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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: Sun Jul 13 02:04:25 2025

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