Fluorine in PDB 8i30: Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J

Enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J, PDB code: 8i30 was solved by R.Zeng, C.Huang, L.W.Xie, K.Wang, Y.Z.Liu, S.Y.Yang, J.Lei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.78 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.249, 84.697, 51.479, 90, 115.14, 90
R / Rfree (%) 18.7 / 22.6

Other elements in 8i30:

The structure of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J (pdb code 8i30). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J, PDB code: 8i30:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8i30

Go back to Fluorine Binding Sites List in 8i30
Fluorine binding site 1 out of 4 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:50.3
occ:1.00
 F01 A:OF9401 0.0 50.3 1.0
C02 A:OF9401 1.4 51.3 1.0
F03 A:OF9401 2.2 60.8 1.0
C04 A:OF9401 2.3 55.1 1.0
C40 A:OF9401 2.4 53.3 1.0
C05 A:OF9401 2.9 46.7 1.0
C39 A:OF9401 3.0 42.2 1.0
C06 A:OF9401 3.5 52.4 1.0
CB A:MET165 3.6 33.2 1.0
O A:HIS164 3.7 38.2 1.0
CE1 A:HIS41 3.9 44.3 1.0
ND1 A:HIS41 4.0 37.4 1.0
SD A:MET165 4.0 42.6 1.0
CG A:MET165 4.2 34.3 1.0
C A:HIS164 4.3 28.1 1.0
NE2 A:HIS41 4.3 45.4 1.0
CA A:ASP187 4.4 42.2 1.0
C07 A:OF9401 4.5 50.9 1.0
O38 A:OF9401 4.6 48.8 1.0
CG A:HIS41 4.6 41.8 1.0
O26 A:OF9401 4.6 35.4 1.0
CB A:ASP187 4.6 36.0 1.0
CA A:MET165 4.6 32.1 1.0
C A:ASP187 4.7 50.2 1.0
CD2 A:HIS41 4.7 43.5 1.0
CB A:HIS164 4.8 29.9 1.0
N A:MET165 4.9 28.9 1.0
N A:ARG188 4.9 46.9 1.0

Fluorine binding site 2 out of 4 in 8i30

Go back to Fluorine Binding Sites List in 8i30
Fluorine binding site 2 out of 4 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:60.8
occ:1.00
 F03 A:OF9401 0.0 60.8 1.0
C02 A:OF9401 1.4 51.3 1.0
F01 A:OF9401 2.2 50.3 1.0
C40 A:OF9401 2.4 53.3 1.0
C04 A:OF9401 2.4 55.1 1.0
C A:ASP187 3.1 50.2 1.0
N A:ARG188 3.1 46.9 1.0
CE A:MET49 3.2 81.2 1.0
O A:ASP187 3.5 53.0 1.0
CA A:ARG188 3.5 57.8 1.0
CA A:ASP187 3.6 42.2 1.0
C05 A:OF9401 3.7 46.7 1.0
C39 A:OF9401 3.7 42.2 1.0
C A:ARG188 3.9 63.2 1.0
O A:ARG188 4.0 54.6 1.0
CB A:ASP187 4.1 36.0 1.0
C06 A:OF9401 4.2 52.4 1.0
SD A:MET49 4.6 90.8 0.7
N A:GLN189 4.7 73.3 1.0
O A:VAL186 4.7 34.9 1.0
ND1 A:HIS41 4.8 37.4 1.0
SD A:MET165 4.8 42.6 1.0
N A:ASP187 4.9 36.3 1.0
CG A:HIS41 4.9 41.8 1.0
CB A:ARG188 4.9 54.3 1.0

Fluorine binding site 3 out of 4 in 8i30

Go back to Fluorine Binding Sites List in 8i30
Fluorine binding site 3 out of 4 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:66.1
occ:1.00
 F11 A:OF9401 0.0 66.1 1.0
C10 A:OF9401 1.4 58.2 1.0
C09 A:OF9401 2.2 55.0 1.0
F12 A:OF9401 2.3 56.4 1.0
C13 A:OF9401 2.4 52.8 1.0
O A:HOH741 3.2 58.2 1.0
N08 A:OF9401 3.4 55.5 1.0
C14 A:OF9401 3.5 50.3 1.0
C15 A:OF9401 4.6 49.5 1.0
C07 A:OF9401 4.6 50.9 1.0

Fluorine binding site 4 out of 4 in 8i30

Go back to Fluorine Binding Sites List in 8i30
Fluorine binding site 4 out of 4 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:56.4
occ:1.00
 F12 A:OF9401 0.0 56.4 1.0
C10 A:OF9401 1.4 58.2 1.0
C09 A:OF9401 2.2 55.0 1.0
F11 A:OF9401 2.3 66.1 1.0
C13 A:OF9401 2.3 52.8 1.0
C23 A:OF9401 3.0 54.3 1.0
C14 A:OF9401 3.1 50.3 1.0
C24 A:OF9401 3.2 54.9 1.0
N08 A:OF9401 3.2 55.5 1.0
C15 A:OF9401 3.4 49.5 1.0
C22 A:OF9401 3.6 55.6 1.0
N16 A:OF9401 3.8 37.5 1.0
O37 A:OF9401 3.8 51.8 1.0
C19 A:OF9401 3.9 50.7 1.0
C21 A:OF9401 4.2 53.6 1.0
C20 A:OF9401 4.3 47.3 1.0
O A:HOH572 4.5 59.8 1.0
C07 A:OF9401 4.6 50.9 1.0
C17 A:OF9401 4.8 40.8 1.0
C18 A:OF9401 4.8 40.3 1.0
O A:HOH727 4.9 63.2 1.0

Reference:

C.Huang, R.Zeng, J.Qiao, B.Quan, R.Luo, Q.Huang, N.Guo, Y.Li, X.Long, R.Ma, A.Xia, Z.Fang, Y.Wang, Y.Li, Y.Zheng, L.Li, J.Lei, S.Yang. Discovery and Structure-Activity Relationship Studies of Novel Alpha-Ketoamide Derivatives Targeting the Sars-Cov-2 Main Protease. Eur.J.Med.Chem. V. 259 15657 2023.
ISSN: ISSN 0223-5234
PubMed: 37517202
DOI: 10.1016/J.EJMECH.2023.115657
Page generated: Fri Aug 2 20:32:35 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy