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Chlorine in PDB 5ru0: Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000000388514

Enzymatic activity of Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000000388514

All present enzymatic activity of Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000000388514:
3.4.19.12;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000000388514, PDB code: 5ru0 was solved by G.J.Correy, I.D.Young, M.C.Thompson, J.S.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.66 / 1.00
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 88.685, 88.685, 39.515, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 16.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000000388514 (pdb code 5ru0). 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 NSP3 Macrodomain in Complex with ZINC000000388514, PDB code: 5ru0:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5ru0

Go back to Chlorine Binding Sites List in 5ru0
Chlorine binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000000388514


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 NSP3 Macrodomain in Complex with ZINC000000388514 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:32.5
occ:0.52
CL1 A:2CL201 0.0 32.5 0.5
C2 A:2CL201 1.8 32.5 0.5
H71 A:2CL201 2.6 37.5 0.5
C3 A:2CL201 2.7 32.6 0.5
C1 A:2CL201 2.7 32.2 0.5
H3 A:2CL201 2.8 39.1 0.5
C7 A:2CL201 3.0 31.3 0.5
O A:HOH448 3.1 15.0 1.0
HA3 A:GLY130 3.6 16.8 1.0
C8 A:2CL201 3.7 30.1 0.5
O A:HOH301 3.7 17.5 1.0
HG23 A:VAL49 3.7 17.8 1.0
H72 A:2CL201 3.9 37.5 0.5
HA2 A:GLY130 4.0 16.8 1.0
C4 A:2CL201 4.0 32.5 0.5
O2 A:2CL201 4.0 30.5 0.5
C6 A:2CL201 4.0 32.8 0.5
CA A:GLY130 4.3 14.0 1.0
O A:HOH507 4.5 61.4 1.0
HA2 A:GLY48 4.5 15.1 1.0
C5 A:2CL201 4.5 32.7 0.5
O1 A:2CL201 4.6 29.7 0.5
CG2 A:VAL49 4.6 14.8 1.0
H A:VAL49 4.7 13.3 1.0
HG22 A:VAL49 4.7 17.8 1.0
H4 A:2CL201 4.7 39.0 0.5
HB3 A:PHE156 4.8 32.4 1.0
O A:HOH459 4.8 12.1 1.0
H A:ILE131 4.8 16.5 1.0
O A:HOH396 4.9 0.2 1.0
HD1 A:PHE156 4.9 35.7 1.0
HG21 A:VAL49 5.0 17.8 1.0

Chlorine binding site 2 out of 4 in 5ru0

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Chlorine binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000000388514


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 NSP3 Macrodomain in Complex with ZINC000000388514 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:33.2
occ:0.52
CL2 A:2CL201 0.0 33.2 0.5
C6 A:2CL201 1.8 32.8 0.5
H72 A:2CL201 2.7 37.5 0.5
C5 A:2CL201 2.7 32.7 0.5
C1 A:2CL201 2.7 32.2 0.5
H5 A:2CL201 2.8 39.3 0.5
HD21 A:LEU160 2.8 23.1 1.0
HD23 A:LEU160 3.0 23.1 1.0
C7 A:2CL201 3.1 31.3 0.5
HD12 A:LEU126 3.1 18.4 1.0
HB2 A:LEU126 3.2 13.6 1.0
HB3 A:ALA129 3.3 24.6 1.0
CD2 A:LEU160 3.3 19.2 1.0
HB3 A:PRO136 3.3 19.5 1.0
HB1 A:ALA129 3.4 24.6 1.0
O A:HOH391 3.5 15.9 1.0
C8 A:2CL201 3.6 30.1 0.5
O A:HOH445 3.6 19.8 1.0
HD22 A:LEU160 3.7 23.1 1.0
O2 A:2CL201 3.8 30.5 0.5
CB A:ALA129 3.8 20.5 1.0
HG13 A:VAL155 3.8 19.2 1.0
H71 A:2CL201 4.0 37.5 0.5
CD1 A:LEU126 4.0 15.3 1.0
C4 A:2CL201 4.0 32.5 0.5
C2 A:2CL201 4.0 32.5 0.5
CB A:LEU126 4.1 11.3 1.0
HD13 A:LEU126 4.1 18.4 1.0
H A:GLY130 4.1 16.5 1.0
CB A:PRO136 4.1 16.3 1.0
HB2 A:PRO136 4.2 19.5 1.0
HB2 A:ALA129 4.2 24.6 1.0
HG22 A:VAL155 4.2 19.5 1.0
H A:LEU126 4.4 12.6 1.0
HB3 A:LEU126 4.4 13.6 1.0
HD11 A:LEU164 4.4 19.4 1.0
O1 A:2CL201 4.4 29.7 0.5
O A:HOH301 4.5 17.5 1.0
C3 A:2CL201 4.5 32.6 0.5
HG3 A:PRO136 4.5 21.6 1.0
CG A:LEU126 4.6 13.3 1.0
N A:GLY130 4.6 13.7 1.0
CG A:LEU160 4.7 19.2 1.0
CG1 A:VAL155 4.7 16.0 1.0
HG A:LEU160 4.7 23.0 1.0
HD11 A:LEU126 4.7 18.4 1.0
HG A:LEU126 4.7 16.0 1.0
H4 A:2CL201 4.7 39.0 0.5
HG11 A:VAL155 4.8 19.2 1.0
HA A:VAL155 4.8 18.8 1.0
O A:LEU126 4.9 11.8 1.0
CG A:PRO136 5.0 18.0 1.0

Chlorine binding site 3 out of 4 in 5ru0

Go back to Chlorine Binding Sites List in 5ru0
Chlorine binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000000388514


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 NSP3 Macrodomain in Complex with ZINC000000388514 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:45.0
occ:0.58
CL1 B:2CL201 0.0 45.0 0.6
C2 B:2CL201 1.7 44.5 0.6
HZ2 B:LYS102 2.4 46.9 1.0
HB2 B:ASN40 2.5 14.1 1.0
C1 B:2CL201 2.6 44.7 0.6
C3 B:2CL201 2.7 44.0 0.6
H71 B:2CL201 2.8 54.4 0.6
H3 B:2CL201 2.8 52.7 0.6
C7 B:2CL201 3.0 45.3 0.6
NZ B:LYS102 3.0 39.1 1.0
HZ3 B:LYS102 3.1 46.9 1.0
O1 B:2CL201 3.1 45.9 0.6
C8 B:2CL201 3.1 45.8 0.6
HZ1 B:LYS102 3.2 46.9 1.0
CB B:ASN40 3.2 11.7 1.0
HB3 B:ASN40 3.4 14.1 1.0
HD1 B:TYR42 3.4 33.5 1.0
CG B:ASN40 3.5 12.3 1.0
HD22 B:ASN40 3.6 16.0 1.0
O B:HOH431 3.7 15.3 1.0
ND2 B:ASN40 3.7 13.3 1.0
O B:HOH414 3.8 18.7 1.0
C6 B:2CL201 3.9 44.4 0.6
O2 B:2CL201 3.9 46.0 0.6
H72 B:2CL201 4.0 54.4 0.6
C4 B:2CL201 4.0 43.9 0.6
H B:VAL41 4.0 13.8 1.0
OD1 B:ASN40 4.1 14.3 1.0
HG22 B:VAL41 4.1 17.2 1.0
HD21 B:ASN40 4.2 16.0 1.0
CD1 B:TYR42 4.3 27.9 1.0
HE1 B:TYR42 4.3 35.8 1.0
CE B:LYS102 4.3 38.2 1.0
HD3 B:LYS102 4.4 43.7 1.0
C5 B:2CL201 4.4 44.1 0.6
H B:TYR42 4.5 15.9 1.0
O B:HOH454 4.5 19.7 1.0
CA B:ASN40 4.5 11.3 1.0
HD2 B:LYS102 4.6 43.7 1.0
HE2 B:LYS102 4.6 45.9 1.0
N B:VAL41 4.6 11.5 1.0
H4 B:2CL201 4.7 52.6 0.6
CD B:LYS102 4.7 36.4 1.0
CE1 B:TYR42 4.7 29.8 1.0
HA B:ASN40 4.7 13.6 1.0
HB2 B:TYR42 4.8 22.7 1.0
O B:HOH305 4.8 25.2 1.0
C B:ASN40 5.0 11.2 1.0

Chlorine binding site 4 out of 4 in 5ru0

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Chlorine binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000000388514


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 NSP3 Macrodomain in Complex with ZINC000000388514 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:44.7
occ:0.58
CL2 B:2CL201 0.0 44.7 0.6
C6 B:2CL201 1.7 44.4 0.6
H72 B:2CL201 2.3 54.4 0.6
C1 B:2CL201 2.6 44.7 0.6
C5 B:2CL201 2.7 44.1 0.6
C7 B:2CL201 2.8 45.3 0.6
H5 B:2CL201 2.9 52.9 0.6
H71 B:2CL201 3.5 54.4 0.6
HE1 B:TYR42 3.6 35.8 1.0
C2 B:2CL201 3.8 44.5 0.6
CE1 B:TYR42 3.9 29.8 1.0
C8 B:2CL201 4.0 45.8 0.6
C4 B:2CL201 4.0 43.9 0.6
HD1 B:TYR42 4.2 33.5 1.0
CD1 B:TYR42 4.3 27.9 1.0
O1 B:2CL201 4.4 45.9 0.6
C3 B:2CL201 4.4 44.0 0.6
CZ B:TYR42 4.6 30.2 1.0
H4 B:2CL201 4.7 52.6 0.6
O2 B:2CL201 4.9 46.0 0.6
OH B:TYR42 4.9 32.3 1.0

Reference:

G.J.Correy, J.S.Fraser. Fragment Screen Against Sars-Cov-2 Nsp Macrodomain To Be Published.
Page generated: Thu Dec 17 10:33:52 2020

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