Magnesium in PDB 2yne: Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor:
2.3.1.97;

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor, PDB code: 2yne was solved by M.H.Wright, B.Clough, M.D.Rackham, J.A.Brannigan, M.Grainger, A.R.Bottrill, W.P.Heal, M.Broncel, R.A.Serwa, D.Mann, R.J.Leatherbarrow, A.J.Wilkinson, A.A.Holder, E.W.Tate, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.83 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.620, 121.850, 179.160, 90.00, 90.00, 90.00
R / Rfree (%)	17.347 / 21.814

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium atom in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (pdb code 2yne). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor, PDB code: 2yne:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1412 b:23.5 occ:1.00 O2A A:NHW1000 2.8 13.7 1.0 O4A A:NHW1000 2.8 14.7 1.0 O A:LEU169 2.9 16.6 1.0 N A:LYS172 2.9 15.0 1.0 N A:LEU174 3.2 14.7 1.0 N A:SER171 3.4 13.9 1.0 N A:ARG173 3.5 13.4 1.0 CA A:LYS172 3.5 15.5 1.0 CB A:LEU174 3.5 15.8 1.0 C A:LYS172 3.7 14.8 1.0 CB A:LYS172 3.7 16.5 1.0 P1A A:NHW1000 3.7 14.0 1.0 C A:ARG170 3.8 14.6 1.0 CA A:LEU174 3.9 13.5 1.0 CA A:ARG170 3.9 13.2 1.0 O1A A:NHW1000 4.0 13.9 1.0 C A:SER171 4.0 16.2 1.0 C A:LEU169 4.0 14.2 1.0 CD1 A:LEU174 4.0 20.2 1.0 CG A:LEU174 4.0 18.4 1.0 P2A A:NHW1000 4.1 13.6 1.0 CG1 A:VAL165 4.1 10.4 1.0 CA A:SER171 4.1 16.3 1.0 C A:ARG173 4.2 15.2 1.0 O3A A:NHW1000 4.3 13.9 1.0 CA A:ARG173 4.3 14.0 1.0 N A:ALA175 4.4 12.3 1.0 N A:ARG170 4.4 14.0 1.0 O A:LYS172 4.5 15.9 1.0 O6A A:NHW1000 4.6 12.4 1.0 O A:ARG170 4.6 14.1 1.0 CG A:LYS172 4.6 22.0 1.0 C A:LEU174 4.7 12.7 1.0 CG2 A:VAL165 4.8 10.8 1.0 CB A:VAL165 4.8 11.0 1.0

Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1411 b:26.5 occ:1.00 N B:LYS172 2.8 13.7 1.0 O B:LEU169 2.8 17.4 1.0 O2A B:NHW1000 2.9 13.6 1.0 O4A B:NHW1000 3.1 13.0 1.0 N B:LEU174 3.2 12.0 1.0 CB B:LYS172 3.3 15.0 1.0 CA B:LYS172 3.3 13.6 1.0 N B:ARG173 3.4 14.0 1.0 CB B:LEU174 3.4 15.2 1.0 C B:LYS172 3.5 13.2 1.0 N B:SER171 3.6 15.2 1.0 P1A B:NHW1000 3.8 13.5 1.0 C B:ARG170 3.9 15.2 1.0 C B:SER171 3.9 15.4 1.0 CG B:LEU174 3.9 16.7 1.0 CD1 B:LEU174 3.9 16.4 1.0 CA B:LEU174 3.9 12.9 1.0 C B:LEU169 4.0 15.8 1.0 O1A B:NHW1000 4.0 14.2 1.0 CA B:ARG170 4.0 14.8 1.0 CA B:SER171 4.1 15.0 1.0 C B:ARG173 4.2 13.4 1.0 CG1 B:VAL165 4.3 12.7 1.0 P2A B:NHW1000 4.3 13.6 1.0 CG B:LYS172 4.3 15.3 1.0 CA B:ARG173 4.3 12.7 1.0 O B:LYS172 4.4 14.1 1.0 N B:ALA175 4.4 12.1 1.0 O3A B:NHW1000 4.5 13.6 1.0 N B:ARG170 4.5 14.3 1.0 O B:ARG170 4.6 15.7 1.0 C B:LEU174 4.7 13.4 1.0 O6A B:NHW1000 4.7 11.0 1.0 CD B:LYS172 4.9 21.4 1.0

Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1411 b:22.7 occ:1.00 O C:LEU169 2.7 17.2 1.0 N C:LYS172 2.9 17.0 1.0 O2A C:NHW1000 2.9 16.5 1.0 O4A C:NHW1000 3.0 13.0 1.0 N C:LEU174 3.2 11.7 1.0 N C:ARG173 3.5 14.3 1.0 N C:SER171 3.5 17.6 1.0 CA C:LYS172 3.5 17.1 1.0 CB C:LEU174 3.6 15.5 1.0 C C:LYS172 3.6 17.7 1.0 CB C:LYS172 3.7 18.6 1.0 C C:ARG170 3.7 16.9 1.0 P1A C:NHW1000 3.8 14.6 1.0 C C:LEU169 3.9 16.7 1.0 CA C:ARG170 3.9 16.6 1.0 O1A C:NHW1000 3.9 16.2 1.0 CA C:LEU174 3.9 13.9 1.0 C C:SER171 4.0 18.5 1.0 CG C:LEU174 4.0 18.6 1.0 P2A C:NHW1000 4.1 14.0 1.0 CG1 C:VAL165 4.2 11.6 1.0 CA C:SER171 4.2 17.5 1.0 CD1 C:LEU174 4.2 17.9 1.0 C C:ARG173 4.2 14.2 1.0 O3A C:NHW1000 4.3 14.3 1.0 CA C:ARG173 4.4 14.7 1.0 N C:ALA175 4.4 13.3 1.0 N C:ARG170 4.4 15.2 1.0 O C:LYS172 4.4 18.4 1.0 O C:ARG170 4.5 17.6 1.0 CG C:LYS172 4.5 22.4 1.0 O6A C:NHW1000 4.6 13.9 1.0 C C:LEU174 4.7 12.9 1.0 CG2 C:VAL165 4.9 13.8 1.0 CB C:VAL165 4.9 12.8 1.0

M.H.Wright, B.Clough, M.D.Rackham, K.Rangachari, J.A.Brannigan, M.Grainger, D.K.Moss, A.R.Bottrill, W.P.Heal, M.Broncel, R.A.Serwa, D.Brady, D.Mann, R.J.Leatherbarrow, R.Tewari, A.J.Wilkinson, A.A.Holder, E.W.Tate. Validation of N-Myristoyltransferase As An Antimalarial Drug Target Using An Integrated Chemical Biology Approach. Nat.Chem. V. 6 112 2014.
ISSN: ISSN 1755-4330
PubMed: 24451586
DOI: 10.1038/NCHEM.1836