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Chlorine in PDB 8udf: Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7

Enzymatic activity of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7

All present enzymatic activity of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7, PDB code: 8udf was solved by F.Forouhar, H.Liu, A.Zack, S.Iketani, A.Williams, D.R.Vaz, D.L.Habashi, S.J.Resnick, A.Chavez, D.D.Ho, B.R.Stockwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.07 / 1.74
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 98.087, 81.861, 51.856, 90, 114.81, 90
R / Rfree (%) 16.5 / 19.4

Other elements in 8udf:

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7 also contains other interesting chemical elements:

Sodium (Na) 1 atom
Fluorine (F) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7 (pdb code 8udf). 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 3CL Protease with Inhibitor DEL_7, PDB code: 8udf:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8udf

Go back to Chlorine Binding Sites List in 8udf
Chlorine binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7


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 3CL Protease with Inhibitor DEL_7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl701

b:73.3
occ:1.00
 CL1 A:WB0701 0.0 73.3 1.0
C18 A:WB0701 1.7 59.1 1.0
C17 A:WB0701 2.7 41.9 1.0
C19 A:WB0701 2.8 54.0 1.0
ND1 A:HIS347 3.3 37.5 1.0
CB A:ASP493 3.4 26.6 1.0
CA A:ASP493 3.5 32.1 1.0
C A:ASP493 3.5 36.2 1.0
CE A:MET355 3.6 66.9 1.0
CG A:HIS347 3.6 34.6 1.0
N A:ARG494 3.8 31.6 1.0
CE1 A:HIS347 3.8 35.0 1.0
O A:ASP493 3.8 35.4 1.0
CB A:HIS347 3.9 30.8 1.0
C16 A:WB0701 4.0 42.8 1.0
C20 A:WB0701 4.1 50.2 1.0
O A:HIS470 4.3 31.4 1.0
CD2 A:HIS347 4.3 36.2 1.0
CA A:ARG494 4.4 34.2 1.0
NE2 A:HIS347 4.4 35.6 1.0
O A:HOH900 4.5 27.1 1.0
C15 A:WB0701 4.5 42.3 1.0
SD A:MET355 4.6 63.7 1.0
OH A:TYR360 4.6 35.3 1.0
C A:ARG494 4.6 37.0 1.0
CG A:ASP493 4.8 29.2 1.0
CB A:MET471 4.8 27.8 1.0
O A:ARG494 4.8 35.4 1.0
SD A:MET471 4.8 57.5 1.0
N A:ASP493 4.9 28.2 1.0

Chlorine binding site 2 out of 4 in 8udf

Go back to Chlorine Binding Sites List in 8udf
Chlorine binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7


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 3CL Protease with Inhibitor DEL_7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl701

b:48.8
occ:1.00
 CL2 A:WB0701 0.0 48.8 1.0
C16 A:WB0701 1.7 42.8 1.0
C17 A:WB0701 2.7 41.9 1.0
C15 A:WB0701 2.7 42.3 1.0
C14 A:WB0701 3.1 40.1 1.0
CE A:MET471 3.3 49.7 1.0
C10 A:WB0701 3.4 47.0 1.0
C11 A:WB0701 3.5 49.1 1.0
C13 A:WB0701 3.6 37.7 1.0
O A:HOH910 3.9 42.5 1.0
C18 A:WB0701 4.0 59.1 1.0
O A:ARG494 4.0 35.4 1.0
CA A:GLN495 4.0 40.0 1.0
C20 A:WB0701 4.0 50.2 1.0
O A:GLU472 4.1 33.1 1.0
CB A:MET471 4.1 27.8 1.0
N2 A:WB0701 4.2 37.9 1.0
C12 A:WB0701 4.3 42.6 1.0
O A:THR496 4.4 43.1 1.0
C9 A:WB0701 4.5 55.2 1.0
SD A:MET471 4.5 57.5 1.0
CG A:GLN495 4.5 49.1 1.0
C19 A:WB0701 4.5 54.0 1.0
N A:THR496 4.6 39.5 1.0
CB A:GLN495 4.6 44.0 1.0
C A:ARG494 4.7 37.0 1.0
C6 A:WB0701 4.7 47.0 1.0
C A:GLN495 4.7 41.2 1.0
N A:GLN495 4.7 35.5 1.0
N3 A:WB0701 4.8 37.2 1.0
CG A:MET471 4.9 35.9 1.0

Chlorine binding site 3 out of 4 in 8udf

Go back to Chlorine Binding Sites List in 8udf
Chlorine binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7


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 3CL Protease with Inhibitor DEL_7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl702

b:69.9
occ:1.00
 O A:HOH1005 2.2 36.9 0.5
O A:HOH887 3.3 49.9 1.0
N A:LYS311 3.4 26.2 1.0
NE A:ARG310 3.5 40.9 1.0
O A:HOH811 3.7 44.2 1.0
CB A:LYS311 4.0 35.9 1.0
CA A:ARG310 4.1 27.9 1.0
NH2 A:ARG310 4.2 50.9 1.0
C A:ARG310 4.3 24.2 1.0
CZ A:ARG310 4.3 51.3 1.0
CA A:LYS311 4.3 25.8 1.0
CD A:ARG310 4.3 42.4 1.0
CB A:ARG310 4.6 34.3 1.0
O A:PHE309 4.8 31.8 1.0
CG A:LYS311 5.0 41.0 1.0

Chlorine binding site 4 out of 4 in 8udf

Go back to Chlorine Binding Sites List in 8udf
Chlorine binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7


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 3CL Protease with Inhibitor DEL_7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl703

b:62.4
occ:1.00
 N A:PHE409 3.3 23.1 1.0
CA A:LYS408 4.0 28.7 1.0
CB A:PHE409 4.1 21.8 1.0
O A:PHE409 4.1 29.0 1.0
C A:LYS408 4.1 23.2 1.0
CA A:PHE409 4.2 20.5 1.0
CB A:LYS408 4.4 34.0 1.0
CG A:PHE409 4.5 25.8 1.0
C A:PHE409 4.6 23.3 1.0
O A:HOH974 4.7 59.2 1.0
O A:HOH927 4.7 62.8 1.0
O A:HOH955 4.7 58.9 1.0
CD2 A:PHE409 4.9 31.3 1.0
CG A:LYS408 5.0 41.9 1.0

Reference:

H.Liu, A.Zack, F.Forouhar, S.Iketani, A.Williams, D.R.Vaz, D.L.Habashi, K.Choi, S.J.Resnick, A.Chavez, D.D.Ho, B.R.Stockwell. Development of Small Molecule Non-Covalent Coronavirus 3CL Protease Inhibitors From Dna-Encoded Chemical Library Screening To Be Published.
Page generated: Sat Feb 8 17:20:35 2025

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