Zinc in PDB 8ov4: Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin
Enzymatic activity of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin
All present enzymatic activity of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin:
2.1.1.57;
Protein crystallography data
The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin, PDB code: 8ov4
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)
|
48.73 /
1.93
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
168.05,
168.05,
51.71,
90,
90,
120
|
R / Rfree (%)
|
17.9 /
20.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin
(pdb code 8ov4). 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 Toyocamycin, PDB code: 8ov4:
Jump to Zinc binding site number:
1;
2;
Zinc binding site 1 out
of 2 in 8ov4
Go back to
Zinc Binding Sites List in 8ov4
Zinc binding site 1 out
of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin
![](/pictures/ZN/pdb/ov/8ov4-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/ov/8ov4-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 Toyocamycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn4402
b:47.6
occ:1.00
|
NE2
|
B:HIS4336
|
2.1
|
65.0
|
1.0
|
SG
|
B:CYS4343
|
2.2
|
50.4
|
1.0
|
SG
|
B:CYS4327
|
2.2
|
46.6
|
1.0
|
SG
|
B:CYS4330
|
2.3
|
42.5
|
1.0
|
H
|
B:CYS4330
|
2.9
|
60.4
|
1.0
|
HB3
|
B:CYS4327
|
2.9
|
59.8
|
1.0
|
CB
|
B:CYS4327
|
3.0
|
49.6
|
1.0
|
CE1
|
B:HIS4336
|
3.0
|
60.1
|
1.0
|
HB2
|
B:CYS4343
|
3.1
|
70.6
|
1.0
|
CD2
|
B:HIS4336
|
3.1
|
63.8
|
1.0
|
HB2
|
B:CYS4327
|
3.2
|
59.8
|
1.0
|
HE1
|
B:HIS4336
|
3.2
|
72.4
|
1.0
|
HD2
|
B:HIS4336
|
3.3
|
76.8
|
1.0
|
CB
|
B:CYS4343
|
3.3
|
58.6
|
1.0
|
HB2
|
B:CYS4330
|
3.3
|
56.8
|
1.0
|
CB
|
B:CYS4330
|
3.4
|
47.2
|
1.0
|
N
|
B:CYS4330
|
3.5
|
50.2
|
1.0
|
HB2
|
B:TYR4329
|
3.6
|
62.7
|
1.0
|
HB2
|
B:LYS4346
|
3.8
|
55.6
|
1.0
|
HB3
|
B:CYS4343
|
3.9
|
70.6
|
1.0
|
CA
|
B:CYS4330
|
3.9
|
45.3
|
1.0
|
H
|
B:LYS4346
|
4.1
|
48.1
|
1.0
|
HA
|
B:CYS4330
|
4.1
|
54.6
|
1.0
|
HA
|
B:CYS4343
|
4.1
|
85.2
|
1.0
|
ND1
|
B:HIS4336
|
4.2
|
71.6
|
1.0
|
HB3
|
B:CYS4330
|
4.2
|
56.8
|
1.0
|
CG
|
B:HIS4336
|
4.2
|
74.3
|
1.0
|
CA
|
B:CYS4343
|
4.3
|
70.8
|
1.0
|
O
|
B:HOH4540
|
4.4
|
63.4
|
1.0
|
HD2
|
B:TYR4329
|
4.4
|
72.0
|
1.0
|
HB2
|
B:LEU4345
|
4.4
|
54.6
|
1.0
|
H
|
B:LEU4345
|
4.5
|
61.5
|
1.0
|
CA
|
B:CYS4327
|
4.5
|
50.2
|
1.0
|
CB
|
B:TYR4329
|
4.5
|
52.0
|
1.0
|
HA
|
B:ALA4324
|
4.5
|
45.1
|
1.0
|
C
|
B:TYR4329
|
4.6
|
52.6
|
1.0
|
H
|
B:TYR4329
|
4.6
|
52.0
|
1.0
|
CB
|
B:LYS4346
|
4.7
|
46.2
|
1.0
|
N
|
B:LYS4346
|
4.8
|
39.9
|
1.0
|
HB3
|
B:LYS4346
|
4.8
|
55.6
|
1.0
|
HA
|
B:CYS4327
|
4.9
|
60.5
|
1.0
|
C
|
B:CYS4327
|
4.9
|
45.0
|
1.0
|
O
|
B:HOH4550
|
4.9
|
66.2
|
1.0
|
CA
|
B:TYR4329
|
4.9
|
49.3
|
1.0
|
HD1
|
B:HIS4336
|
4.9
|
86.2
|
1.0
|
N
|
B:TYR4329
|
4.9
|
43.1
|
1.0
|
H
|
B:ASP4344
|
5.0
|
79.0
|
1.0
|
O
|
B:CYS4327
|
5.0
|
42.2
|
1.0
|
HB3
|
B:TYR4329
|
5.0
|
62.7
|
1.0
|
|
Zinc binding site 2 out
of 2 in 8ov4
Go back to
Zinc Binding Sites List in 8ov4
Zinc binding site 2 out
of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin
![](/pictures/ZN/pdb/ov/8ov4-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/ov/8ov4-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 Toyocamycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn4403
b:68.7
occ:1.00
|
SG
|
B:CYS4370
|
2.3
|
67.1
|
1.0
|
SG
|
B:CYS4381
|
2.3
|
68.5
|
1.0
|
SG
|
B:CYS4373
|
2.4
|
62.3
|
1.0
|
SG
|
B:CYS4383
|
2.4
|
82.7
|
1.0
|
HB2
|
B:CYS4383
|
2.9
|
109.0
|
1.0
|
HB3
|
B:CYS4370
|
2.9
|
82.5
|
1.0
|
CB
|
B:CYS4370
|
3.0
|
68.6
|
1.0
|
HB2
|
B:CYS4370
|
3.0
|
82.5
|
1.0
|
H
|
B:CYS4373
|
3.1
|
77.6
|
1.0
|
CB
|
B:CYS4383
|
3.2
|
90.6
|
1.0
|
H
|
B:CYS4383
|
3.3
|
106.3
|
1.0
|
HB3
|
B:CYS4373
|
3.3
|
69.0
|
1.0
|
HB2
|
B:CYS4381
|
3.4
|
86.7
|
1.0
|
CB
|
B:CYS4381
|
3.5
|
72.0
|
1.0
|
CB
|
B:CYS4373
|
3.5
|
57.3
|
1.0
|
O
|
B:HOH4534
|
3.5
|
67.5
|
1.0
|
HA
|
B:CYS4381
|
3.6
|
87.7
|
1.0
|
HB
|
B:VAL4372
|
3.7
|
91.5
|
1.0
|
N
|
B:CYS4373
|
3.8
|
64.5
|
1.0
|
HB3
|
B:CYS4383
|
3.9
|
109.0
|
1.0
|
N
|
B:CYS4383
|
4.0
|
88.4
|
1.0
|
CA
|
B:CYS4381
|
4.0
|
73.0
|
1.0
|
HZ2
|
B:LYS4377
|
4.0
|
121.5
|
1.0
|
H
|
B:SER4382
|
4.1
|
83.4
|
1.0
|
HD3
|
B:LYS4377
|
4.2
|
105.8
|
1.0
|
CA
|
B:CYS4383
|
4.2
|
91.3
|
1.0
|
HB2
|
B:CYS4373
|
4.2
|
69.0
|
1.0
|
CA
|
B:CYS4373
|
4.3
|
68.4
|
1.0
|
HB3
|
B:CYS4381
|
4.3
|
86.7
|
1.0
|
H
|
B:VAL4372
|
4.3
|
75.2
|
1.0
|
CA
|
B:CYS4370
|
4.4
|
66.6
|
1.0
|
N
|
B:SER4382
|
4.5
|
69.4
|
1.0
|
HB2
|
B:MET4375
|
4.5
|
60.6
|
1.0
|
C
|
B:CYS4381
|
4.6
|
71.1
|
1.0
|
H
|
B:MET4375
|
4.6
|
67.4
|
1.0
|
CB
|
B:VAL4372
|
4.6
|
76.1
|
1.0
|
HA
|
B:CYS4383
|
4.7
|
109.8
|
1.0
|
HD2
|
B:LYS4377
|
4.7
|
105.8
|
1.0
|
H
|
B:GLY4374
|
4.7
|
78.8
|
1.0
|
HA
|
B:CYS4370
|
4.8
|
80.2
|
1.0
|
NZ
|
B:LYS4377
|
4.8
|
101.0
|
1.0
|
CD
|
B:LYS4377
|
4.9
|
88.0
|
1.0
|
C
|
B:VAL4372
|
4.9
|
67.1
|
1.0
|
C
|
B:CYS4370
|
4.9
|
65.0
|
1.0
|
HZ3
|
B:LYS4377
|
4.9
|
121.5
|
1.0
|
N
|
B:VAL4372
|
5.0
|
62.5
|
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 Thesars-Cov-2 Methyltransferase NSP10-16 To Be Published.
Page generated: Fri Jul 28 07:22:05 2023
|