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Bromine in PDB 5sro: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (R) and (S) Isomers

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (R) and (S) Isomers

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (R) and (S) Isomers:
3.4.19.121;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (R) and (S) Isomers, PDB code: 5sro was solved by G.J.Correy, J.S.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.69 / 1.05
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 88.753, 88.753, 39.576, 90, 90, 90
R / Rfree (%) 13.6 / 15.3

Other elements in 5sro:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (R) and (S) Isomers also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (R) and (S) Isomers (pdb code 5sro). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (R) and (S) Isomers, PDB code: 5sro:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 5sro

Go back to Bromine Binding Sites List in 5sro
Bromine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (R) and (S) Isomers


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (R) and (S) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br201

b:15.4
occ:0.06
 BR14 A:RCR201 0.0 15.4 0.1
O A:HOH558 0.3 50.9 0.9
H151 A:RD6202 1.9 17.3 0.1
C11 A:RCR201 1.9 15.2 0.1
H101 A:RD6202 2.3 18.2 0.1
O A:HOH546 2.5 37.5 0.8
O A:HOH474 2.6 50.2 0.8
N15 A:RD6202 2.6 14.4 0.1
O A:HOH450 2.7 15.2 0.8
O A:HOH503 2.7 11.7 0.2
C10 A:RCR201 2.8 15.1 0.1
HB2 A:ALA52 2.8 14.7 0.8
H101 A:RCR201 2.9 18.1 0.1
C12 A:RCR201 2.9 15.1 0.1
HB2 A:ALA52 3.0 11.8 0.2
C10 A:RD6202 3.0 15.2 0.1
H121 A:RCR201 3.0 18.1 0.1
C09 A:RD6202 3.1 14.8 0.1
HB1 A:ALA52 3.3 11.8 0.2
HB1 A:ALA52 3.6 14.7 0.8
CB A:ALA52 3.6 9.9 0.2
CB A:ALA52 3.6 12.3 0.8
C16 A:RD6202 4.0 14.3 0.1
C09 A:RCR201 4.1 15.0 0.1
C13 A:RCR201 4.2 15.1 0.1
HA A:ALA52 4.2 12.6 0.8
HB3 A:ALA52 4.3 11.8 0.2
HB3 A:ALA52 4.3 14.7 0.8
HA A:ALA52 4.3 11.6 0.2
C11 A:RD6202 4.3 15.6 0.1
O A:HOH517 4.3 45.5 1.0
HZ A:PHE156 4.4 21.1 0.2
O A:HOH548 4.4 29.6 0.8
C08 A:RD6202 4.5 14.6 0.1
CA A:ALA52 4.5 10.6 0.8
CA A:ALA52 4.6 9.7 0.2
CZ A:PHE156 4.6 17.6 0.2
N17 A:RD6202 4.7 14.1 0.1
C08 A:RCR201 4.7 15.0 0.1
O A:HOH382 4.7 22.9 0.8
HE1 A:PHE156 4.9 21.1 0.2
CE1 A:PHE156 4.9 17.6 0.2
C07 A:RD6202 4.9 14.3 0.1

Bromine binding site 2 out of 2 in 5sro

Go back to Bromine Binding Sites List in 5sro
Bromine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (R) and (S) Isomers


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562509 - (R) and (S) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br202

b:16.6
occ:0.10
 BR14 A:RD6202 0.0 16.6 0.1
OD1 A:ASP22 1.2 20.6 0.8
H151 A:RCR201 1.9 17.8 0.1
C11 A:RD6202 2.0 15.6 0.1
CG A:ASP22 2.2 20.7 0.8
HB A:VAL24 2.2 21.2 0.8
H A:VAL24 2.3 18.4 0.8
HG23 A:VAL24 2.5 22.4 0.8
H101 A:RCR201 2.5 18.1 0.1
N15 A:RCR201 2.7 14.8 0.1
O A:HOH474 2.7 50.2 0.8
OD2 A:ASP22 2.7 22.7 0.8
OD1 A:ASP22 2.7 19.5 0.2
CG2 A:VAL24 2.9 18.7 0.8
CB A:VAL24 2.9 17.7 0.8
C10 A:RD6202 2.9 15.2 0.1
C12 A:RD6202 2.9 15.2 0.1
H A:VAL24 2.9 21.6 0.2
HG21 A:VAL24 2.9 22.4 0.8
H101 A:RD6202 3.0 18.2 0.1
H121 A:RD6202 3.0 18.2 0.1
N A:VAL24 3.1 15.4 0.8
C10 A:RCR201 3.1 15.1 0.1
C09 A:RCR201 3.2 15.0 0.1
CG A:ASP22 3.2 19.4 0.2
HG22 A:ILE23 3.2 21.1 0.2
HG23 A:VAL24 3.3 21.0 0.2
OD2 A:ASP22 3.4 19.4 0.2
HD1 A:PHE156 3.4 20.9 0.2
HE1 A:PHE156 3.4 21.1 0.2
HB A:VAL24 3.5 21.3 0.2
H A:ILE23 3.5 22.0 0.2
HG22 A:ILE23 3.6 17.1 0.8
CB A:ASP22 3.6 18.5 0.8
CA A:VAL24 3.6 16.6 0.8
HB1 A:ALA52 3.6 14.7 0.8
H A:ILE23 3.7 17.7 0.8
H A:GLU25 3.7 22.5 0.8
N A:ILE23 3.8 14.8 0.8
N A:VAL24 3.8 18.1 0.2
HA A:ASP22 3.8 19.9 0.8
C A:ASP22 3.8 15.3 0.8
HG22 A:VAL24 3.8 22.4 0.8
C16 A:RCR201 3.9 14.8 0.1
HA A:ASP22 3.9 22.6 0.2
N A:ILE23 3.9 18.4 0.2
CE1 A:PHE156 3.9 17.6 0.2
CD1 A:PHE156 3.9 17.4 0.2
CG2 A:VAL24 3.9 17.6 0.2
CA A:ASP22 3.9 16.6 0.8
HG21 A:VAL24 4.0 21.0 0.2
HB1 A:ALA52 4.0 11.8 0.2
HB3 A:ASP22 4.1 22.2 0.8
CB A:VAL24 4.1 17.8 0.2
HB2 A:ASP22 4.2 22.2 0.8
CG2 A:ILE23 4.2 17.6 0.2
CG1 A:VAL24 4.2 18.9 0.8
C A:ILE23 4.2 14.6 0.8
C09 A:RD6202 4.2 14.8 0.1
C13 A:RD6202 4.2 14.9 0.1
HA A:VAL24 4.3 19.9 0.8
HG23 A:ILE23 4.3 17.1 0.8
C A:ASP22 4.3 18.6 0.2
O A:HOH370 4.3 41.0 1.0
HG11 A:VAL24 4.3 22.6 0.8
CB A:ASP22 4.3 19.2 0.2
HB3 A:ALA52 4.3 14.7 0.8
N A:GLU25 4.3 18.8 0.8
CG2 A:ILE23 4.4 14.3 0.8
CA A:ASP22 4.4 18.9 0.2
N17 A:RCR201 4.4 14.7 0.1
CB A:ALA52 4.4 12.3 0.8
C11 A:RCR201 4.4 15.2 0.1
HG23 A:ILE23 4.4 21.1 0.2
O A:ASP22 4.4 16.2 0.8
HG12 A:VAL24 4.4 22.6 0.8
CA A:ILE23 4.5 14.3 0.8
C A:VAL24 4.5 17.3 0.8
C08 A:RCR201 4.5 15.0 0.1
CA A:VAL24 4.6 18.2 0.2
CA A:ILE23 4.7 17.9 0.2
HB3 A:ALA52 4.7 11.8 0.2
H A:GLU25 4.7 23.8 0.2
HB2 A:ALA52 4.7 14.7 0.8
C A:ILE23 4.7 18.0 0.2
HG21 A:ILE23 4.7 21.1 0.2
HB2 A:ASP22 4.7 23.0 0.2
CB A:ALA52 4.8 9.9 0.2
C08 A:RD6202 4.8 14.6 0.1
HG22 A:VAL24 4.8 21.0 0.2
O A:HOH422 4.8 21.6 0.9
C07 A:RCR201 4.9 14.9 0.1
HG2 A:GLU25 4.9 32.0 0.8
HG13 A:VAL24 4.9 22.6 0.8
CB A:ILE23 4.9 17.6 0.2
O A:HOH548 5.0 29.6 0.8

Reference:

G.J.Correy, J.S.Fraser. Ligand Screen Against Sars-Cov-2 NSP3 Macrodomain To Be Published.
Page generated: Thu Jul 11 00:57:36 2024

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