Atomistry » Fluorine » PDB 7re1-7rrz » 7rme
Atomistry »
  Fluorine »
    PDB 7re1-7rrz »
      7rme »

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: Fri Aug 2 12:19:17 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy