.0
|
SG
|
B:CYS19
|
2.3
|
40.8
|
1.0
|
CD2
|
B:HIS33
|
2.9
|
32.2
|
1.0
|
CG
|
B:HIS39
|
3.0
|
55.0
|
1.0
|
CE1
|
B:HIS33
|
3.0
|
33.5
|
1.0
|
CE1
|
B:HIS39
|
3.1
|
52.7
|
1.0
|
CB
|
B:HIS39
|
3.2
|
50.2
|
1.0
|
CB
|
B:CYS16
|
3.4
|
43.7
|
1.0
|
CB
|
B:CYS19
|
3.4
|
41.1
|
1.0
|
N
|
B:CYS19
|
3.5
|
50.5
|
1.0
|
CA
|
B:CYS19
|
3.8
|
46.3
|
1.0
|
CG
|
B:HIS33
|
4.1
|
36.0
|
1.0
|
ND1
|
B:HIS33
|
4.1
|
32.1
|
1.0
|
CD2
|
B:HIS39
|
4.1
|
51.6
|
1.0
|
NE2
|
B:HIS39
|
4.2
|
53.5
|
1.0
|
C
|
B:ALA18
|
4.2
|
50.8
|
1.0
|
CB
|
B:ALA18
|
4.5
|
45.6
|
1.0
|
CB
|
B:ALA110
|
4.5
|
39.6
|
1.0
|
CA
|
B:HIS39
|
4.7
|
47.2
|
1.0
|
CA
|
B:CYS16
|
4.8
|
41.4
|
1.0
|
CA
|
B:ALA18
|
4.8
|
47.7
|
1.0
|
N
|
B:ALA18
|
4.9
|
46.9
|
1.0
|
CE2
|
B:PHE106
|
5.0
|
38.6
|
1.0
|
|
Zinc binding site 5 out
of 6 in 5rmk
Go back to
Zinc Binding Sites List in 5rmk
Zinc binding site 5 out
of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn703
b:50.2
occ:1.00
|
SG
|
B:CYS29
|
2.2
|
44.1
|
1.0
|
SG
|
B:CYS5
|
2.3
|
54.4
|
1.0
|
SG
|
B:CYS26
|
2.4
|
54.9
|
1.0
|
CB
|
B:CYS8
|
2.8
|
70.8
|
1.0
|
CB
|
B:CYS29
|
3.0
|
45.7
|
1.0
|
SG
|
B:CYS8
|
3.0
|
88.1
|
1.0
|
CB
|
B:CYS5
|
3.3
|
60.6
|
1.0
|
CB
|
B:CYS26
|
3.5
|
52.2
|
1.0
|
N
|
B:CYS8
|
3.8
|
70.8
|
1.0
|
CA
|
B:CYS8
|
3.9
|
72.7
|
1.0
|
N
|
B:CYS26
|
3.9
|
58.2
|
1.0
|
N
|
B:CYS29
|
4.1
|
46.1
|
1.0
|
CA
|
B:CYS29
|
4.2
|
44.3
|
1.0
|
CA
|
B:CYS26
|
4.3
|
54.4
|
1.0
|
CB
|
B:LEU7
|
4.4
|
74.4
|
1.0
|
C
|
B:LEU7
|
4.6
|
70.7
|
1.0
|
CA
|
B:GLY99
|
4.7
|
67.4
|
1.0
|
N
|
B:GLY99
|
4.7
|
67.9
|
1.0
|
OG
|
B:SER10
|
4.7
|
62.6
|
1.0
|
CB
|
B:SER10
|
4.7
|
59.4
|
1.0
|
CA
|
B:CYS5
|
4.8
|
63.3
|
1.0
|
OG
|
B:SER100
|
4.8
|
63.5
|
1.0
|
C
|
B:CYS26
|
4.9
|
54.0
|
1.0
|
C
|
B:CYS8
|
4.9
|
66.8
|
1.0
|
CA
|
B:LEU7
|
4.9
|
68.9
|
1.0
|
N
|
B:LEU7
|
4.9
|
59.6
|
1.0
|
O
|
B:CYS26
|
5.0
|
50.4
|
1.0
|
|
Zinc binding site 6 out
of 6 in 5rmk
Go back to
Zinc Binding Sites List in 5rmk
Zinc binding site 6 out
of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn704
b:64.5
occ:1.00
|
SG
|
B:CYS50
|
2.2
|
58.5
|
1.0
|
ND1
|
B:HIS75
|
2.2
|
68.7
|
1.0
|
SG
|
B:CYS55
|
2.3
|
64.0
|
1.0
|
SG
|
B:CYS72
|
2.6
|
58.0
|
1.0
|
CG
|
B:HIS75
|
3.2
|
69.4
|
1.0
|
CB
|
B:CYS50
|
3.2
|
62.8
|
1.0
|
CE1
|
B:HIS75
|
3.2
|
72.2
|
1.0
|
CB
|
B:CYS55
|
3.3
|
74.1
|
1.0
|
CB
|
B:CYS72
|
3.3
|
59.7
|
1.0
|
CB
|
B:HIS75
|
3.4
|
68.1
|
1.0
|
N
|
B:CYS72
|
3.7
|
56.3
|
1.0
|
CB
|
B:ALA52
|
3.9
|
78.6
|
1.0
|
CA
|
B:CYS72
|
4.1
|
60.8
|
1.0
|
CD2
|
B:HIS75
|
4.3
|
72.9
|
1.0
|
NE2
|
B:HIS75
|
4.3
|
72.3
|
1.0
|
N
|
B:HIS75
|
4.4
|
60.7
|
1.0
|
CG2
|
B:VAL57
|
4.5
|
78.4
|
1.0
|
CA
|
B:HIS75
|
4.5
|
64.4
|
1.0
|
CA
|
B:CYS50
|
4.6
|
68.9
|
1.0
|
C
|
B:CYS72
|
4.7
|
63.9
|
1.0
|
CA
|
B:CYS55
|
4.7
|
79.1
|
1.0
|
CB
|
B:VAL57
|
4.7
|
80.1
|
1.0
|
O
|
B:CYS72
|
4.8
|
57.9
|
1.0
|
C
|
B:TYR71
|
4.9
|
58.1
|
1.0
|
C
|
B:SER74
|
4.9
|
66.5
|
1.0
|
|
Reference:
J.A.Newman,
Y.Yosaatmadja,
A.Douangamath,
A.Aimon,
A.J.Powell,
A.Dias,
D.Fearon,
L.Dunnett,
J.Brandao-Neto,
T.Krojer,
R.Skyner,
T.Gorrie-Stone,
W.Thompson,
F.Von Delft,
C.H.Arrowsmith,
A.Edwards,
C.Bountra,
O.Gileadi.
Pandda Analysis Group Deposition To Be Published.
Page generated: Mon Oct 28 04:29:04 2024
|