Chlorine in PDB 7grg: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3, PDB code: 7grg was solved by C.-Y.Huang, A.Metz, M.Sharpe, A.Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.81 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.78, 100.18, 104.17, 90, 90, 90
R / Rfree (%) 20.2 / 23.6

Other elements in 7grg:

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3 (pdb code 7grg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3, PDB code: 7grg:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 7grg

Go back to Chlorine Binding Sites List in 7grg
Chlorine binding site 1 out of 5 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1501

b:41.8
occ:0.77
 CL04 A:Y2C1501 0.0 41.8 0.8
C03 A:Y2C1501 1.8 26.3 0.8
C05 A:Y2C1501 2.7 23.0 0.8
C02 A:Y2C1501 2.8 32.0 0.8
N01 A:Y2C1501 3.0 38.5 0.8
O B:HOH883 3.1 37.0 1.0
O A:HOH1626 3.5 34.7 1.0
OE1 A:GLU166 3.6 24.4 1.0
N B:SER1 3.7 20.9 1.0
O A:PHE140 3.8 22.7 1.0
CD A:GLU166 3.9 26.4 1.0
N06 A:Y2C1501 4.0 17.6 0.8
C08 A:Y2C1501 4.0 33.6 0.8
OE2 A:GLU166 4.0 27.8 1.0
N A:ASN142 4.0 23.6 0.5
N A:ASN142 4.1 23.7 0.5
C A:LEU141 4.2 24.4 1.0
CA A:LEU141 4.2 21.6 1.0
O A:HOH1856 4.3 43.8 1.0
ND2 A:ASN142 4.4 37.4 0.5
OD1 A:ASN142 4.4 35.7 0.5
CB A:GLU166 4.5 20.4 1.0
C07 A:Y2C1501 4.5 29.4 0.8
CG A:ASN142 4.5 29.5 0.5
C A:PHE140 4.7 20.8 1.0
CG A:GLU166 4.8 20.7 1.0
CA A:ASN142 4.8 26.2 0.5
O A:LEU141 4.8 19.5 1.0
CA A:ASN142 4.9 26.2 0.5
N A:LEU141 4.9 17.9 1.0
CA B:SER1 5.0 28.1 1.0

Chlorine binding site 2 out of 5 in 7grg

Go back to Chlorine Binding Sites List in 7grg
Chlorine binding site 2 out of 5 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1501

b:53.1
occ:0.77
 CL09 A:Y2C1501 0.0 53.1 0.8
C08 A:Y2C1501 1.8 33.6 0.8
C02 A:Y2C1501 2.8 32.0 0.8
C07 A:Y2C1501 2.8 29.4 0.8
N01 A:Y2C1501 3.0 38.5 0.8
O A:HOH1808 3.2 30.4 1.0
SG A:CYS145 3.4 21.2 1.0
OD1 A:ASN142 3.5 28.9 0.5
O A:HOH1825 3.6 20.8 1.0
O A:HOH1789 3.8 25.8 1.0
N06 A:Y2C1501 4.0 17.6 0.8
C03 A:Y2C1501 4.0 26.3 0.8
OD1 A:ASN142 4.1 35.7 0.5
O A:HOH1879 4.3 35.4 1.0
CA A:ASN142 4.5 26.2 0.5
C05 A:Y2C1501 4.5 23.0 0.8
CA A:ASN142 4.6 26.2 0.5
CG A:ASN142 4.6 32.4 0.5
N A:GLY143 4.7 20.4 1.0
O A:HOH1856 4.9 43.8 1.0
O A:HIS164 5.0 18.3 1.0
CG A:ASN142 5.0 29.5 0.5

Chlorine binding site 3 out of 5 in 7grg

Go back to Chlorine Binding Sites List in 7grg
Chlorine binding site 3 out of 5 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl602

b:45.3
occ:0.67
 CL04 B:Y2C602 0.0 45.3 0.7
C03 B:Y2C602 1.8 27.1 0.7
C05 B:Y2C602 2.7 30.3 0.7
C02 B:Y2C602 2.8 42.2 0.7
O B:HOH737 3.0 39.5 1.0
N01 B:Y2C602 3.1 40.9 0.7
OE1 B:GLU166 3.5 23.7 1.0
O B:PHE140 3.6 24.9 1.0
O A:HOH1758 3.6 37.9 1.0
N A:SER1 3.6 21.5 1.0
OE2 B:GLU166 3.7 25.4 1.0
CD B:GLU166 3.8 30.4 1.0
CA B:LEU141 3.9 27.2 1.0
N06 B:Y2C602 4.0 16.8 0.7
N B:ASN142 4.0 29.1 1.0
C B:LEU141 4.0 35.3 1.0
C08 B:Y2C602 4.1 35.8 0.7
C B:PHE140 4.4 23.5 1.0
C07 B:Y2C602 4.5 30.0 0.7
N B:LEU141 4.6 27.6 1.0
CB B:GLU166 4.7 19.4 1.0
O B:LEU141 4.7 24.7 1.0
CA B:ASN142 4.8 29.9 1.0
CG B:GLU166 4.8 22.5 1.0
CA A:SER1 5.0 22.9 1.0
CD2 B:LEU141 5.0 27.2 1.0

Chlorine binding site 4 out of 5 in 7grg

Go back to Chlorine Binding Sites List in 7grg
Chlorine binding site 4 out of 5 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl602

b:57.4
occ:0.67
 CL09 B:Y2C602 0.0 57.4 0.7
C08 B:Y2C602 1.8 35.8 0.7
O B:HOH875 2.6 38.2 1.0
C07 B:Y2C602 2.8 30.0 0.7
C02 B:Y2C602 2.8 42.2 0.7
N01 B:Y2C602 3.0 40.9 0.7
O B:HOH879 3.4 27.0 1.0
SG B:CYS145 3.8 23.4 1.0
ND2 B:ASN142 3.8 50.6 1.0
N06 B:Y2C602 4.0 16.8 0.7
C03 B:Y2C602 4.1 27.1 0.7
O B:HOH870 4.1 25.9 1.0
C05 B:Y2C602 4.5 30.3 0.7
CA B:ASN142 4.7 29.9 1.0
CG B:ASN142 4.9 45.8 1.0
O B:HIS164 4.9 17.2 1.0

Chlorine binding site 5 out of 5 in 7grg

Go back to Chlorine Binding Sites List in 7grg
Chlorine binding site 5 out of 5 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl605

b:18.0
occ:1.00
 N B:THR224 3.3 23.1 1.0
CA B:PHE223 3.7 18.5 1.0
O B:THR224 3.8 25.8 1.0
CB B:PHE223 3.9 17.1 1.0
CD1 B:PHE223 3.9 18.8 1.0
C B:PHE223 4.0 26.0 1.0
CG2 B:THR224 4.2 26.4 1.0
CA B:THR224 4.4 22.1 1.0
CG B:PHE223 4.4 19.6 1.0
C B:THR224 4.4 20.3 1.0
CB B:THR224 4.8 27.6 1.0
O B:ARG222 4.8 20.8 1.0
N B:PHE223 4.9 20.6 1.0
CE1 B:PHE223 5.0 15.8 1.0

Reference:

C.Y.Huang, A.Metz, R.Lange, N.Artico, C.Potot, J.Hazemann, M.Muller, M.Dos Santos, A.Chambovey, D.Ritz, D.Eris, S.Meyer, G.Bourquin, M.Sharpe, A.Mac Sweeney. Fragment-Based Screening Targeting An Open Form of the Sars-Cov-2 Main Protease Binding Pocket. Acta Crystallogr D Struct V. 80 123 2024BIOL.
ISSN: ISSN 2059-7983
PubMed: 38289714
DOI: 10.1107/S2059798324000329
Page generated: Mon Jul 29 22:10:54 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy