Magnesium in PDB 5o48: P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound

All present enzymatic activity of P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound:
2.3.1.97;

The structure of P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound, PDB code: 5o48 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)	100.67 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.565, 121.983, 178.247, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20

The structure of P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Magnesium atom in the P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound (pdb code 5o48). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound, PDB code: 5o48:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:17.8 occ:1.00 O2A A:NHW501 2.8 10.2 1.0 O A:LEU169 2.8 12.4 1.0 N A:LYS172 2.9 11.3 1.0 O5A A:NHW501 2.9 10.8 1.0 N A:LEU174 3.2 11.4 1.0 N A:ARG173 3.4 10.5 1.0 N A:SER171 3.5 11.0 1.0 CA A:LYS172 3.5 11.1 1.0 CB A:LEU174 3.6 11.4 1.0 C A:LYS172 3.6 11.5 1.0 P1A A:NHW501 3.7 11.1 1.0 CB A:LYS172 3.8 10.8 1.0 C A:ARG170 3.8 11.9 1.0 CG A:LEU174 3.9 16.5 1.0 O1A A:NHW501 3.9 11.5 1.0 CA A:LEU174 3.9 11.1 1.0 C A:SER171 3.9 13.2 1.0 CA A:ARG170 4.0 10.2 1.0 C A:LEU169 4.0 11.3 1.0 CD1 A:LEU174 4.0 17.1 1.0 P2A A:NHW501 4.1 10.3 1.0 CA A:SER171 4.1 11.8 1.0 CG1 A:VAL165 4.1 9.1 1.0 C A:ARG173 4.2 11.9 1.0 CA A:ARG173 4.3 11.6 1.0 O3A A:NHW501 4.3 10.3 1.0 N A:ALA175 4.4 9.6 1.0 N A:ARG170 4.4 9.8 1.0 O A:LYS172 4.5 13.2 1.0 O A:ARG170 4.6 11.8 1.0 O6A A:NHW501 4.6 11.7 1.0 C A:LEU174 4.7 10.3 1.0 CG A:LYS172 4.7 14.0 1.0 CG2 A:VAL165 4.7 8.0 1.0 CB A:VAL165 4.8 8.8 1.0

Magnesium binding site 2 out of 3 in the P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:22.2 occ:1.00 O B:LEU169 2.8 12.9 1.0 N B:LYS172 2.9 13.8 1.0 O2A B:NHW501 2.9 10.4 1.0 O5A B:NHW501 3.0 10.1 1.0 N B:LEU174 3.2 9.6 1.0 N B:ARG173 3.4 12.1 1.0 CB B:LEU174 3.5 11.2 1.0 CB B:LYS172 3.5 15.9 1.0 CA B:LYS172 3.5 15.0 1.0 N B:SER171 3.5 11.1 1.0 C B:LYS172 3.6 12.7 1.0 CD1 B:LEU174 3.8 14.9 1.0 C B:ARG170 3.8 12.7 1.0 P1A B:NHW501 3.8 11.3 1.0 CG B:LEU174 3.9 13.4 1.0 C B:LEU169 3.9 12.3 1.0 CA B:LEU174 3.9 10.3 1.0 C B:SER171 3.9 15.0 1.0 O1A B:NHW501 4.0 11.7 1.0 CA B:ARG170 4.0 12.1 1.0 CG1 B:VAL165 4.0 12.4 1.0 CA B:SER171 4.2 13.5 1.0 C B:ARG173 4.2 12.0 1.0 P2A B:NHW501 4.2 10.7 1.0 CG B:LYS172 4.4 18.2 1.0 O3A B:NHW501 4.4 10.1 1.0 CA B:ARG173 4.4 10.9 1.0 N B:ARG170 4.4 12.4 1.0 N B:ALA175 4.4 10.1 1.0 O B:LYS172 4.4 14.1 1.0 O B:ARG170 4.6 12.5 1.0 O6A B:NHW501 4.6 9.9 1.0 C B:LEU174 4.7 10.2 1.0 CG2 B:VAL165 4.9 10.3 1.0 CB B:VAL165 4.9 11.5 1.0

Magnesium binding site 3 out of 3 in the P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg505 b:20.6 occ:1.00 O C:LEU169 2.8 14.1 1.0 N C:LYS172 2.8 15.1 1.0 O5A C:NHW501 3.0 12.7 1.0 O2A C:NHW501 3.0 12.4 1.0 N C:LEU174 3.2 11.2 1.0 N C:ARG173 3.4 13.8 1.0 CA C:LYS172 3.5 14.9 1.0 N C:SER171 3.5 16.4 1.0 C C:LYS172 3.6 14.3 1.0 CB C:LYS172 3.6 14.8 1.0 CB C:LEU174 3.7 11.9 1.0 C C:ARG170 3.7 14.8 1.0 P1A C:NHW501 3.8 12.3 1.0 O1A C:NHW501 3.8 13.7 1.0 C C:SER171 3.9 17.0 1.0 CA C:ARG170 3.9 13.3 1.0 C C:LEU169 3.9 13.8 1.0 CA C:LEU174 3.9 10.9 1.0 CD1 C:LEU174 4.0 13.5 1.0 CG C:LEU174 4.0 12.7 1.0 CG1 C:VAL165 4.1 11.9 1.0 CA C:SER171 4.1 16.9 1.0 P2A C:NHW501 4.1 12.0 1.0 C C:ARG173 4.2 12.1 1.0 CA C:ARG173 4.3 12.6 1.0 O3A C:NHW501 4.3 10.6 1.0 N C:ALA175 4.4 10.4 1.0 N C:ARG170 4.4 13.1 1.0 O C:ARG170 4.5 14.2 1.0 O C:LYS172 4.5 15.1 1.0 CG C:LYS172 4.5 19.1 1.0 C C:LEU174 4.7 10.6 1.0 O6A C:NHW501 4.7 10.6 1.0 CB C:VAL165 4.8 12.3 1.0 CG2 C:VAL165 4.8 11.1 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