Manganese in PDB 7ex9: 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;

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

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

Chlorine

(Cl)

4 atoms

The binding sites of Manganese 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 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 28, PDB code: 7ex9:
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 28


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 28 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:21.9 occ:0.68 O9 A:U28203 1.9 21.3 1.0 O6 A:U28203 2.0 15.0 1.0 OD1 A:ASP79 2.0 14.5 1.0 OD1 A:ASN52 2.2 17.7 1.0 O A:HOH304 2.2 17.1 1.0 O A:HOH359 2.2 16.8 1.0 C08 A:U28203 3.0 23.5 1.0 C5 A:U28203 3.1 22.4 1.0 CG A:ASP79 3.1 16.7 1.0 CG A:ASN52 3.2 20.4 1.0 C7 A:U28203 3.5 22.4 1.0 ND2 A:ASN52 3.6 22.7 1.0 OD2 A:ASP79 3.7 13.9 1.0 MN A:MN202 3.8 14.7 1.0 OD1 A:ASN51 3.8 27.4 1.0 OD1 A:ASP92 4.2 17.2 1.0 CE1 A:HIS34 4.2 14.3 1.0 CA A:ASP79 4.2 13.6 1.0 CB A:ASP79 4.3 13.3 1.0 O A:THR77 4.3 17.4 1.0 C10 A:U28203 4.4 30.4 1.0 NE2 A:HIS34 4.4 14.4 1.0 N A:ASP79 4.4 14.3 1.0 C3 A:U28203 4.4 22.8 1.0 CB A:ASN52 4.5 15.9 1.0 O A:HOH367 4.6 28.8 1.0 C13 A:U28203 4.7 31.9 1.0 OD2 A:ASP92 4.7 17.7 1.0 C14 A:U28203 4.7 37.5 1.0 O2 A:U28203 4.7 17.7 1.0 CA A:ASN52 4.8 16.7 1.0 CG A:ASP92 4.8 18.9 1.0 N A:ASN52 4.8 15.9 1.0 O A:HOH374 4.9 30.7 1.0 C A:PRO78 5.0 14.5 1.0

Manganese binding site 2 out of 2 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 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 28 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:14.7 occ:1.00 O2 A:U28203 2.1 17.7 1.0 OD2 A:ASP79 2.2 13.9 1.0 OD2 A:ASP92 2.2 17.7 1.0 O A:TYR93 2.3 13.8 1.0 NE2 A:HIS34 2.3 14.4 1.0 O6 A:U28203 2.4 15.0 1.0 C1 A:U28203 3.0 26.9 0.2 C3 A:U28203 3.1 22.8 1.0 CG A:ASP79 3.1 16.7 1.0 CG A:ASP92 3.1 18.9 1.0 C5 A:U28203 3.2 22.4 1.0 CD2 A:HIS34 3.2 14.8 1.0 CE1 A:HIS34 3.3 14.3 1.0 OD1 A:ASP79 3.4 14.5 1.0 C A:TYR93 3.4 14.7 1.0 N A:TYR93 3.5 13.8 1.0 OD1 A:ASP92 3.6 17.2 1.0 MN A:MN201 3.8 21.9 0.7 CA A:TYR93 3.9 13.2 1.0 O A:HOH374 4.0 30.7 1.0 O4 A:U28203 4.2 28.0 1.0 CB A:ASP92 4.2 14.8 1.0 CB A:TYR93 4.2 14.4 1.0 C A:ASP92 4.2 14.5 1.0 O A:HOH359 4.3 16.8 1.0 NZ A:LYS94 4.3 21.7 1.0 ND1 A:HIS34 4.4 15.4 1.0 CG A:HIS34 4.4 16.4 1.0 CB A:ASP79 4.5 13.3 1.0 CA A:ASP92 4.5 13.5 1.0 C7 A:U28203 4.5 22.4 1.0 CE A:LYS94 4.5 19.4 1.0 N A:LYS94 4.5 15.2 1.0 O A:HOH304 4.7 17.1 1.0 CD A:LYS94 4.8 21.1 1.0 CG A:TYR93 4.8 14.4 1.0 CD2 A:TYR93 4.8 13.2 1.0 CA A:LYS94 5.0 15.4 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