Manganese in PDB 7ex3: 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;

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

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

Chlorine	(Cl)	4 atoms
Fluorine	(F)	1 atom

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 3, PDB code: 7ex3:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 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 Manganese with other atoms in the Mn 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:Mn201 b:26.8 occ:0.57 O9 A:IA3203 2.0 25.7 1.0 OD1 A:ASN52 2.0 26.6 1.0 O6 A:IA3203 2.1 23.9 1.0 O A:HOH306 2.1 22.4 1.0 OD1 A:ASP79 2.2 23.6 1.0 O A:HOH323 2.3 22.2 1.0 CG A:ASN52 2.9 26.3 1.0 C8 A:IA3203 2.9 25.4 1.0 C5 A:IA3203 3.0 25.6 1.0 ND2 A:ASN52 3.2 24.6 1.0 CG A:ASP79 3.3 22.6 1.0 C7 A:IA3203 3.3 25.0 1.0 OD2 A:ASP79 3.8 24.1 1.0 OD1 A:ASN51 4.0 25.9 1.0 MN A:MN202 4.0 20.4 1.0 O A:HOH374 4.2 28.9 1.0 O A:THR77 4.3 22.4 1.0 C10 A:IA3203 4.3 24.7 1.0 OD1 A:ASP92 4.3 22.8 1.0 CE1 A:HIS34 4.4 23.6 1.0 CB A:ASN52 4.4 24.6 1.0 C3 A:IA3203 4.4 26.6 1.0 CB A:ASP79 4.4 20.6 1.0 CA A:ASP79 4.5 19.7 1.0 NE2 A:HIS34 4.5 21.4 1.0 O A:HOH329 4.6 25.2 1.0 N A:ASP79 4.6 20.4 1.0 C19 A:IA3203 4.6 28.3 1.0 C18 A:IA3203 4.7 24.7 1.0 CA A:ASN52 4.8 23.2 1.0 C11 A:IA3203 4.8 24.1 1.0 N A:ASN52 4.8 23.7 1.0 C20 A:IA3203 4.9 28.3 1.0 O2 A:IA3203 4.9 26.5 1.0 OD2 A:ASP92 4.9 22.0 1.0

Manganese binding site 2 out of 2 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 Manganese with other atoms in the Mn 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:Mn202 b:20.4 occ:1.00 O2 A:IA3203 2.1 26.5 1.0 OD2 A:ASP92 2.2 22.0 1.0 OD2 A:ASP79 2.2 24.1 1.0 O6 A:IA3203 2.3 23.9 1.0 O A:TYR93 2.3 22.6 1.0 NE2 A:HIS34 2.4 21.4 1.0 C1 A:IA3203 2.7 31.2 1.0 C3 A:IA3203 2.8 26.6 1.0 C5 A:IA3203 3.0 25.6 1.0 CG A:ASP92 3.1 26.8 1.0 CG A:ASP79 3.2 22.6 1.0 CD2 A:HIS34 3.2 21.8 1.0 C A:TYR93 3.4 22.8 1.0 OD1 A:ASP79 3.5 23.6 1.0 CE1 A:HIS34 3.5 23.6 1.0 N A:TYR93 3.5 19.9 1.0 OD1 A:ASP92 3.6 22.8 1.0 CA A:TYR93 3.9 22.5 1.0 O A:HOH332 3.9 30.5 1.0 O4 A:IA3203 4.0 31.3 1.0 MN A:MN201 4.0 26.8 0.6 CB A:TYR93 4.2 21.6 1.0 C A:ASP92 4.3 22.1 1.0 CB A:ASP92 4.3 24.0 1.0 C7 A:IA3203 4.3 25.0 1.0 CE A:LYS94 4.4 26.7 1.0 CG A:HIS34 4.4 23.7 1.0 NZ A:LYS94 4.5 25.6 1.0 CB A:ASP79 4.5 20.6 1.0 O A:HOH323 4.5 22.2 1.0 ND1 A:HIS34 4.5 21.9 1.0 N A:LYS94 4.5 19.6 1.0 CA A:ASP92 4.6 23.1 1.0 O A:HOH306 4.6 22.4 1.0 CD2 A:TYR93 4.8 22.9 1.0 CD A:LYS94 4.8 26.0 1.0 CG A:TYR93 4.8 19.1 1.0 CA A:LYS94 4.9 21.5 1.0

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