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Bromine in PDB 9cjp: X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir

Enzymatic activity of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir

All present enzymatic activity of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir:
3.4.22.69;

Protein crystallography data

The structure of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir, PDB code: 9cjp was solved by M.A.Esler, K.Shi, R.S.Harris, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.83 / 1.71
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.095, 105.665, 53.1, 90, 103.61, 90
R / Rfree (%) 18 / 22.6

Other elements in 9cjp:

The structure of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir (pdb code 9cjp). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir, PDB code: 9cjp:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in 9cjp

Go back to Bromine Binding Sites List in 9cjp
Bromine binding site 1 out of 3 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br403

b:74.9
occ:1.00
NE A:ARG4 3.5 38.9 1.0
NH2 A:ARG4 3.8 33.8 1.0
N A:LYS5 3.9 26.2 1.0
CB A:LYS5 4.0 25.5 1.0
CZ A:ARG4 4.1 40.1 1.0
NZ B:LYS5 4.2 40.7 1.0
CD A:ARG4 4.5 39.9 1.0
CA A:LYS5 4.6 23.5 1.0
CA A:ARG4 4.7 31.9 1.0
C A:ARG4 4.8 31.6 1.0
CB A:ARG4 5.0 29.1 1.0

Bromine binding site 2 out of 3 in 9cjp

Go back to Bromine Binding Sites List in 9cjp
Bromine binding site 2 out of 3 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br403

b:75.4
occ:1.00
O B:HOH533 2.2 57.6 1.0
O B:HOH539 3.6 30.8 1.0
ND2 B:ASN228 3.7 55.1 1.0
OG1 B:THR226 3.8 36.6 1.0
CB B:ASN228 4.1 43.0 1.0
CB B:THR226 4.2 29.1 1.0
CG B:ASN228 4.4 47.1 1.0
CG2 B:THR226 4.5 35.9 1.0
OD1 B:ASP229 4.7 48.0 1.0
OD2 B:ASP229 5.0 54.7 1.0
CG B:ASP229 5.0 50.2 1.0

Bromine binding site 3 out of 3 in 9cjp

Go back to Bromine Binding Sites List in 9cjp
Bromine binding site 3 out of 3 in the X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br404

b:97.9
occ:1.00
NH2 B:ARG279 3.4 62.5 1.0
CB B:TRP218 3.9 33.1 1.0
CZ B:ARG279 4.3 47.2 1.0
CA B:TRP218 4.3 38.7 1.0
NH1 B:ARG279 4.3 54.6 1.0
N B:TRP218 4.7 42.9 1.0

Reference:

M.A.Esler, K.Shi, R.S.Harris, H.Aihara. X-Ray Crystal Structure of Sars-Cov-2 Main Protease Quadruple Mutants in Complex with Nirmatrelvir To Be Published.
Page generated: Mon Aug 4 17:38:20 2025

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