Magnesium in PDB 5o6h: Human NMT1 in Complex with Myristoyl-Coa and Inhibitor Imp-917

All present enzymatic activity of Human NMT1 in Complex with Myristoyl-Coa and Inhibitor Imp-917:
2.3.1.97;

The structure of Human NMT1 in Complex with Myristoyl-Coa and Inhibitor Imp-917, PDB code: 5o6h was solved by J.A.Brannigan, A.J.Wilkinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.00 / 1.29
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.138, 178.852, 58.465, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.3

The structure of Human NMT1 in Complex with Myristoyl-Coa and Inhibitor Imp-917 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Magnesium atom in the Human NMT1 in Complex with Myristoyl-Coa and Inhibitor Imp-917 (pdb code 5o6h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human NMT1 in Complex with Myristoyl-Coa and Inhibitor Imp-917, PDB code: 5o6h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human NMT1 in Complex with Myristoyl-Coa and Inhibitor Imp-917


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human NMT1 in Complex with Myristoyl-Coa and Inhibitor Imp-917 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2006 b:21.6 occ:1.00 O A:LEU254 2.8 15.7 1.0 O1A A:MYA2001 2.9 12.8 1.0 N A:LYS257 3.0 17.1 1.0 O5A A:MYA2001 3.0 13.5 1.0 N A:VAL259 3.2 13.8 1.0 N A:ARG258 3.3 17.0 1.0 N A:SER256 3.5 16.4 1.0 CB A:VAL259 3.5 14.2 1.0 C A:LYS257 3.5 16.8 1.0 CA A:LYS257 3.6 15.8 1.0 CB A:LYS257 3.6 17.8 1.0 CG2 A:VAL259 3.6 18.0 1.0 C A:ARG255 3.7 16.9 1.0 P1A A:MYA2001 3.8 12.7 1.0 CA A:VAL259 3.9 13.2 1.0 C A:LEU254 3.9 15.5 1.0 O2A A:MYA2001 3.9 14.1 1.0 CA A:ARG255 3.9 15.4 1.0 C A:SER256 4.0 17.1 1.0 CG1 A:VAL250 4.0 13.0 1.0 C A:ARG258 4.1 16.7 1.0 P2A A:MYA2001 4.1 13.1 1.0 CA A:ARG258 4.2 17.7 1.0 CA A:SER256 4.2 16.3 1.0 N A:ALA260 4.3 11.8 1.0 O A:LYS257 4.3 19.0 1.0 N A:ARG255 4.4 14.7 1.0 O3A A:MYA2001 4.4 13.0 1.0 CG A:LYS257 4.5 21.9 1.0 O A:ARG255 4.6 18.3 1.0 C A:VAL259 4.6 13.4 1.0 O6A A:MYA2001 4.7 12.3 1.0 CG1 A:VAL259 4.9 15.8 1.0 CB A:VAL250 4.9 11.0 1.0 CG2 A:VAL250 4.9 11.5 1.0

Magnesium binding site 2 out of 2 in the Human NMT1 in Complex with Myristoyl-Coa and Inhibitor Imp-917


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human NMT1 in Complex with Myristoyl-Coa and Inhibitor Imp-917 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2008 b:20.3 occ:1.00 O B:LEU254 2.8 13.1 1.0 O1A B:MYA2001 2.9 11.4 1.0 N B:LYS257 2.9 14.6 1.0 O5A B:MYA2001 3.1 12.0 1.0 N B:VAL259 3.2 12.4 1.0 N B:ARG258 3.3 13.7 1.0 C B:LYS257 3.5 14.7 1.0 N B:SER256 3.5 14.3 1.0 CA B:LYS257 3.5 13.8 1.0 CB B:VAL259 3.5 12.1 1.0 CG2 B:VAL259 3.6 15.8 1.0 CB B:LYS257 3.7 16.1 1.0 C B:ARG255 3.8 13.8 1.0 P1A B:MYA2001 3.8 11.6 1.0 O2A B:MYA2001 3.8 12.6 1.0 CA B:VAL259 3.9 13.0 1.0 C B:LEU254 3.9 13.7 1.0 C B:SER256 4.0 15.4 1.0 CG1 B:VAL250 4.0 12.5 1.0 CA B:ARG255 4.0 12.9 1.0 C B:ARG258 4.1 14.6 1.0 CA B:SER256 4.2 14.9 1.0 CA B:ARG258 4.2 13.8 1.0 P2A B:MYA2001 4.2 11.7 1.0 O B:LYS257 4.3 16.0 1.0 N B:ALA260 4.3 12.1 1.0 O3A B:MYA2001 4.4 11.4 1.0 N B:ARG255 4.5 13.6 1.0 CG B:LYS257 4.6 19.6 1.0 O B:ARG255 4.6 15.8 1.0 C B:VAL259 4.6 10.8 1.0 O6A B:MYA2001 4.7 11.3 1.0 CG2 B:VAL250 4.8 11.0 1.0 CB B:VAL250 4.8 10.4 1.0 CG B:LEU254 4.9 10.9 0.5 CG1 B:VAL259 4.9 14.2 1.0

A.Mousnier, A.S.Bell, D.P.Swieboda, J.Morales-Sanfrutos, I.Perez-Dorado, J.A.Brannigan, J.Newman, M.Ritzefeld, J.A.Hutton, A.Guedan, A.S.Asfor, S.W.Robinson, I.Hopkins-Navratilova, A.J.Wilkinson, S.L.Johnston, R.J.Leatherbarrow, T.J.Tuthill, R.Solari, E.W.Tate. Fragment-Derived Inhibitors of Human N-Myristoyltransferase Block Capsid Assembly and Replication of the Common Cold Virus. Nat Chem V. 10 599 2018.
ISSN: ESSN 1755-4349
PubMed: 29760414
DOI: 10.1038/S41557-018-0039-2