Zinc in PDB 8otr: Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sam Analog Bdh 33959089

Enzymatic activity of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sam Analog Bdh 33959089

All present enzymatic activity of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sam Analog Bdh 33959089:
2.1.1.57;

Protein crystallography data

The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sam Analog Bdh 33959089, PDB code: 8otr 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) 41.99 / 1.77
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.6, 167.6, 51.48, 90, 90, 120
R / Rfree (%) 18.8 / 21

Other elements in 8otr:

The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sam Analog Bdh 33959089 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sam Analog Bdh 33959089 (pdb code 8otr). 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 Sam Analog Bdh 33959089, PDB code: 8otr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8otr

Go back to Zinc Binding Sites List in 8otr
Zinc binding site 1 out of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sam Analog Bdh 33959089


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 Sam Analog Bdh 33959089 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4401

b:39.3
occ:1.00
NE2 B:HIS4336 2.0 43.7 1.0
SG B:CYS4327 2.3 36.3 1.0
SG B:CYS4343 2.3 38.8 1.0
SG B:CYS4330 2.3 38.0 1.0
CE1 B:HIS4336 3.0 42.1 1.0
CD2 B:HIS4336 3.1 43.0 1.0
CB B:CYS4327 3.1 39.3 1.0
CB B:CYS4343 3.3 45.3 1.0
CB B:CYS4330 3.4 33.7 1.0
N B:CYS4330 3.6 38.0 1.0
CA B:CYS4330 4.0 35.2 1.0
ND1 B:HIS4336 4.1 43.3 1.0
CG B:HIS4336 4.2 53.2 1.0
O2 B:EDO4404 4.3 55.7 1.0
CA B:CYS4343 4.4 45.6 1.0
CB B:TYR4329 4.5 40.4 1.0
CA B:CYS4327 4.6 36.5 1.0
C B:TYR4329 4.6 38.1 1.0
C2 B:EDO4404 4.7 59.6 1.0
CB B:LYS4346 4.8 35.9 1.0
N B:LYS4346 4.9 32.8 1.0
CA B:TYR4329 4.9 37.4 1.0
C B:CYS4327 5.0 37.7 1.0
N B:TYR4329 5.0 34.2 1.0

Zinc binding site 2 out of 2 in 8otr

Go back to Zinc Binding Sites List in 8otr
Zinc binding site 2 out of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sam Analog Bdh 33959089


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 Sam Analog Bdh 33959089 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4402

b:58.5
occ:1.00
SG B:CYS4370 2.3 56.7 1.0
SG B:CYS4381 2.3 61.5 1.0
SG B:CYS4383 2.4 68.7 1.0
SG B:CYS4373 2.4 54.6 1.0
CB B:CYS4370 3.1 53.8 1.0
CB B:CYS4383 3.3 72.4 1.0
CB B:CYS4373 3.4 52.9 1.0
CB B:CYS4381 3.4 56.8 1.0
N B:CYS4373 3.8 51.8 1.0
N B:CYS4383 4.0 79.3 1.0
O B:HOH4549 4.1 60.3 1.0
CA B:CYS4381 4.1 61.3 1.0
O B:HOH4557 4.2 59.5 1.0
CA B:CYS4373 4.2 53.4 1.0
CA B:CYS4383 4.2 82.2 1.0
CA B:CYS4370 4.5 53.2 1.0
N B:SER4382 4.5 68.5 1.0
NZ B:LYS4377 4.6 72.8 1.0
C B:CYS4381 4.6 66.0 1.0
CB B:VAL4372 4.6 63.3 1.0
CE B:LYS4377 4.7 76.8 1.0
C B:VAL4372 4.8 56.0 1.0
C B:CYS4373 4.9 56.8 1.0
N B:GLY4374 5.0 53.5 1.0
CG1 B:VAL4372 5.0 61.1 1.0

Reference:

V.Kremling, D.Oberthuer, O.Yefanov, M.Galchenkova, P.Middendorf, S.Falke, Y.Fernandez Garcia, C.Ehrt, 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: Thu Oct 31 08:56:58 2024

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