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Chlorine in PDB 7ex9: Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 28

Enzymatic activity of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 28

All present enzymatic activity of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 28:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 28, PDB code: 7ex9 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) 22.42 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.855, 70.763, 70.923, 90, 90, 90
R / Rfree (%) 18.5 / 20.2

Other elements in 7ex9:

The structure of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 28 also contains other interesting chemical elements:

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 28 (pdb code 7ex9). 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 28, PDB code: 7ex9:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7ex9

Go back to Chlorine Binding Sites List in 7ex9
Chlorine binding site 1 out of 4 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 28


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 28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:26.3
occ:1.00
 C16 A:U28203 3.0 41.2 1.0
OH A:TYR109 3.1 20.4 1.0
N A:THR77 3.2 19.3 1.0
NZ A:LYS108 3.5 38.2 1.0
CB A:VAL76 3.6 20.2 1.0
CE1 A:TYR109 3.7 20.3 1.0
CA A:VAL76 3.8 19.9 1.0
CZ A:TYR109 3.9 21.4 1.0
CE A:LYS108 4.0 29.8 1.0
OG1 A:THR77 4.0 21.2 1.0
C A:VAL76 4.0 18.5 1.0
C A:THR77 4.1 16.3 1.0
CG1 A:VAL76 4.1 22.0 1.0
O A:THR77 4.1 17.4 1.0
CA A:THR77 4.1 15.5 1.0
N15 A:U28203 4.4 39.6 1.0
O A:HOH397 4.5 46.6 1.0
N A:PRO78 4.6 16.3 1.0
CB A:THR77 4.7 18.1 1.0
CD A:LYS108 4.8 26.9 1.0
CG2 A:VAL76 4.9 18.7 1.0
C14 A:U28203 5.0 37.5 1.0
O A:HOH359 5.0 16.8 1.0

Chlorine binding site 2 out of 4 in 7ex9

Go back to Chlorine Binding Sites List in 7ex9
Chlorine binding site 2 out of 4 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 28


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 28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:28.9
occ:1.00
 O A:HOH402 3.2 22.0 1.0
O A:HOH347 3.2 40.8 1.0
N A:TRP83 3.4 17.0 1.0
NH2 A:ARG50 3.5 20.6 1.0
NH1 A:ARG50 3.8 17.4 1.0
CA A:ILE82 3.9 16.9 1.0
O A:TYR81 3.9 14.5 1.0
O A:HOH411 4.0 37.0 1.0
CZ A:ARG50 4.1 21.0 1.0
C A:ILE82 4.1 17.4 1.0
CE2 A:TYR81 4.2 18.5 1.0
O A:TRP83 4.3 25.9 1.0
CB A:TRP83 4.3 23.1 1.0
CA A:TRP83 4.3 22.8 1.0
CD2 A:TYR81 4.4 15.5 1.0
O A:HOH366 4.5 20.4 1.0
C A:TYR81 4.7 15.8 1.0
O A:HOH432 4.7 26.7 1.0
CG2 A:ILE82 4.7 21.1 1.0
C A:TRP83 4.7 26.7 1.0
N A:ILE82 4.7 16.5 1.0
CB A:ILE82 4.8 17.6 1.0
CZ A:TYR81 5.0 21.2 1.0

Chlorine binding site 3 out of 4 in 7ex9

Go back to Chlorine Binding Sites List in 7ex9
Chlorine binding site 3 out of 4 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 28


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 28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:33.9
occ:1.00
 N A:ARG17 3.0 24.1 1.0
O A:HOH423 3.1 34.2 1.0
OG1 A:THR18 3.4 27.4 1.0
N A:THR18 3.5 25.4 1.0
CB A:VAL21 3.8 23.2 1.0
CG2 A:VAL21 3.8 27.6 1.0
CA A:ARG17 3.8 25.7 1.0
CG2 A:VAL16 3.9 23.4 1.0
CB A:ARG17 3.9 28.3 1.0
CA A:VAL16 3.9 23.4 1.0
C A:VAL16 4.0 23.0 1.0
CG1 A:VAL21 4.0 24.8 1.0
C A:ARG17 4.1 27.5 1.0
CG2 A:THR18 4.1 25.6 1.0
CB A:THR18 4.2 25.1 1.0
CA A:THR18 4.4 22.8 1.0
CG A:ARG17 4.5 30.5 1.0
CB A:VAL16 4.5 20.4 1.0
O A:ALA15 4.7 26.5 1.0
O A:THR18 4.8 22.4 1.0

Chlorine binding site 4 out of 4 in 7ex9

Go back to Chlorine Binding Sites List in 7ex9
Chlorine binding site 4 out of 4 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 28


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 28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:24.7
occ:0.80
 O A:HOH326 2.9 24.8 1.0
C1 A:U28203 3.0 26.9 0.2
N A:VAL95 3.1 15.0 1.0
O A:VAL95 3.4 17.8 1.0
O A:HOH357 3.5 24.7 1.0
O A:HOH337 3.6 29.8 1.0
CD2 A:HIS34 3.8 14.8 1.0
CA A:LYS94 3.9 15.4 1.0
C A:LYS94 4.0 15.8 1.0
O A:HOH426 4.0 37.2 1.0
C A:VAL95 4.1 18.0 1.0
CA A:VAL95 4.1 14.3 1.0
CB A:HIS34 4.2 15.9 1.0
CG A:HIS34 4.4 16.4 1.0
O2 A:U28203 4.4 17.7 1.0
CD A:LYS94 4.4 21.1 1.0
CB A:LYS94 4.5 15.3 1.0
CB A:VAL95 4.5 14.9 1.0
O A:TYR93 4.8 13.8 1.0
O4 A:U28203 4.8 28.0 1.0
NE2 A:HIS34 4.9 14.4 1.0
C3 A:U28203 4.9 22.8 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 20:38:21 2024

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