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Chlorine in PDB 7ex3: Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3

Enzymatic activity of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3

All present enzymatic activity of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3, PDB code: 7ex3 was solved by W.Kuang, Z.Hu, P.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.63 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.666, 70.873, 71.253, 90, 90, 90
R / Rfree (%) 19 / 22.6

Other elements in 7ex3:

The structure of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3 also contains other interesting chemical elements:

Fluorine (F) 1 atom
Manganese (Mn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3 (pdb code 7ex3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3, PDB code: 7ex3:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7ex3

Go back to Chlorine Binding Sites List in 7ex3
Chlorine binding site 1 out of 4 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:30.0
occ:1.00
 CL1 A:IA3203 0.0 30.0 1.0
C15 A:IA3203 1.8 26.3 1.0
C17 A:IA3203 2.7 24.4 1.0
C14 A:IA3203 2.7 25.9 1.0
O A:LEU30 3.4 25.2 1.0
O A:HOH367 3.5 27.2 1.0
O A:HOH364 3.7 36.7 1.0
C A:LEU30 3.7 26.1 1.0
O A:HOH311 3.8 28.5 1.0
N A:GLU31 3.9 24.3 1.0
CA A:GLU31 3.9 22.8 1.0
C18 A:IA3203 4.0 24.7 1.0
C13 A:IA3203 4.0 27.0 1.0
CB A:HIS34 4.1 22.4 1.0
CB A:LEU30 4.1 24.7 1.0
CA A:LEU30 4.5 25.9 1.0
CG A:HIS34 4.6 23.7 1.0
C12 A:IA3203 4.6 25.3 1.0
CB A:GLU31 4.7 24.0 1.0
C1 A:IA3203 4.8 31.2 1.0
CD2 A:HIS34 4.8 21.8 1.0

Chlorine binding site 2 out of 4 in 7ex3

Go back to Chlorine Binding Sites List in 7ex3
Chlorine binding site 2 out of 4 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:27.1
occ:1.00
 O A:HOH374 3.0 28.9 1.0
OH A:TYR109 3.0 23.7 1.0
NZ A:LYS108 3.2 39.6 1.0
N A:THR77 3.3 22.8 1.0
CB A:VAL76 3.7 26.8 1.0
CE1 A:TYR109 3.8 23.5 1.0
CZ A:TYR109 3.9 23.5 1.0
CA A:VAL76 3.9 25.1 1.0
OG1 A:THR77 3.9 26.1 1.0
O A:HOH365 4.0 40.6 1.0
CG1 A:VAL76 4.1 27.1 1.0
C A:VAL76 4.1 23.7 1.0
CE A:LYS108 4.1 31.9 1.0
C22 A:IA3203 4.1 43.7 1.0
C A:THR77 4.1 23.4 1.0
O A:THR77 4.2 22.4 1.0
CA A:THR77 4.2 21.5 1.0
O A:HOH304 4.6 43.4 1.0
N A:PRO78 4.7 23.8 1.0
CB A:THR77 4.7 26.1 1.0
O A:HOH323 4.8 22.2 1.0
CD A:LYS108 4.9 32.4 1.0
C23 A:IA3203 5.0 47.6 1.0

Chlorine binding site 3 out of 4 in 7ex3

Go back to Chlorine Binding Sites List in 7ex3
Chlorine binding site 3 out of 4 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:36.3
occ:1.00
 CG2 A:THR18 4.4 30.6 1.0

Chlorine binding site 4 out of 4 in 7ex3

Go back to Chlorine Binding Sites List in 7ex3
Chlorine binding site 4 out of 4 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:40.8
occ:1.00
 O A:HOH377 3.0 40.0 1.0
N A:ARG17 3.0 30.9 1.0
OG1 A:THR18 3.4 33.3 1.0
N A:THR18 3.4 33.9 1.0
CG2 A:VAL21 3.7 32.4 1.0
CB A:VAL21 3.7 34.0 1.0
CG2 A:VAL16 3.8 29.1 1.0
CA A:ARG17 3.8 30.1 1.0
CA A:VAL16 3.9 31.4 1.0
C A:VAL16 4.0 30.5 1.0
CG1 A:VAL21 4.0 31.8 1.0
CG2 A:THR18 4.0 30.6 1.0
CB A:ARG17 4.0 36.8 1.0
C A:ARG17 4.1 31.9 1.0
CB A:THR18 4.1 31.6 1.0
CA A:THR18 4.3 29.1 1.0
CB A:VAL16 4.5 30.8 1.0
CG A:ARG17 4.6 36.6 1.0
O A:ALA15 4.7 36.3 1.0
O A:THR18 4.8 33.5 1.0

Reference:

W.Kuang, H.Zhang, Y.Cai, G.Zhang, F.Deng, H.Li, Y.Zhou, M.Wang, P.Gong, Y.Guo, Z.Hu. Structural and Biochemical Basis For Development of Diketo Acid Inhibitors Targeting the Cap-Snatching Endonuclease of the Ebinur Lake Virus (Order: Bunyavirales ). J.Virol. V. 96 17321 2022.
ISSN: ESSN 1098-5514
PubMed: 35266805
DOI: 10.1128/JVI.02173-21
Page generated: Mon Jul 29 20:37:47 2024

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