Fluorine in PDB 7rme: Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-52

Enzymatic activity of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-52

All present enzymatic activity of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-52:
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-3-52, PDB code: 7rme 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) 25.30 / 2.00
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 52.432, 82.164, 91.742, 90, 95.34, 90
R / Rfree (%) 16.3 / 20.4

Other elements in 7rme:

The structure of Room Temperature X-Ray Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Hl-3-52 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-3-52 (pdb code 7rme). 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-3-52, PDB code: 7rme:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7rme

Go back to Fluorine Binding Sites List in 7rme
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-3-52


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-3-52 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:50.6
occ:1.00
 F25 A:5Z3401 0.0 50.6 1.0
C24 A:5Z3401 1.4 48.1 1.0
F27 A:5Z3401 2.2 52.4 1.0
F26 A:5Z3401 2.2 48.2 1.0
C14 A:5Z3401 2.4 44.6 1.0
C A:ARG188 3.0 49.1 1.0
C13 A:5Z3401 3.0 48.3 1.0
CL16 A:5Z3401 3.1 48.2 1.0
CA A:ARG188 3.2 44.3 1.0
O A:ARG188 3.2 43.4 1.0
N A:GLN189 3.3 57.2 1.0
N A:ARG188 3.4 29.9 1.0
C15 A:5Z3401 3.5 46.5 1.0
C A:ASP187 3.8 37.3 1.0
CA A:GLN189 3.9 60.4 1.0
O A:ASP187 4.2 30.7 1.0
CB A:GLN189 4.3 67.3 1.0
C12 A:5Z3401 4.3 43.2 1.0
OE1 A:GLN189 4.4 87.0 1.0
CA A:ASP187 4.4 27.5 1.0
O A:MET49 4.7 58.3 1.0
C10 A:5Z3401 4.7 43.0 1.0
CB A:ARG188 4.7 45.2 1.0
C11 A:5Z3401 5.0 48.5 1.0

Fluorine binding site 2 out of 3 in 7rme

Go back to Fluorine Binding Sites List in 7rme
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-3-52


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-3-52 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:48.2
occ:1.00
 F26 A:5Z3401 0.0 48.2 1.0
C24 A:5Z3401 1.4 48.1 1.0
F27 A:5Z3401 2.2 52.4 1.0
F25 A:5Z3401 2.2 50.6 1.0
C14 A:5Z3401 2.4 44.6 1.0
C A:ASP187 3.0 37.3 1.0
C13 A:5Z3401 3.0 48.3 1.0
CA A:ASP187 3.1 27.5 1.0
CL16 A:5Z3401 3.2 48.2 1.0
CB A:ASP187 3.3 23.2 1.0
O A:ASP187 3.3 30.7 1.0
N A:ARG188 3.4 29.9 1.0
C15 A:5Z3401 3.4 46.5 1.0
CD2 A:HIS41 3.8 34.6 1.0
CA A:ARG188 3.9 44.3 1.0
CG A:HIS41 4.3 36.1 1.0
C12 A:5Z3401 4.3 43.2 1.0
C A:ARG188 4.3 49.1 1.0
CB A:HIS41 4.4 28.9 1.0
SD A:MET165 4.4 44.4 1.0
O A:ARG188 4.5 43.4 1.0
N A:ASP187 4.5 27.4 1.0
OH A:TYR54 4.6 32.9 1.0
CG A:ASP187 4.6 24.7 1.0
C10 A:5Z3401 4.7 43.0 1.0
O A:VAL186 4.7 27.2 1.0
NE2 A:HIS41 4.7 35.0 1.0
C11 A:5Z3401 5.0 48.5 1.0

Fluorine binding site 3 out of 3 in 7rme

Go back to Fluorine Binding Sites List in 7rme
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-3-52


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-3-52 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:52.4
occ:1.00
 F27 A:5Z3401 0.0 52.4 1.0
C24 A:5Z3401 1.3 48.1 1.0
F26 A:5Z3401 2.2 48.2 1.0
F25 A:5Z3401 2.2 50.6 1.0
C14 A:5Z3401 2.4 44.6 1.0
C15 A:5Z3401 2.7 46.5 1.0
SD A:MET165 3.4 44.4 1.0
CB A:MET165 3.5 26.9 1.0
C13 A:5Z3401 3.7 48.3 1.0
CG A:MET165 4.0 28.3 1.0
C10 A:5Z3401 4.1 43.0 1.0
O A:ARG188 4.3 43.4 1.0
N A:ARG188 4.5 29.9 1.0
CA A:ASP187 4.5 27.5 1.0
CL16 A:5Z3401 4.5 48.2 1.0
O A:HIS164 4.6 28.0 1.0
C A:ARG188 4.6 49.1 1.0
C A:ASP187 4.6 37.3 1.0
CE A:MET165 4.7 32.3 1.0
O A:HOH567 4.8 37.9 1.0
CA A:MET165 4.8 26.1 1.0
CD2 A:HIS41 4.8 34.6 1.0
C12 A:5Z3401 4.8 43.2 1.0
C8 A:5Z3401 4.8 43.5 1.0
CA A:ARG188 4.9 44.3 1.0
O A:VAL186 4.9 27.2 1.0
N7 A:5Z3401 5.0 42.8 1.0
C11 A:5Z3401 5.0 48.5 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: Thu Nov 25 09:15:28 2021

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