Magnesium in PDB 5mu6: Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound

All present enzymatic activity of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound:
2.3.1.97;

The structure of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound, PDB code: 5mu6 was solved by I.Perez-Dorado, A.S.Bell, E.W.Tate, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.18 / 1.88
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.730, 180.730, 58.990, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.7

The structure of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Magnesium atom in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound (pdb code 5mu6). 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 N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound, PDB code: 5mu6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:22.8 occ:1.00 O A:LEU254 2.5 16.3 1.0 N A:LYS257 2.8 17.7 1.0 O4A A:MYA501 2.9 14.5 1.0 O2A A:MYA501 3.0 16.0 1.0 N A:SER256 3.2 15.0 1.0 N A:VAL259 3.4 13.0 1.0 CA A:LYS257 3.5 14.9 1.0 N A:ARG258 3.5 15.7 1.0 C A:ARG255 3.5 12.9 1.0 C A:LYS257 3.6 15.9 1.0 C A:LEU254 3.6 11.1 1.0 CA A:ARG255 3.7 11.6 1.0 CB A:VAL259 3.7 12.3 1.0 CB A:LYS257 3.7 14.6 1.0 CG2 A:VAL259 3.8 16.6 1.0 C A:SER256 3.8 12.4 1.0 P1A A:MYA501 3.9 14.7 1.0 O1A A:MYA501 4.0 15.3 1.0 CA A:SER256 4.0 12.5 1.0 CA A:VAL259 4.1 11.0 1.0 N A:ARG255 4.1 11.5 1.0 P2A A:MYA501 4.2 10.2 1.0 CG1 A:VAL250 4.2 10.2 1.0 O A:ARG255 4.2 16.4 1.0 O A:LYS257 4.3 17.7 1.0 CA A:ARG258 4.3 17.3 1.0 C A:ARG258 4.3 14.5 1.0 O3A A:MYA501 4.5 13.1 1.0 CG A:LYS257 4.5 17.3 1.0 N A:ALA260 4.6 12.5 1.0 O6A A:MYA501 4.7 12.2 1.0 CA A:LEU254 4.9 11.3 1.0 C A:VAL259 4.9 14.6 1.0 CB A:LEU254 4.9 10.4 1.0 CG1 A:VAL259 5.0 13.4 1.0 O A:SER256 5.0 15.3 1.0

Magnesium binding site 2 out of 2 in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Imp-1088 Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:21.4 occ:1.00 O B:LEU254 2.6 16.1 1.0 N B:LYS257 2.9 18.8 1.0 O2A B:MYA501 3.0 12.4 1.0 O4A B:MYA501 3.1 10.7 1.0 N B:VAL259 3.2 13.3 1.0 CB B:VAL259 3.4 11.0 1.0 N B:SER256 3.5 15.2 1.0 CA B:LYS257 3.5 13.1 1.0 CG2 B:VAL259 3.5 14.6 1.0 N B:ARG258 3.5 16.5 1.0 C B:LYS257 3.6 14.4 1.0 CB B:LYS257 3.6 13.2 1.0 C B:LEU254 3.7 14.4 1.0 C B:ARG255 3.7 15.1 1.0 CA B:ARG255 3.8 10.6 1.0 CA B:VAL259 3.9 11.8 1.0 CG1 B:VAL250 4.0 13.3 1.0 C B:SER256 4.0 13.7 1.0 P1A B:MYA501 4.0 16.5 1.0 CA B:SER256 4.2 17.3 1.0 O1A B:MYA501 4.2 18.7 1.0 N B:ARG255 4.2 12.8 1.0 C B:ARG258 4.3 11.2 1.0 CG B:LYS257 4.3 18.0 1.0 P2A B:MYA501 4.3 11.6 1.0 O B:LYS257 4.3 18.2 1.0 CA B:ARG258 4.4 15.5 1.0 O B:ARG255 4.5 16.6 1.0 N B:ALA260 4.5 9.5 1.0 O3A B:MYA501 4.7 14.8 1.0 C B:VAL259 4.8 13.4 1.0 CG2 B:VAL250 4.8 7.3 1.0 CG1 B:VAL259 4.8 11.6 1.0 CB B:VAL250 4.8 11.6 1.0 O6A B:MYA501 4.8 12.0 1.0 CA B:LEU254 4.9 12.2 1.0 CB B:LEU254 5.0 15.1 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