Atomistry » Zinc » PDB 8brv-8c8s » 8c5m
Atomistry »
  Zinc »
    PDB 8brv-8c8s »
      8c5m »

Zinc in PDB 8c5m: Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Mta

Enzymatic activity of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Mta

All present enzymatic activity of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Mta:
2.1.1.57;

Protein crystallography data

The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Mta, PDB code: 8c5m was solved by V.Kremling, J.Sprenger, D.Oberthuer, S.Falke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.43 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.955, 166.955, 51.394, 90, 90, 120
R / Rfree (%) 18.4 / 21.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Mta (pdb code 8c5m). 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 Mta, PDB code: 8c5m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8c5m

Go back to Zinc Binding Sites List in 8c5m
Zinc binding site 1 out of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Mta


Mono view


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 Mta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4401

b:33.9
occ:1.00
NE2 B:HIS4336 2.1 39.6 1.0
SG B:CYS4327 2.3 32.1 1.0
SG B:CYS4343 2.3 33.6 1.0
SG B:CYS4330 2.3 32.9 1.0
CD2 B:HIS4336 3.1 38.0 1.0
CE1 B:HIS4336 3.1 37.2 1.0
CB B:CYS4327 3.1 32.0 1.0
CB B:CYS4343 3.3 40.6 1.0
CB B:CYS4330 3.4 28.6 1.0
N B:CYS4330 3.6 29.9 1.0
CA B:CYS4330 4.0 30.5 1.0
HO2 B:EDO4406 4.0 70.1 1.0
ND1 B:HIS4336 4.2 39.1 1.0
CG B:HIS4336 4.2 46.0 1.0
O2 B:EDO4406 4.3 58.4 1.0
CA B:CYS4343 4.5 44.7 1.0
CB B:TYR4329 4.5 35.9 1.0
CA B:CYS4327 4.5 33.1 1.0
C B:TYR4329 4.6 37.1 1.0
CB B:LYS4346 4.8 33.5 1.0
H12 B:EDO4406 4.8 72.6 1.0
N B:LYS4346 4.9 29.6 1.0
C B:CYS4327 4.9 34.0 1.0
CA B:TYR4329 4.9 34.5 1.0
O B:CYS4327 5.0 28.9 1.0
N B:TYR4329 5.0 28.6 1.0

Zinc binding site 2 out of 2 in 8c5m

Go back to Zinc Binding Sites List in 8c5m
Zinc binding site 2 out of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Mta


Mono view


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 Mta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4402

b:53.5
occ:1.00
SG B:CYS4381 2.3 55.5 1.0
SG B:CYS4370 2.3 52.5 1.0
SG B:CYS4373 2.4 51.8 1.0
SG B:CYS4383 2.4 57.5 1.0
CB B:CYS4370 3.1 46.9 1.0
CB B:CYS4383 3.2 60.2 1.0
CB B:CYS4373 3.4 48.4 1.0
CB B:CYS4381 3.5 49.9 1.0
N B:CYS4373 3.8 51.0 1.0
CA B:CYS4381 4.1 53.7 1.0
N B:CYS4383 4.1 67.2 1.0
CA B:CYS4373 4.2 53.4 1.0
O B:HOH4540 4.2 54.0 1.0
CA B:CYS4383 4.3 69.1 1.0
O B:HOH4568 4.4 64.0 1.0
NZ B:LYS4377 4.4 59.2 1.0
CA B:CYS4370 4.5 47.5 1.0
N B:SER4382 4.6 58.0 1.0
CB B:VAL4372 4.6 57.1 1.0
C B:CYS4381 4.6 55.6 1.0
C B:VAL4372 4.9 53.9 1.0
C B:CYS4373 4.9 51.0 1.0

Reference:

V.Kremling, J.Sprenger, D.Oberthuer, S.Falke, O.Yefanov, M.Galchenkova, P.Middendorf, Y.Fernandez Garcia, C.Ehrt, A.Kiene, B.Klopprogge, H.Chapman. Crystal Structures of Tubercidin and Adenosine Bound to the Active Site of the Sars-Cov-2 Methyltransferase NSP10-16 To Be Published.
Page generated: Wed Oct 30 18:34:57 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy