Manganese in PDB 7ex4: Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 5

All present enzymatic activity of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 5:
2.7.7.48;

The structure of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 5, PDB code: 7ex4 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)	35.41 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.933, 70.566, 70.882, 90, 90, 90
R / Rfree (%)	20.5 / 23.6

The structure of Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 5 also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Bromine	(Br)	1 atom

The binding sites of Manganese atom in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 5 (pdb code 7ex4). 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 5, PDB code: 7ex4:
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 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:34.3 occ:0.77 O9 A:IA5203 2.0 26.9 1.0 OD1 A:ASP79 2.1 24.2 1.0 O6 A:IA5203 2.1 29.4 1.0 OD1 A:ASN52 2.1 22.1 1.0 O A:HOH304 2.1 24.4 1.0 O A:HOH332 2.3 23.8 1.0 C8 A:IA5203 3.0 28.3 1.0 CG A:ASN52 3.1 28.2 1.0 C5 A:IA5203 3.1 28.2 1.0 CG A:ASP79 3.3 22.3 1.0 ND2 A:ASN52 3.4 28.4 1.0 C7 A:IA5203 3.4 28.1 1.0 OD1 A:ASN51 3.8 28.8 1.0 OD2 A:ASP79 3.9 21.5 1.0 MN A:MN202 4.0 19.9 1.0 O A:HOH379 4.1 43.0 1.0 O A:THR77 4.3 24.0 1.0 CE1 A:HIS34 4.3 23.0 1.0 CA A:ASP79 4.3 22.1 1.0 C10 A:IA5203 4.3 28.4 1.0 OD1 A:ASP92 4.3 25.6 1.0 CB A:ASP79 4.4 19.6 1.0 CB A:ASN52 4.4 24.3 1.0 C3 A:IA5203 4.5 29.9 1.0 N A:ASP79 4.5 22.0 1.0 NE2 A:HIS34 4.5 23.6 1.0 O A:HOH315 4.6 24.2 1.0 C19 A:IA5203 4.7 32.6 1.0 C18 A:IA5203 4.7 27.1 1.0 N A:ASN52 4.8 24.7 1.0 CA A:ASN52 4.8 25.0 1.0 O A:HOH319 4.8 38.2 1.0 O2 A:IA5203 4.8 30.5 1.0 C11 A:IA5203 4.9 28.8 1.0 OD2 A:ASP92 5.0 27.4 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Ebinur Lake Virus Cap Snatching Endonuclease in Complex with Inhibitor 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:19.9 occ:0.96 OD2 A:ASP79 2.2 21.5 1.0 C1 A:IA5203 2.2 26.2 1.0 OD2 A:ASP92 2.3 27.4 1.0 O2 A:IA5203 2.4 30.5 1.0 O A:TYR93 2.4 20.4 1.0 NE2 A:HIS34 2.4 23.6 1.0 O6 A:IA5203 2.4 29.4 1.0 CG A:ASP79 3.1 22.3 1.0 CG A:ASP92 3.2 26.2 1.0 C3 A:IA5203 3.2 29.9 1.0 C5 A:IA5203 3.2 28.2 1.0 CD2 A:HIS34 3.3 22.1 1.0 OD1 A:ASP79 3.3 24.2 1.0 CE1 A:HIS34 3.4 23.0 1.0 C A:TYR93 3.4 23.4 1.0 N A:TYR93 3.6 23.7 1.0 OD1 A:ASP92 3.6 25.6 1.0 O A:HOH319 3.7 38.2 1.0 CA A:TYR93 3.9 23.0 1.0 MN A:MN201 4.0 34.3 0.8 CB A:TYR93 4.2 24.2 1.0 O4 A:IA5203 4.3 34.8 1.0 C A:ASP92 4.3 24.9 1.0 CB A:ASP92 4.3 23.7 1.0 CG A:HIS34 4.4 22.3 1.0 ND1 A:HIS34 4.5 19.5 1.0 CB A:ASP79 4.5 19.6 1.0 O A:HOH332 4.5 23.8 1.0 C7 A:IA5203 4.5 28.1 1.0 NZ A:LYS94 4.5 26.3 1.0 N A:LYS94 4.6 21.7 1.0 CA A:ASP92 4.6 23.3 1.0 CE A:LYS94 4.7 26.5 1.0 O A:HOH304 4.7 24.4 1.0 CD2 A:TYR93 4.8 22.2 1.0 CG A:TYR93 4.8 23.2 1.0 CD A:LYS94 4.8 26.2 1.0 CA A:LYS94 5.0 20.2 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