Magnesium in PDB 8s8x: Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin and M7GPPPA-Rna (CAP0-Rna)

Enzymatic activity of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin and M7GPPPA-Rna (CAP0-Rna)

All present enzymatic activity of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin and M7GPPPA-Rna (CAP0-Rna):
2.1.1.57;

Protein crystallography data

The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin and M7GPPPA-Rna (CAP0-Rna), PDB code: 8s8x was solved by V.Kremling, J.Sprenger, D.Oberthuer, T.E.S.Scheer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.06 / 1.99
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.11, 168.11, 52.11, 90, 90, 120
R / Rfree (%) 18.9 / 22.3

Other elements in 8s8x:

The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin and M7GPPPA-Rna (CAP0-Rna) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin and M7GPPPA-Rna (CAP0-Rna) (pdb code 8s8x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin and M7GPPPA-Rna (CAP0-Rna), PDB code: 8s8x:

Magnesium binding site 1 out of 1 in 8s8x

Go back to Magnesium Binding Sites List in 8s8x
Magnesium binding site 1 out of 1 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin and M7GPPPA-Rna (CAP0-Rna)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin and M7GPPPA-Rna (CAP0-Rna) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7203

b:54.6
occ:1.00
 O A:HOH7383 2.2 52.7 1.0
O C:HOH204 2.3 44.8 1.0
OD1 A:ASN6996 2.4 36.4 1.0
O C:HOH201 2.5 40.0 1.0
O A:HOH7355 2.6 50.0 1.0
O C:HOH208 2.9 61.4 1.0
CG A:ASN6996 3.4 35.2 1.0
HD22 A:ASN6996 3.5 39.8 1.0
HB2 A:SER6999 3.7 49.7 1.0
ND2 A:ASN6996 3.9 33.1 1.0
OP2 C:U2 4.0 43.1 1.0
O A:HOH7351 4.1 47.8 1.0
OP1 C:U2 4.2 44.0 1.0
HA A:ASN6996 4.2 50.7 1.0
O C:HOH203 4.4 46.6 1.0
OG A:SER6998 4.5 44.1 1.0
HB3 A:SER6999 4.5 49.7 1.0
CB A:SER6999 4.5 41.4 1.0
HG A:SER6998 4.6 53.0 1.0
O31 C:GTA1 4.6 44.6 1.0
HE3 A:MET6840 4.6 69.3 1.0
O A:ASP6830 4.7 54.1 1.0
P C:U2 4.7 45.4 1.0
HD21 A:ASN6996 4.7 39.8 1.0
HA2 A:GLY6829 4.7 64.4 1.0
CB A:ASN6996 4.7 39.7 1.0
HG2 A:MET6840 4.8 58.1 1.0
CA A:ASN6996 5.0 42.2 1.0
HG A:SER6831 5.0 78.0 1.0
HG A:SER6999 5.0 50.4 1.0

Reference:

V.Kremling, S.Falke, Y.Fernandez-Garcia, C.Ehrt, A.Kiene, B.Klopprogge, T.E.S.Scheer, F.Barthels, P.Middendorf, S.Kuehn, S.Guenther, M.Rarey, H.N.Chapman, D.Oberthuer, J.Sprenger. Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Natural and Drug-Like Purine Analogs For Guiding Structure-Based Drug Development To Be Published.
Page generated: Fri Oct 4 19:15:15 2024

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