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Fluorine in PDB 7rmz: Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-63

Enzymatic activity of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-63

All present enzymatic activity of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-63:
3.4.22.69;

Protein crystallography data

The structure of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-63, PDB code: 7rmz was solved by A.Kovalevsky, D.W.Kneller, L.Coates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.02 / 2.10
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 52.284, 82.224, 91.243, 90, 95.5, 90
R / Rfree (%) 15.2 / 18.9

Other elements in 7rmz:

The structure of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-63 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-63 (pdb code 7rmz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-63, PDB code: 7rmz:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7rmz

Go back to Fluorine Binding Sites List in 7rmz
Fluorine binding site 1 out of 3 in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-63


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-63 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:45.4
occ:1.00
 F25 A:5ZJ401 0.0 45.4 1.0
C24 A:5ZJ401 1.4 45.3 1.0
F26 A:5ZJ401 2.2 42.7 1.0
F27 A:5ZJ401 2.2 42.1 1.0
C13 A:5ZJ401 2.4 45.7 1.0
O A:ASP187 2.9 32.0 1.0
C14 A:5ZJ401 3.0 43.6 1.0
OH A:TYR54 3.1 30.7 1.0
CL23 A:5ZJ401 3.1 46.8 1.0
C A:ASP187 3.1 37.2 1.0
CB A:HIS41 3.3 24.8 1.0
C12 A:5ZJ401 3.5 36.4 1.0
N A:ARG188 3.7 27.7 1.0
CB A:ASP187 3.7 21.1 1.0
CA A:ASP187 3.7 25.0 1.0
CA A:ARG188 3.9 43.9 1.0
CG A:HIS41 3.9 37.9 1.0
CD2 A:HIS41 4.0 31.9 1.0
C15 A:5ZJ401 4.3 37.5 1.0
CZ A:TYR54 4.4 28.2 1.0
C A:ARG188 4.6 48.2 1.0
CG A:ASP187 4.6 25.6 1.0
CA A:HIS41 4.6 28.7 1.0
C11 A:5ZJ401 4.7 41.7 1.0
O A:HOH556 4.9 22.2 1.0
CG A:PRO52 4.9 49.7 1.0
OD2 A:ASP187 5.0 27.3 1.0
CG A:MET49 5.0 61.4 1.0
SG A:CYS44 5.0 47.0 1.0
N A:GLN189 5.0 59.8 1.0

Fluorine binding site 2 out of 3 in 7rmz

Go back to Fluorine Binding Sites List in 7rmz
Fluorine binding site 2 out of 3 in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-63


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-63 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:42.7
occ:1.00
 F26 A:5ZJ401 0.0 42.7 1.0
C24 A:5ZJ401 1.4 45.3 1.0
F25 A:5ZJ401 2.2 45.4 1.0
F27 A:5ZJ401 2.2 42.1 1.0
C13 A:5ZJ401 2.4 45.7 1.0
C14 A:5ZJ401 3.0 43.6 1.0
CL23 A:5ZJ401 3.1 46.8 1.0
CA A:ARG188 3.3 43.9 1.0
N A:GLN189 3.4 59.8 1.0
CG A:MET49 3.4 61.4 1.0
CG A:GLN189 3.4 80.1 1.0
C12 A:5ZJ401 3.4 36.4 1.0
C A:ARG188 3.5 48.2 1.0
O A:MET49 3.5 53.3 1.0
N A:ARG188 3.8 27.7 1.0
CB A:MET49 3.9 54.0 1.0
O A:ASP187 3.9 32.0 1.0
CA A:MET49 3.9 54.8 1.0
C A:ASP187 4.0 37.2 1.0
C A:MET49 4.2 59.4 1.0
CB A:GLN189 4.3 65.3 1.0
CA A:GLN189 4.3 59.3 1.0
C15 A:5ZJ401 4.3 37.5 1.0
O A:ARG188 4.3 45.2 1.0
CB A:ARG188 4.5 45.2 1.0
CD A:GLN189 4.5 84.7 1.0
OH A:TYR54 4.5 30.7 1.0
NE2 A:GLN189 4.6 62.9 1.0
C11 A:5ZJ401 4.6 41.7 1.0
CG A:PRO52 4.7 49.7 1.0
SD A:MET49 4.9 92.8 1.0

Fluorine binding site 3 out of 3 in 7rmz

Go back to Fluorine Binding Sites List in 7rmz
Fluorine binding site 3 out of 3 in the Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-63


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-63 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:42.1
occ:1.00
 F27 A:5ZJ401 0.0 42.1 1.0
C24 A:5ZJ401 1.4 45.3 1.0
F26 A:5ZJ401 2.2 42.7 1.0
F25 A:5ZJ401 2.2 45.4 1.0
C13 A:5ZJ401 2.4 45.7 1.0
C12 A:5ZJ401 2.7 36.4 1.0
CG A:MET49 3.2 61.4 1.0
CB A:HIS41 3.5 24.8 1.0
SG A:CYS44 3.5 47.0 1.0
OH A:TYR54 3.6 30.7 1.0
CB A:CYS44 3.7 41.6 1.0
C14 A:5ZJ401 3.7 43.6 1.0
C11 A:5ZJ401 4.1 41.7 1.0
CA A:MET49 4.1 54.8 1.0
CB A:MET49 4.2 54.0 1.0
CG A:HIS41 4.3 37.9 1.0
O A:ASP187 4.4 32.0 1.0
CA A:HIS41 4.5 28.7 1.0
CL23 A:5ZJ401 4.5 46.8 1.0
SD A:MET49 4.5 92.8 1.0
O A:HIS41 4.5 29.2 1.0
CG A:PRO52 4.5 49.7 1.0
O A:MET49 4.7 53.3 1.0
CZ A:TYR54 4.8 28.2 1.0
C15 A:5ZJ401 4.8 37.5 1.0
CA A:ARG188 4.9 43.9 1.0
C A:ASP187 4.9 37.2 1.0
C A:MET49 5.0 59.4 1.0
CD2 A:HIS41 5.0 31.9 1.0
C10 A:5ZJ401 5.0 37.6 1.0

Reference:

D.W.Kneller, H.Li, S.Galanie, G.Phillips, A.Labbe, K.L.Weiss, Q.Zhang, M.A.Arnould, A.Clyde, H.Ma, A.Ramanathan, C.B.Jonsson, M.S.Head, L.Coates, J.M.Louis, P.V.Bonnesen, A.Kovalevsky. Structural, Electronic, and Electrostatic Determinants For Inhibitor Binding to Subsites S1 and S2 in Sars-Cov-2 Main Protease. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34705466
DOI: 10.1021/ACS.JMEDCHEM.1C01475
Page generated: Fri Aug 2 12:19:17 2024

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