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Chlorine in PDB 8bsd: Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Tubercidin

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

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

Protein crystallography data

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

Resolution Low / High (Å) 37.54 / 1.95
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.47, 167.47, 51.51, 90, 90, 120
R / Rfree (%) 18 / 20.8

Other elements in 8bsd:

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

Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Tubercidin (pdb code 8bsd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Tubercidin, PDB code: 8bsd:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8bsd

Go back to Chlorine Binding Sites List in 8bsd
Chlorine binding site 1 out of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Tubercidin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Tubercidin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl7229

b:61.3
occ:1.00
H A:ASP7018 2.6 41.8 1.0
HE2 A:MET7022 3.0 45.6 1.0
HA A:ILE7017 3.1 52.6 1.0
HG23 A:ILE7017 3.2 46.8 1.0
N A:ASP7018 3.4 34.9 1.0
HB3 A:ASP7018 3.4 40.5 1.0
CE A:MET7022 3.8 38.0 1.0
O A:HOH7480 3.9 58.7 1.0
HE1 A:MET7022 3.9 45.6 1.0
O A:ASP7018 3.9 35.4 1.0
CA A:ILE7017 3.9 43.9 1.0
HB A:VAL7021 4.0 44.7 1.0
HG12 A:ILE7017 4.0 45.3 1.0
CG2 A:ILE7017 4.1 39.0 1.0
CB A:ASP7018 4.1 33.8 1.0
HB2 A:MET7022 4.1 38.2 1.0
HG12 A:VAL7021 4.2 43.7 1.0
C A:ILE7017 4.2 35.2 1.0
CA A:ASP7018 4.2 38.8 1.0
HE3 A:MET7022 4.2 45.6 1.0
HB2 A:ASP7018 4.3 40.5 1.0
O A:GLN7016 4.5 53.6 1.0
C A:ASP7018 4.5 37.4 1.0
CB A:ILE7017 4.5 39.7 1.0
NH1 A:ARG6817 4.6 71.5 1.0
HG22 A:ILE7017 4.6 46.8 1.0
HG11 A:VAL7021 4.6 43.7 1.0
HG21 A:ILE7017 4.7 46.8 1.0
HH11 A:ARG6817 4.7 85.8 1.0
CZ A:ARG6817 4.7 90.3 1.0
CG1 A:VAL7021 4.7 36.4 1.0
HD3 A:ARG6817 4.7 94.1 1.0
CG1 A:ILE7017 4.7 37.8 1.0
HH12 A:ARG6817 4.7 85.8 1.0
CB A:VAL7021 4.8 37.2 1.0
H A:MET7022 4.8 38.8 1.0
NE A:ARG6817 4.9 92.6 1.0
HD22 A:ASN7025 4.9 39.2 1.0

Chlorine binding site 2 out of 2 in 8bsd

Go back to Chlorine Binding Sites List in 8bsd
Chlorine binding site 2 out of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Tubercidin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Tubercidin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl7230

b:67.6
occ:1.00
H A:ASN6941 2.5 50.1 1.0
HB3 A:ASN6941 3.0 50.6 1.0
O A:HOH7485 3.1 61.9 1.0
HG2 A:GLU6940 3.3 88.7 1.0
N A:ASN6941 3.3 41.8 1.0
HG3 A:GLU6940 3.4 88.7 1.0
HA A:GLU6940 3.4 52.2 1.0
HD23 A:LEU6820 3.5 52.0 1.0
CB A:ASN6941 3.8 42.2 1.0
CG A:GLU6940 3.8 73.9 1.0
HB2 A:ASN6941 3.9 50.6 1.0
CA A:ASN6941 4.1 46.1 1.0
HD21 A:LEU6820 4.1 52.0 1.0
CA A:GLU6940 4.2 43.5 1.0
H22 A:EDO7205 4.2 76.2 1.0
HG A:LEU6820 4.2 50.6 1.0
CD2 A:LEU6820 4.2 43.4 1.0
C A:GLU6940 4.2 49.4 1.0
O A:ASN6941 4.4 40.9 1.0
C A:ASN6941 4.6 36.8 1.0
CB A:GLU6940 4.6 45.7 1.0
HB3 A:LEU6820 4.7 51.0 1.0
CG A:LEU6820 4.7 42.2 1.0
O A:HOH7369 4.7 57.1 1.0
O2 A:EDO7205 4.7 51.7 1.0
HO2 A:EDO7205 4.8 62.0 1.0
O A:HOH7350 4.9 34.4 1.0
H12 A:EDO7205 4.9 68.7 1.0
C2 A:EDO7205 4.9 63.5 1.0
HA A:ASN6941 4.9 55.3 1.0
HD21 A:ASN6941 4.9 39.9 1.0
CD A:GLU6940 5.0 87.6 1.0

Reference:

V.Kremling, D.Oberthuer, J.Sprenger. Crystal Structures of Tubercidin Bound to the Active Site of the Sars-Cov-2 Methyltransferase NSP10-16 To Be Published.
Page generated: Sun Jul 13 09:43:30 2025

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