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Chlorine in PDB 7gs6: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-29

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-29

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-29:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-29, PDB code: 7gs6 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) 56.16 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.99, 99.62, 104.44, 90, 90, 90
R / Rfree (%) 19 / 22.8

Other elements in 7gs6:

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-29 also contains other interesting chemical elements:

Magnesium (Mg) 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-29 (pdb code 7gs6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-29, PDB code: 7gs6:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 7gs6

Go back to Chlorine Binding Sites List in 7gs6
Chlorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-29


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-29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:72.6
occ:1.00
 CL A:XXN602 0.0 72.6 1.0
C3 A:XXN602 1.8 61.4 1.0
C4 A:XXN602 2.8 55.1 1.0
C2 A:XXN602 2.8 60.3 1.0
N A:XXN602 3.2 50.7 1.0
C5 A:XXN602 4.0 52.6 1.0
C1 A:XXN602 4.1 56.2 1.0
ND2 A:ASN142 4.2 62.8 1.0
O A:HOH956 4.3 44.9 1.0
O A:HOH909 4.5 37.5 1.0
C7 A:XXN602 4.5 51.6 1.0
C6 A:XXN602 4.5 51.4 1.0

Chlorine binding site 2 out of 6 in 7gs6

Go back to Chlorine Binding Sites List in 7gs6
Chlorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-29


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-29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:51.8
occ:1.00
 CL1 A:XXN602 0.0 51.8 1.0
C6 A:XXN602 1.8 51.4 1.0
C5 A:XXN602 2.7 52.6 1.0
O A:HOH819 2.8 39.5 1.0
C1 A:XXN602 2.8 56.2 1.0
O A:LEU141 3.0 22.4 1.0
OG A:SER144 3.0 25.8 1.0
C A:XXN602 3.4 46.3 1.0
O A:XXN602 3.6 32.6 1.0
N A:SER144 3.7 18.3 1.0
C A:LEU141 3.7 27.1 1.0
SG A:CYS145 3.7 27.7 1.0
N A:CYS145 3.8 18.0 1.0
CA A:ASN142 3.9 34.5 1.0
N A:GLY143 4.0 25.5 1.0
C4 A:XXN602 4.0 55.1 1.0
C2 A:XXN602 4.0 60.3 1.0
NE2 A:HIS163 4.1 17.5 1.0
N A:ASN142 4.1 32.3 1.0
CB A:SER144 4.1 24.1 1.0
CD2 A:HIS163 4.2 16.4 1.0
CA A:SER144 4.2 18.7 1.0
C A:SER144 4.3 16.8 1.0
C A:ASN142 4.3 34.8 1.0
CB A:PHE140 4.5 22.3 1.0
C3 A:XXN602 4.5 61.4 1.0
N A:LEU141 4.7 26.0 1.0
C A:GLY143 4.7 19.3 1.0
CA A:CYS145 4.7 15.0 1.0
C A:PHE140 4.7 32.9 1.0
CA A:LEU141 4.7 25.1 1.0
C7 A:XXN602 4.8 51.6 1.0
O A:PHE140 4.8 33.2 1.0
CB A:CYS145 4.9 18.3 1.0
CA A:GLY143 4.9 22.6 1.0

Chlorine binding site 3 out of 6 in 7gs6

Go back to Chlorine Binding Sites List in 7gs6
Chlorine binding site 3 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-29


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-29 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:85.4
occ:1.00
 CL B:XXN404 0.0 85.4 1.0
C3 B:XXN404 1.8 77.0 1.0
C2 B:XXN404 2.7 62.8 1.0
C4 B:XXN404 2.8 78.8 1.0
N B:XXN404 3.0 59.9 1.0
C1 B:XXN404 4.0 65.9 1.0
C5 B:XXN404 4.1 70.0 1.0
O B:DMS403 4.3 59.6 1.0
C7 B:XXN404 4.4 64.1 1.0
O B:HOH631 4.5 35.5 1.0
C6 B:XXN404 4.6 71.5 1.0
O B:HOH603 4.8 53.6 1.0
C B:XXN404 4.9 46.3 1.0

Chlorine binding site 4 out of 6 in 7gs6

Go back to Chlorine Binding Sites List in 7gs6
Chlorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-29


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-29 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:56.4
occ:1.00
 CL1 B:XXN404 0.0 56.4 1.0
C6 B:XXN404 1.8 71.5 1.0
C5 B:XXN404 2.7 70.0 1.0
C1 B:XXN404 2.8 65.9 1.0
OE2 B:GLU166 3.0 65.6 1.0
N B:GLY143 3.1 40.5 1.0
C B:XXN404 3.5 46.3 1.0
N B:SER144 3.6 29.1 1.0
O B:XXN404 3.6 51.2 1.0
CG B:GLU166 3.7 42.1 1.0
CA B:ASN142 3.8 54.8 1.0
CD B:GLU166 3.8 57.2 1.0
OG B:SER144 3.8 53.5 1.0
C B:ASN142 3.9 49.7 1.0
CA B:GLY143 3.9 44.8 1.0
CB B:ASN142 3.9 62.9 1.0
SG B:CYS145 4.0 32.8 1.0
NE2 B:HIS163 4.0 29.9 1.0
C4 B:XXN404 4.0 78.8 1.0
C2 B:XXN404 4.1 62.8 1.0
N B:CYS145 4.1 23.6 1.0
C B:GLY143 4.2 25.1 1.0
CA B:SER144 4.5 27.7 1.0
C3 B:XXN404 4.6 77.0 1.0
CD2 B:HIS163 4.6 34.4 1.0
C B:SER144 4.7 19.9 1.0
C7 B:XXN404 4.8 64.1 1.0
CB B:SER144 4.8 28.8 1.0
ND2 B:ASN142 4.8 66.5 1.0
O B:HOH603 4.9 53.6 1.0
CG B:ASN142 4.9 67.2 1.0

Chlorine binding site 5 out of 6 in 7gs6

Go back to Chlorine Binding Sites List in 7gs6
Chlorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-29


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-29 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:48.8
occ:1.00
 CL B:XXN405 0.0 48.8 1.0
C3 B:XXN405 1.8 38.1 1.0
C2 B:XXN405 2.7 40.5 1.0
C4 B:XXN405 2.8 35.5 1.0
O B:ASN51 2.9 71.8 1.0
N B:XXN405 3.2 39.9 1.0
N B:TYR54 3.4 37.0 1.0
C B:ASN53 3.4 49.5 1.0
CA B:TYR54 3.6 29.2 1.0
O B:ASN53 3.6 33.9 1.0
N B:ASN53 3.6 42.6 1.0
C B:ASN51 3.6 65.4 1.0
CB B:ASN51 3.6 75.9 1.0
OD1 B:ASP48 3.8 93.2 1.0
C1 B:XXN405 4.0 34.6 1.0
C5 B:XXN405 4.0 29.2 1.0
CA B:ASN53 4.1 47.8 1.0
C B:PRO52 4.2 58.1 1.0
CA B:ASN51 4.2 67.6 1.0
CB B:TYR54 4.3 27.9 1.0
CG B:ASN51 4.4 70.9 1.0
C7 B:XXN405 4.5 55.0 1.0
N B:PRO52 4.5 53.0 1.0
O B:ASP48 4.5 72.8 1.0
C6 B:XXN405 4.5 34.3 1.0
OD1 B:ASN51 4.6 47.5 1.0
O B:HOH577 4.6 36.6 1.0
CA B:PRO52 4.7 51.3 1.0
O B:PRO52 4.8 60.1 1.0
C B:TYR54 4.8 28.3 1.0
N B:ASN51 4.8 65.6 1.0
CG B:ASP48 4.9 87.8 1.0
C B:XXN405 5.0 53.0 1.0

Chlorine binding site 6 out of 6 in 7gs6

Go back to Chlorine Binding Sites List in 7gs6
Chlorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-29


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-29 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:36.7
occ:1.00
 CL1 B:XXN405 0.0 36.7 1.0
C6 B:XXN405 1.8 34.3 1.0
C1 B:XXN405 2.7 34.6 1.0
C5 B:XXN405 2.8 29.2 1.0
O B:ASP187 3.2 23.9 1.0
C B:XXN405 3.3 53.0 1.0
O B:XXN405 3.3 36.8 1.0
O B:HOH561 3.4 29.4 1.0
CG B:ASP187 3.5 24.5 1.0
C B:ASP187 3.5 27.5 1.0
OD1 B:ASP187 3.5 22.1 1.0
OD2 B:ASP187 3.6 18.4 1.0
SG B:CYS44 3.6 32.5 1.0
N B:ARG188 3.8 31.6 1.0
CA B:ARG188 3.9 28.6 1.0
C2 B:XXN405 4.0 40.5 1.0
CB B:HIS41 4.0 19.8 1.0
C4 B:XXN405 4.0 35.5 1.0
CB B:ASP187 4.1 19.9 1.0
CG B:ARG188 4.2 41.2 1.0
NE B:ARG40 4.3 21.1 1.0
CA B:ASP187 4.4 19.4 1.0
CA B:HIS41 4.4 16.8 1.0
C3 B:XXN405 4.5 38.1 1.0
NH2 B:ARG40 4.5 17.4 1.0
C7 B:XXN405 4.6 55.0 1.0
CB B:ARG188 4.6 35.8 1.0
CZ B:ARG40 4.7 20.8 1.0
CG B:ARG40 4.8 15.8 1.0
O B:HOH571 4.8 16.8 1.0
CD2 B:TYR54 4.9 23.3 1.0
N B:HIS41 4.9 13.9 1.0
N B:XXN405 4.9 39.9 1.0
CB B:CYS44 5.0 29.7 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 22:13:39 2024

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