Chlorine in PDB 7rm2: Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Mcule-Csr-494190-S1

Enzymatic activity of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Mcule-Csr-494190-S1

All present enzymatic activity of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Mcule-Csr-494190-S1:
3.4.22.69;

Protein crystallography data

The structure of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Mcule-Csr-494190-S1, PDB code: 7rm2 was solved by A.Kovalevsky, D.W.Kneller, L.Coates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.09 / 2.00
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 52.403, 81.889, 91.706, 90, 95.37, 90
R / Rfree (%) 16.6 / 19

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Mcule-Csr-494190-S1 (pdb code 7rm2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Mcule-Csr-494190-S1, PDB code: 7rm2:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7rm2

Go back to Chlorine Binding Sites List in 7rm2
Chlorine binding site 1 out of 2 in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Mcule-Csr-494190-S1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Mcule-Csr-494190-S1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:38.6
occ:1.00
CL24 A:5YJ401 0.0 38.6 1.0
C14 A:5YJ401 1.8 37.2 1.0
C15 A:5YJ401 2.7 35.1 1.0
C13 A:5YJ401 2.7 36.4 1.0
C23 A:5YJ401 3.0 37.4 1.0
SG A:CYS44 3.4 51.9 0.3
CB A:CYS44 3.5 41.7 0.7
CG A:MET49 3.7 79.0 1.0
CB A:CYS44 3.7 41.6 0.3
O A:HOH562 3.9 36.2 1.0
O A:HIS41 3.9 31.7 1.0
C12 A:5YJ401 4.0 36.9 1.0
C10 A:5YJ401 4.0 34.9 1.0
CB A:HIS41 4.2 27.3 1.0
SG A:CYS44 4.4 39.6 0.7
CB A:MET49 4.4 68.4 1.0
SD A:MET49 4.4 92.7 1.0
C A:CYS44 4.5 47.2 0.3
C11 A:5YJ401 4.5 35.1 1.0
O A:CYS44 4.6 46.6 0.3
CA A:MET49 4.6 66.0 1.0
CG A:HIS41 4.6 31.1 1.0
CA A:CYS44 4.7 42.6 0.3
O A:THR45 4.7 70.2 1.0
CA A:CYS44 4.7 42.3 0.7
ND1 A:HIS41 4.7 29.6 1.0
C A:CYS44 4.7 47.2 0.7
O A:CYS44 4.8 46.8 0.7
CG A:GLN189 4.8 57.9 1.0
C A:HIS41 4.8 29.5 1.0
CA A:HIS41 5.0 29.0 1.0

Chlorine binding site 2 out of 2 in 7rm2

Go back to Chlorine Binding Sites List in 7rm2
Chlorine binding site 2 out of 2 in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Mcule-Csr-494190-S1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Mcule-Csr-494190-S1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:34.5
occ:1.00
CL25 A:5YJ401 0.0 34.5 1.0
C12 A:5YJ401 1.8 36.9 1.0
C11 A:5YJ401 2.7 35.1 1.0
C13 A:5YJ401 2.7 36.4 1.0
C23 A:5YJ401 3.1 37.4 1.0
C A:ASP187 3.5 32.4 1.0
N A:ARG188 3.5 31.6 1.0
CA A:ASP187 3.6 26.6 1.0
C A:ARG188 3.9 49.1 1.0
SD A:MET165 3.9 32.8 1.0
O A:ASP187 3.9 30.9 1.0
C14 A:5YJ401 4.0 37.2 1.0
CB A:ASP187 4.0 23.9 1.0
O A:ARG188 4.0 46.2 1.0
C10 A:5YJ401 4.0 34.9 1.0
CA A:ARG188 4.1 43.3 1.0
N A:GLN189 4.2 58.9 1.0
CD2 A:HIS41 4.2 28.1 1.0
NE2 A:GLN189 4.3 59.7 1.0
CG A:GLN189 4.3 57.9 1.0
CB A:MET165 4.4 22.1 1.0
C15 A:5YJ401 4.5 35.1 1.0
CA A:GLN189 4.7 59.5 1.0
CG A:HIS41 4.7 31.1 1.0
CD A:GLN189 4.7 68.7 1.0
O A:VAL186 4.7 23.9 1.0
CG A:MET165 4.9 22.3 1.0
N A:ASP187 4.9 25.9 1.0
NE2 A:HIS41 4.9 28.4 1.0
CB A:HIS41 4.9 27.3 1.0

Reference:

D.W.Kneller, H.Li, S.Galanie, G.Phillips, A.Labbe, K.L.Weiss, Q.Zhang, M.A.Arnould, A.Clyde, H.Ma, A.Ramanathan, C.B.Jonsson, M.S.Head, L.Coates, J.M.Louis, P.V.Bonnesen, A.Kovalevsky. Structural, Electronic, and Electrostatic Determinants For Inhibitor Binding to Subsites S1 and S2 in Sars-Cov-2 Main Protease. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34705466
DOI: 10.1021/ACS.JMEDCHEM.1C01475
Page generated: Thu Nov 25 08:55:45 2021

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