Zinc in PDB 8ov1: Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Adp
Enzymatic activity of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Adp
All present enzymatic activity of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Adp:
2.1.1.57;
Protein crystallography data
The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Adp, PDB code: 8ov1
was solved by
V.Kremling,
J.Sprenger,
D.Oberthuer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.87 /
1.67
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
167.495,
167.495,
51.5,
90,
90,
120
|
R / Rfree (%)
|
17.4 /
18.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Adp
(pdb code 8ov1). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the
Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Adp, PDB code: 8ov1:
Jump to Zinc binding site number:
1;
2;
Zinc binding site 1 out
of 2 in 8ov1
Go back to
Zinc Binding Sites List in 8ov1
Zinc binding site 1 out
of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Adp
![](/pictures/ZN/pdb/ov/8ov1-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/ov/8ov1-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn4402
b:27.6
occ:1.00
|
NE2
|
B:HIS4336
|
2.1
|
25.9
|
1.0
|
SG
|
B:CYS4327
|
2.3
|
29.1
|
1.0
|
SG
|
B:CYS4343
|
2.3
|
28.5
|
1.0
|
SG
|
B:CYS4330
|
2.3
|
27.7
|
1.0
|
H
|
B:CYS4330
|
3.0
|
29.2
|
1.0
|
CE1
|
B:HIS4336
|
3.0
|
32.5
|
1.0
|
HB2
|
B:CYS4343
|
3.1
|
34.3
|
1.0
|
HB3
|
B:CYS4327
|
3.1
|
30.5
|
1.0
|
CD2
|
B:HIS4336
|
3.1
|
37.2
|
1.0
|
CB
|
B:CYS4327
|
3.2
|
25.4
|
1.0
|
HE1
|
B:HIS4336
|
3.2
|
39.0
|
1.0
|
HB2
|
B:CYS4330
|
3.3
|
26.8
|
1.0
|
HD2
|
B:HIS4336
|
3.3
|
44.6
|
1.0
|
CB
|
B:CYS4343
|
3.3
|
28.6
|
1.0
|
CB
|
B:CYS4330
|
3.3
|
22.3
|
1.0
|
HB2
|
B:CYS4327
|
3.3
|
30.5
|
1.0
|
N
|
B:CYS4330
|
3.6
|
24.4
|
1.0
|
HB2
|
B:TYR4329
|
3.7
|
33.3
|
1.0
|
HB3
|
B:CYS4343
|
3.9
|
34.3
|
1.0
|
CA
|
B:CYS4330
|
4.0
|
24.6
|
1.0
|
HB2
|
B:LYS4346
|
4.0
|
31.8
|
1.0
|
HA
|
B:CYS4330
|
4.2
|
29.6
|
1.0
|
HB3
|
B:CYS4330
|
4.2
|
26.8
|
1.0
|
ND1
|
B:HIS4336
|
4.2
|
31.0
|
1.0
|
CG
|
B:HIS4336
|
4.2
|
33.8
|
1.0
|
O2
|
B:EDO4405
|
4.2
|
39.5
|
1.0
|
HA
|
B:CYS4343
|
4.3
|
36.6
|
1.0
|
HB2
|
B:LEU4345
|
4.3
|
31.7
|
1.0
|
H
|
B:LYS4346
|
4.3
|
30.6
|
1.0
|
CA
|
B:CYS4343
|
4.4
|
30.5
|
1.0
|
HA
|
B:ALA4324
|
4.5
|
26.2
|
1.0
|
HD2
|
B:TYR4329
|
4.6
|
42.9
|
1.0
|
CB
|
B:TYR4329
|
4.6
|
27.7
|
1.0
|
H
|
B:TYR4329
|
4.6
|
31.4
|
1.0
|
C
|
B:TYR4329
|
4.6
|
27.5
|
1.0
|
CA
|
B:CYS4327
|
4.6
|
25.1
|
1.0
|
H
|
B:LEU4345
|
4.6
|
31.2
|
1.0
|
H12
|
B:EDO4405
|
4.7
|
67.4
|
1.0
|
HO2
|
B:EDO4405
|
4.7
|
47.5
|
1.0
|
CB
|
B:LYS4346
|
4.9
|
26.4
|
1.0
|
HD1
|
B:HIS4336
|
4.9
|
37.2
|
1.0
|
HD12
|
B:LEU4345
|
5.0
|
38.9
|
1.0
|
N
|
B:LYS4346
|
5.0
|
25.5
|
1.0
|
HB3
|
B:LYS4346
|
5.0
|
31.8
|
1.0
|
C
|
B:CYS4327
|
5.0
|
28.0
|
1.0
|
CA
|
B:TYR4329
|
5.0
|
24.7
|
1.0
|
N
|
B:TYR4329
|
5.0
|
26.1
|
1.0
|
HA
|
B:CYS4327
|
5.0
|
30.2
|
1.0
|
|
Zinc binding site 2 out
of 2 in 8ov1
Go back to
Zinc Binding Sites List in 8ov1
Zinc binding site 2 out
of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Adp
![](/pictures/ZN/pdb/ov/8ov1-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/ov/8ov1-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn4403
b:42.4
occ:1.00
|
SG
|
B:CYS4381
|
2.2
|
45.1
|
1.0
|
SG
|
B:CYS4370
|
2.3
|
42.9
|
1.0
|
SG
|
B:CYS4383
|
2.3
|
43.2
|
1.0
|
SG
|
B:CYS4373
|
2.4
|
38.0
|
1.0
|
HB2
|
B:CYS4383
|
2.9
|
62.7
|
1.0
|
HB3
|
B:CYS4373
|
3.0
|
44.5
|
1.0
|
HB3
|
B:CYS4370
|
3.0
|
54.1
|
1.0
|
CB
|
B:CYS4370
|
3.1
|
45.0
|
1.0
|
HB2
|
B:CYS4370
|
3.1
|
54.1
|
1.0
|
H
|
B:CYS4373
|
3.2
|
47.5
|
1.0
|
CB
|
B:CYS4383
|
3.2
|
52.2
|
1.0
|
CB
|
B:CYS4373
|
3.3
|
37.0
|
1.0
|
H
|
B:CYS4383
|
3.4
|
60.0
|
1.0
|
HB2
|
B:CYS4381
|
3.4
|
53.1
|
1.0
|
CB
|
B:CYS4381
|
3.5
|
44.2
|
1.0
|
HB
|
B:VAL4372
|
3.6
|
64.2
|
1.0
|
HA
|
B:CYS4381
|
3.7
|
56.4
|
1.0
|
HZ3
|
B:LYS4377
|
3.7
|
91.2
|
1.0
|
N
|
B:CYS4373
|
3.8
|
39.6
|
1.0
|
HB3
|
B:CYS4383
|
3.9
|
62.7
|
1.0
|
HE2
|
B:LYS4377
|
4.0
|
96.0
|
1.0
|
N
|
B:CYS4383
|
4.0
|
50.0
|
1.0
|
HB2
|
B:CYS4373
|
4.1
|
44.5
|
1.0
|
O
|
B:HOH4531
|
4.1
|
45.6
|
1.0
|
CA
|
B:CYS4381
|
4.1
|
47.0
|
1.0
|
H
|
B:SER4382
|
4.1
|
53.6
|
1.0
|
CA
|
B:CYS4373
|
4.1
|
46.8
|
1.0
|
O
|
B:HOH4582
|
4.2
|
53.6
|
1.0
|
CA
|
B:CYS4383
|
4.2
|
55.5
|
1.0
|
HB3
|
B:CYS4381
|
4.3
|
53.1
|
1.0
|
NZ
|
B:LYS4377
|
4.4
|
76.0
|
1.0
|
HZ1
|
B:LYS4377
|
4.4
|
91.2
|
1.0
|
H
|
B:VAL4372
|
4.4
|
56.2
|
1.0
|
HB2
|
B:MET4375
|
4.5
|
45.9
|
1.0
|
HD3
|
B:LYS4377
|
4.5
|
76.7
|
1.0
|
N
|
B:SER4382
|
4.5
|
44.6
|
1.0
|
CA
|
B:CYS4370
|
4.6
|
43.0
|
1.0
|
CB
|
B:VAL4372
|
4.6
|
53.5
|
1.0
|
H
|
B:MET4375
|
4.6
|
45.1
|
1.0
|
HA
|
B:CYS4383
|
4.6
|
66.6
|
1.0
|
C
|
B:CYS4381
|
4.6
|
42.4
|
1.0
|
CE
|
B:LYS4377
|
4.6
|
80.0
|
1.0
|
H
|
B:GLY4374
|
4.8
|
49.5
|
1.0
|
C
|
B:VAL4372
|
4.9
|
45.4
|
1.0
|
HA
|
B:CYS4370
|
4.9
|
51.5
|
1.0
|
HG12
|
B:VAL4372
|
4.9
|
62.6
|
1.0
|
HA
|
B:CYS4373
|
4.9
|
56.1
|
1.0
|
C
|
B:CYS4373
|
4.9
|
45.9
|
1.0
|
|
Reference:
V.Kremling,
D.Oberthuer,
O.Yefanov,
M.Galchenkova,
P.Middendorf,
Y.Fernandez Garcia,
C.Ehrt,
S.Falke,
A.Kiene,
B.Klopprogge,
H.Chapman,
J.Sprenger.
Crystal Structures of Tubercidin and Adenosine Bound to the Active Site of the Sars-Cov-2 Methyltransferase NSP10-16 To Be Published.
Page generated: Fri Jul 28 07:22:05 2023
|