Zinc in PDB 6zsl: Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution
Enzymatic activity of Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution
Protein crystallography data
The structure of Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution, PDB code: 6zsl
was solved by
J.A.Newman,
Y.Yosaatmadja,
A.Douangamath,
C.H.Arrowsmith,
F.Von Delft,
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)
|
57.56 /
1.94
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
59.151,
70.120,
84.558,
102.47,
95.65,
112.79
|
R / Rfree (%)
|
20.9 /
25.3
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution
(pdb code 6zsl). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution, PDB code: 6zsl:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 6zsl
Go back to
Zinc Binding Sites List in 6zsl
Zinc binding site 1 out
of 6 in the Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution
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-Cov-2 Helicase at 1.94 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn701
b:47.2
occ:1.00
|
ND1
|
B:HIS39
|
2.1
|
44.5
|
1.0
|
NE2
|
B:HIS33
|
2.2
|
44.5
|
1.0
|
SG
|
B:CYS16
|
2.2
|
48.5
|
1.0
|
SG
|
B:CYS19
|
2.4
|
43.9
|
1.0
|
CG
|
B:HIS39
|
3.0
|
48.2
|
1.0
|
CE1
|
B:HIS39
|
3.1
|
49.6
|
1.0
|
CD2
|
B:HIS33
|
3.1
|
38.6
|
1.0
|
CE1
|
B:HIS33
|
3.2
|
45.7
|
1.0
|
CB
|
B:CYS16
|
3.3
|
55.1
|
1.0
|
CB
|
B:HIS39
|
3.3
|
44.8
|
1.0
|
CB
|
B:CYS19
|
3.4
|
35.6
|
1.0
|
N
|
B:CYS19
|
3.4
|
46.8
|
1.0
|
CA
|
B:CYS19
|
3.8
|
45.8
|
1.0
|
NE2
|
B:HIS39
|
4.2
|
47.7
|
1.0
|
CD2
|
B:HIS39
|
4.2
|
47.7
|
1.0
|
CG
|
B:HIS33
|
4.3
|
43.3
|
1.0
|
ND1
|
B:HIS33
|
4.3
|
39.9
|
1.0
|
C
|
B:ALA18
|
4.3
|
47.2
|
1.0
|
CB
|
B:ALA110
|
4.5
|
44.4
|
1.0
|
CB
|
B:ALA18
|
4.6
|
45.0
|
1.0
|
CA
|
B:CYS16
|
4.7
|
56.7
|
1.0
|
CA
|
B:HIS39
|
4.8
|
37.8
|
1.0
|
N
|
B:ALA18
|
4.8
|
49.4
|
1.0
|
CA
|
B:ALA18
|
4.8
|
52.3
|
1.0
|
CE2
|
B:PHE106
|
4.8
|
37.1
|
1.0
|
C
|
B:CYS16
|
4.9
|
50.1
|
1.0
|
CZ
|
B:PHE106
|
5.0
|
43.8
|
1.0
|
|
Zinc binding site 2 out
of 6 in 6zsl
Go back to
Zinc Binding Sites List in 6zsl
Zinc binding site 2 out
of 6 in the Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution
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-Cov-2 Helicase at 1.94 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn702
b:66.8
occ:1.00
|
SG
|
B:CYS26
|
2.4
|
77.2
|
1.0
|
SG
|
B:CYS8
|
2.4
|
79.9
|
1.0
|
SG
|
B:CYS5
|
2.5
|
69.1
|
1.0
|
SG
|
B:CYS29
|
2.6
|
67.5
|
1.0
|
CB
|
B:CYS8
|
3.0
|
68.9
|
1.0
|
CB
|
B:CYS29
|
3.0
|
53.1
|
1.0
|
CB
|
B:CYS26
|
3.3
|
56.0
|
1.0
|
CB
|
B:CYS5
|
3.6
|
73.1
|
1.0
|
N
|
B:CYS8
|
3.7
|
76.6
|
1.0
|
N
|
B:CYS26
|
3.9
|
61.3
|
1.0
|
CA
|
B:CYS8
|
4.0
|
77.4
|
1.0
|
N
|
B:CYS29
|
4.0
|
62.4
|
1.0
|
CA
|
B:CYS26
|
4.1
|
65.9
|
1.0
|
CA
|
B:CYS29
|
4.1
|
54.9
|
1.0
|
N
|
B:GLY99
|
4.2
|
75.3
|
1.0
|
CA
|
B:GLY99
|
4.2
|
74.5
|
1.0
|
CB
|
B:LEU7
|
4.5
|
68.7
|
1.0
|
C
|
B:LEU7
|
4.5
|
66.7
|
1.0
|
OG
|
B:SER100
|
4.7
|
64.5
|
1.0
|
C
|
B:CYS26
|
4.7
|
61.4
|
1.0
|
C
|
B:GLY99
|
4.7
|
75.6
|
1.0
|
O
|
B:CYS26
|
4.8
|
55.5
|
1.0
|
CA
|
B:LEU7
|
4.9
|
67.6
|
1.0
|
CA
|
B:CYS5
|
5.0
|
76.9
|
1.0
|
|
Zinc binding site 3 out
of 6 in 6zsl
Go back to
Zinc Binding Sites List in 6zsl
Zinc binding site 3 out
of 6 in the Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution
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-Cov-2 Helicase at 1.94 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn703
b:69.0
occ:1.00
|
ND1
|
B:HIS75
|
2.0
|
69.1
|
1.0
|
SG
|
B:CYS55
|
2.3
|
75.6
|
1.0
|
SG
|
B:CYS50
|
2.4
|
68.0
|
1.0
|
SG
|
B:CYS72
|
2.5
|
60.6
|
1.0
|
CE1
|
B:HIS75
|
2.9
|
77.1
|
1.0
|
CG
|
B:HIS75
|
3.1
|
67.7
|
1.0
|
CB
|
B:CYS55
|
3.1
|
85.4
|
1.0
|
CB
|
B:CYS72
|
3.5
|
53.5
|
1.0
|
CB
|
B:CYS50
|
3.5
|
61.6
|
1.0
|
CB
|
B:HIS75
|
3.5
|
65.8
|
1.0
|
CB
|
B:ALA52
|
3.8
|
77.6
|
1.0
|
N
|
B:CYS72
|
3.9
|
54.5
|
1.0
|
NE2
|
B:HIS75
|
4.0
|
76.2
|
1.0
|
CD2
|
B:HIS75
|
4.1
|
68.7
|
1.0
|
CA
|
B:CYS72
|
4.3
|
52.7
|
1.0
|
N
|
B:HIS75
|
4.5
|
61.3
|
1.0
|
CG2
|
B:VAL57
|
4.5
|
64.5
|
1.0
|
CA
|
B:CYS55
|
4.6
|
86.8
|
1.0
|
CA
|
B:HIS75
|
4.6
|
67.3
|
1.0
|
CB
|
B:VAL57
|
4.7
|
61.4
|
1.0
|
CA
|
B:CYS50
|
4.9
|
67.5
|
1.0
|
C
|
B:CYS72
|
5.0
|
60.2
|
1.0
|
|
Zinc binding site 4 out
of 6 in 6zsl
Go back to
Zinc Binding Sites List in 6zsl
Zinc binding site 4 out
of 6 in the Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution
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-Cov-2 Helicase at 1.94 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn701
b:56.0
occ:1.00
|
ND1
|
A:HIS75
|
2.1
|
56.6
|
1.0
|
SG
|
A:CYS55
|
2.2
|
61.1
|
1.0
|
SG
|
A:CYS50
|
2.3
|
48.4
|
1.0
|
SG
|
A:CYS72
|
2.5
|
57.4
|
1.0
|
CE1
|
A:HIS75
|
3.0
|
56.5
|
1.0
|
CB
|
A:CYS55
|
3.1
|
53.8
|
1.0
|
CB
|
A:CYS50
|
3.2
|
53.7
|
1.0
|
CG
|
A:HIS75
|
3.2
|
53.9
|
1.0
|
CB
|
A:CYS72
|
3.4
|
57.6
|
1.0
|
CB
|
A:HIS75
|
3.7
|
53.8
|
1.0
|
N
|
A:CYS72
|
3.8
|
47.1
|
1.0
|
NE2
|
A:HIS75
|
4.2
|
46.3
|
1.0
|
CA
|
A:CYS72
|
4.2
|
53.4
|
1.0
|
CD2
|
A:HIS75
|
4.3
|
52.6
|
1.0
|
CB
|
A:ALA52
|
4.3
|
53.9
|
1.0
|
CG2
|
A:VAL57
|
4.4
|
53.1
|
1.0
|
CA
|
A:CYS55
|
4.6
|
54.9
|
1.0
|
CB
|
A:VAL57
|
4.6
|
55.7
|
1.0
|
N
|
A:HIS75
|
4.6
|
56.4
|
1.0
|
CA
|
A:CYS50
|
4.6
|
49.9
|
1.0
|
CA
|
A:HIS75
|
4.8
|
51.3
|
1.0
|
C
|
A:CYS72
|
4.9
|
64.1
|
1.0
|
C
|
A:TYR71
|
5.0
|
50.2
|
1.0
|
|
Zinc binding site 5 out
of 6 in 6zsl
Go back to
Zinc Binding Sites List in 6zsl
Zinc binding site 5 out
of 6 in the Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution
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-Cov-2 Helicase at 1.94 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn702
b:45.7
occ:1.00
|
NE2
|
A:HIS33
|
2.0
|
28.4
|
1.0
|
ND1
|
A:HIS39
|
2.0
|
40.5
|
1.0
|
SG
|
A:CYS16
|
2.3
|
47.9
|
1.0
|
SG
|
A:CYS19
|
2.4
|
48.0
|
1.0
|
CE1
|
A:HIS39
|
2.9
|
50.4
|
1.0
|
CD2
|
A:HIS33
|
2.9
|
51.7
|
1.0
|
CE1
|
A:HIS33
|
3.0
|
47.8
|
1.0
|
CG
|
A:HIS39
|
3.0
|
56.1
|
1.0
|
N
|
A:CYS19
|
3.3
|
50.3
|
1.0
|
CB
|
A:CYS16
|
3.4
|
46.3
|
1.0
|
CB
|
A:HIS39
|
3.4
|
50.5
|
1.0
|
CB
|
A:CYS19
|
3.4
|
36.5
|
1.0
|
CA
|
A:CYS19
|
3.7
|
45.1
|
1.0
|
NE2
|
A:HIS39
|
4.0
|
50.3
|
1.0
|
ND1
|
A:HIS33
|
4.1
|
49.9
|
1.0
|
CD2
|
A:HIS39
|
4.1
|
50.3
|
1.0
|
CG
|
A:HIS33
|
4.1
|
44.4
|
1.0
|
C
|
A:ALA18
|
4.1
|
49.0
|
1.0
|
CB
|
A:ALA18
|
4.2
|
52.9
|
1.0
|
CB
|
A:ALA110
|
4.5
|
47.7
|
1.0
|
CA
|
A:ALA18
|
4.6
|
54.2
|
1.0
|
N
|
A:ALA18
|
4.6
|
52.0
|
1.0
|
CA
|
A:CYS16
|
4.7
|
51.1
|
1.0
|
CA
|
A:HIS39
|
4.8
|
51.5
|
1.0
|
C
|
A:CYS16
|
5.0
|
50.6
|
1.0
|
CE2
|
A:PHE106
|
5.0
|
50.4
|
1.0
|
O
|
A:ALA18
|
5.0
|
61.1
|
1.0
|
|
Zinc binding site 6 out
of 6 in 6zsl
Go back to
Zinc Binding Sites List in 6zsl
Zinc binding site 6 out
of 6 in the Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution
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-Cov-2 Helicase at 1.94 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn703
b:70.1
occ:1.00
|
SG
|
A:CYS5
|
2.3
|
69.7
|
1.0
|
SG
|
A:CYS26
|
2.4
|
70.3
|
1.0
|
SG
|
A:CYS29
|
2.4
|
73.5
|
1.0
|
SG
|
A:CYS8
|
2.5
|
84.8
|
1.0
|
CB
|
A:CYS29
|
3.0
|
69.0
|
1.0
|
CB
|
A:CYS26
|
3.2
|
68.9
|
1.0
|
CB
|
A:CYS5
|
3.3
|
70.5
|
1.0
|
CB
|
A:CYS8
|
3.4
|
75.7
|
1.0
|
N
|
A:CYS26
|
3.6
|
59.0
|
1.0
|
N
|
A:CYS8
|
3.7
|
76.2
|
1.0
|
CA
|
A:CYS26
|
4.0
|
68.7
|
1.0
|
CA
|
A:CYS8
|
4.1
|
79.8
|
1.0
|
CB
|
A:LEU7
|
4.2
|
67.2
|
1.0
|
CA
|
A:CYS29
|
4.2
|
65.5
|
1.0
|
N
|
A:CYS29
|
4.2
|
69.0
|
1.0
|
C
|
A:LEU7
|
4.5
|
72.1
|
1.0
|
C
|
A:CYS26
|
4.7
|
69.3
|
1.0
|
CA
|
A:LEU7
|
4.8
|
69.2
|
1.0
|
CA
|
A:CYS5
|
4.8
|
73.3
|
1.0
|
C
|
A:CYS8
|
4.8
|
77.9
|
1.0
|
C
|
A:LEU25
|
4.8
|
64.4
|
1.0
|
N
|
A:LEU7
|
4.8
|
67.4
|
1.0
|
O
|
A:CYS26
|
4.8
|
70.4
|
1.0
|
|
Reference:
J.A.Newman,
Y.Yosaatmadja,
A.Douangamath,
C.H.Arrowsmith,
F.Von Delft,
A.Edwards,
C.Bountra,
O.Gileadi.
Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution To Be Published.
Page generated: Tue Oct 29 15:58:30 2024
|