Chlorine in PDB 7gry: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-21

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-21

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-21:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-21, PDB code: 7gry 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) 56.64 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.68, 99.16, 103.5, 90, 90, 90
R / Rfree (%) 18 / 21.7

Other elements in 7gry:

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-21 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-21 (pdb code 7gry). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-21, PDB code: 7gry:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7gry

Go back to Chlorine Binding Sites List in 7gry
Chlorine binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-21


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-21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:18.0
occ:1.00
 N A:GLN107 3.2 15.1 1.0
NE2 A:GLN110 3.3 16.2 1.0
O A:HOH762 3.3 35.7 1.0
CA A:ILE106 3.7 14.3 1.0
CG A:GLN110 3.8 10.3 1.0
CB A:GLN110 3.9 12.6 1.0
CB A:ILE106 3.9 15.3 1.0
CB A:GLN107 3.9 23.8 1.0
C A:ILE106 4.0 15.6 1.0
CD A:GLN110 4.0 15.8 1.0
CA A:GLN107 4.1 15.1 1.0
CG A:GLN107 4.2 21.9 1.0
CG2 A:ILE106 4.2 16.3 1.0
O A:HOH533 4.4 31.9 1.0
O A:GLN107 4.5 14.5 1.0
C A:GLN107 4.8 15.8 1.0
O A:ARG105 4.8 20.8 1.0
O A:HOH756 4.8 28.7 1.0

Chlorine binding site 2 out of 4 in 7gry

Go back to Chlorine Binding Sites List in 7gry
Chlorine binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-21


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-21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:34.5
occ:1.00
 N A:ALA285 3.2 20.0 1.0
OG A:SER284 3.3 42.4 1.0
N B:ALA285 3.3 20.3 1.0
OG B:SER284 3.5 29.6 1.0
N A:LEU286 3.7 22.6 1.0
N B:LEU286 3.8 20.8 1.0
CA A:ALA285 3.9 20.6 1.0
CB A:ALA285 4.0 22.9 1.0
CG B:LEU286 4.0 28.5 1.0
CA B:SER284 4.0 21.4 1.0
CA A:SER284 4.0 18.6 1.0
C A:ALA285 4.1 18.6 1.0
C A:SER284 4.1 19.4 1.0
CA B:ALA285 4.1 22.1 1.0
C B:SER284 4.1 21.9 1.0
CG A:LEU286 4.1 27.6 1.0
CB B:LEU286 4.2 25.3 1.0
CB A:SER284 4.2 23.6 1.0
CB B:SER284 4.2 23.3 1.0
C B:ALA285 4.3 25.2 1.0
CB B:ALA285 4.3 28.9 1.0
CD1 B:LEU286 4.3 26.9 1.0
CB A:LEU286 4.4 19.2 1.0
CA B:LEU286 4.6 17.2 1.0
CD1 A:LEU286 4.6 28.4 1.0
CA A:LEU286 4.7 20.2 1.0
O A:ALA285 5.0 21.4 1.0

Chlorine binding site 3 out of 4 in 7gry

Go back to Chlorine Binding Sites List in 7gry
Chlorine binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-21


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-21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:103.2
occ:1.00
 CL07 B:XZO405 0.0 103.2 1.0
C06 B:XZO405 1.8 76.5 1.0
C01 B:XZO405 2.7 68.4 1.0
C05 B:XZO405 2.8 66.1 1.0
OE1 B:GLN189 3.1 60.2 0.9
C02 B:XZO405 4.0 68.9 1.0
C04 B:XZO405 4.0 75.6 1.0
CD B:GLN189 4.1 64.0 0.9
N B:ALA191 4.2 39.2 0.3
NE2 B:GLN189 4.4 69.4 0.9
C B:THR190 4.5 41.8 0.6
C03 B:XZO405 4.5 71.6 1.0
CA B:ALA191 4.7 36.6 0.3
N B:THR190 4.8 43.9 0.4
CA B:THR190 4.8 41.2 0.6
CA B:THR190 4.8 41.2 0.4
C B:THR190 4.9 41.1 0.4
CB B:ALA191 4.9 35.5 0.3
O B:THR190 4.9 42.5 0.4

Chlorine binding site 4 out of 4 in 7gry

Go back to Chlorine Binding Sites List in 7gry
Chlorine binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-21


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-21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:82.8
occ:1.00
 CL08 B:XZO405 0.0 82.8 1.0
C04 B:XZO405 1.8 75.6 1.0
C05 B:XZO405 2.7 66.1 1.0
C03 B:XZO405 2.8 71.6 1.0
CB B:PRO168 3.7 24.9 1.0
CA B:PRO168 3.8 22.0 1.0
CG B:PRO168 3.9 37.0 1.0
C06 B:XZO405 4.0 76.5 1.0
C02 B:XZO405 4.0 68.9 1.0
N B:PRO168 4.5 26.9 1.0
C01 B:XZO405 4.5 68.4 1.0
O B:HOH553 4.6 39.9 1.0
CD B:PRO168 4.8 24.8 1.0
O B:PRO168 4.9 30.2 1.0
C B:PRO168 4.9 22.8 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 22:12:20 2024

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