Magnesium in PDB 5o6j: Human NMT1 in Complex with Myristoyl-Coa and Inhibitor Imp-1031

All present enzymatic activity of Human NMT1 in Complex with Myristoyl-Coa and Inhibitor Imp-1031:
2.3.1.97;

The structure of Human NMT1 in Complex with Myristoyl-Coa and Inhibitor Imp-1031, PDB code: 5o6j 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)	80.00 / 1.45
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.918, 177.285, 58.298, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 24.4

The structure of Human NMT1 in Complex with Myristoyl-Coa and Inhibitor Imp-1031 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-1031 (pdb code 5o6j). 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-1031, PDB code: 5o6j:
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-1031


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-1031 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2005 b:29.2 occ:1.00 O A:LEU254 2.6 20.7 1.0 O1A A:MYA2001 2.9 16.3 1.0 O5A A:MYA2001 3.0 18.2 1.0 N A:LYS257 3.0 21.6 1.0 N A:VAL259 3.2 16.4 1.0 N A:ARG258 3.4 20.3 1.0 N A:SER256 3.5 17.2 1.0 CB A:VAL259 3.5 16.4 1.0 CA A:LYS257 3.6 19.8 1.0 C A:LYS257 3.6 21.2 1.0 CB A:LYS257 3.7 20.0 1.0 CG2 A:VAL259 3.7 21.3 1.0 C A:ARG255 3.7 18.0 1.0 C A:LEU254 3.7 16.1 1.0 P1A A:MYA2001 3.7 17.5 1.0 CA A:ARG255 3.8 16.6 1.0 CA A:VAL259 3.9 14.4 1.0 O2A A:MYA2001 3.9 16.3 1.0 CG1 A:VAL250 4.0 13.2 1.0 C A:SER256 4.1 22.1 1.0 P2A A:MYA2001 4.1 16.6 1.0 C A:ARG258 4.2 21.0 1.0 CA A:SER256 4.2 22.7 1.0 N A:ARG255 4.2 18.0 1.0 CA A:ARG258 4.2 20.2 1.0 N A:ALA260 4.3 15.2 1.0 O A:LYS257 4.4 23.5 1.0 O3A A:MYA2001 4.4 17.3 1.0 O A:ARG255 4.4 21.2 1.0 C A:VAL259 4.6 15.8 1.0 CG A:LYS257 4.6 23.3 1.0 O6A A:MYA2001 4.7 16.3 1.0 CG2 A:VAL250 4.8 14.5 1.0 CG1 A:VAL259 4.8 15.3 1.0 CB A:VAL250 4.8 13.0 1.0 CA A:LEU254 5.0 21.7 1.0

Magnesium binding site 2 out of 2 in the Human NMT1 in Complex with Myristoyl-Coa and Inhibitor Imp-1031


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-1031 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2005 b:25.5 occ:1.00 O B:LEU254 2.8 19.7 1.0 O1A B:MYA2001 2.8 14.4 1.0 O5A B:MYA2001 2.9 16.7 1.0 N B:LYS257 3.0 21.9 1.0 N B:VAL259 3.2 16.8 1.0 N B:ARG258 3.4 19.6 1.0 N B:SER256 3.4 17.2 1.0 CB B:VAL259 3.5 16.8 1.0 C B:LYS257 3.5 20.6 1.0 CG2 B:VAL259 3.6 20.9 1.0 CA B:LYS257 3.6 20.3 1.0 P1A B:MYA2001 3.7 15.8 1.0 O2A B:MYA2001 3.7 16.7 1.0 C B:ARG255 3.8 19.0 1.0 CA B:VAL259 3.8 14.8 1.0 CB B:LYS257 3.8 22.6 1.0 C B:LEU254 3.9 17.2 1.0 C B:SER256 4.0 23.7 1.0 CA B:ARG255 4.0 18.7 1.0 CG1 B:VAL250 4.0 13.0 1.0 P2A B:MYA2001 4.0 17.3 1.0 CA B:SER256 4.1 22.8 1.0 C B:ARG258 4.1 19.9 1.0 CA B:ARG258 4.1 20.4 1.0 N B:ALA260 4.2 11.9 1.0 O3A B:MYA2001 4.3 16.5 1.0 O B:LYS257 4.3 20.4 1.0 N B:ARG255 4.4 18.3 1.0 O B:ARG255 4.5 20.1 1.0 C B:VAL259 4.6 14.7 1.0 O6A B:MYA2001 4.6 15.1 1.0 CG2 B:VAL250 4.8 13.7 1.0 CG B:LYS257 4.8 24.0 1.0 CB B:VAL250 4.8 13.5 1.0 CG1 B:VAL259 4.8 16.4 1.0 CG B:LEU254 4.9 19.3 0.5

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