Sodium in PDB 7t7h: Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Inhibitor CP100356

The structure of Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Inhibitor CP100356, PDB code: 7t7h was solved by J.K.Peters, J.D.Gross, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.77 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.77, 82.77, 96.31, 90, 90, 90
R / Rfree (%)	18.7 / 21.9

The binding sites of Sodium atom in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Inhibitor CP100356 (pdb code 7t7h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Inhibitor CP100356, PDB code: 7t7h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Inhibitor CP100356


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Inhibitor CP100356 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:37.3 occ:1.00 O A:HOH422 2.8 39.2 1.0 N A:TYR81 2.9 24.5 1.0 O A:HOH414 3.0 47.3 1.0 O A:HOH467 3.5 27.5 1.0 CB A:TYR81 3.5 25.7 1.0 O A:HOH509 3.7 60.9 1.0 CA A:TYR80 3.8 23.6 1.0 CA A:TYR81 3.8 26.4 1.0 CB A:TYR80 3.8 24.5 1.0 C A:TYR80 3.8 23.9 1.0 CD1 A:TYR80 3.9 23.7 1.0 O A:HOH415 4.4 53.6 1.0 CG A:TYR80 4.4 23.6 1.0 NH1 A:ARG185 4.5 29.6 1.0 O A:PHE103 4.6 25.6 1.0 OD1 A:ASP100 4.6 28.6 1.0 N A:ASN82 4.7 25.1 1.0 C A:TYR81 4.8 27.4 1.0 O A:TYR80 5.0 24.3 1.0 CG A:TYR81 5.0 26.3 1.0 CE1 A:TYR80 5.0 25.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Inhibitor CP100356


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Inhibitor CP100356 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:143.7 occ:1.00 N A:GLU200 2.6 25.4 1.0 O A:ASP197 2.9 27.4 1.0 O A:HOH457 2.9 29.6 1.0 CG A:GLU200 3.0 45.5 1.0 N A:TYR199 3.0 23.2 1.0 C A:ASP197 3.4 27.8 1.0 C A:TYR199 3.5 24.5 1.0 CB A:GLU200 3.5 31.9 1.0 CA A:TYR199 3.5 26.3 1.0 O A:ASP196 3.5 27.2 1.0 CA A:GLU200 3.6 28.2 1.0 O A:HOH453 3.6 40.6 1.0 CB A:TYR199 3.7 25.0 1.0 C A:LYS198 3.7 23.9 1.0 CA A:ASP197 4.0 27.8 1.0 N A:LYS198 4.0 26.4 1.0 CD A:GLU200 4.1 51.6 1.0 O A:HOH472 4.1 34.7 1.0 CA A:LYS198 4.2 25.6 1.0 OE2 A:GLU200 4.3 55.6 1.0 O A:LYS198 4.4 24.5 1.0 C A:ASP196 4.6 27.9 1.0 O A:HOH484 4.6 45.6 1.0 O A:TYR199 4.7 27.1 1.0 C A:GLU200 4.7 26.5 1.0 N A:TYR201 4.7 25.0 1.0 CG A:TYR199 4.8 22.1 1.0 N A:ASP197 4.8 26.9 1.0 CD2 A:TYR199 4.8 25.4 1.0

M.Bednarczyk, J.K.Peters, R.Kasprzyk, J.Starek, M.Warminski, T.Spiewla, J.S.Mugridge, J.D.Gross, J.Jemielity, J.Kowalska. Fluorescence-Based Activity Screening Assay Reveals Small Molecule Inhibitors of Vaccinia Virus Mrna Decapping Enzyme D9. Acs Chem.Biol. V. 17 1460 2022.
ISSN: ESSN 1554-8937
PubMed: 35576528
DOI: 10.1021/ACSCHEMBIO.2C00049