Magnesium in PDB 4c68: Plasmodium Vivax N-Myristoyltransferase in Complex with A Peptidomimetic Inhibitor

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

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Peptidomimetic Inhibitor, PDB code: 4c68 was solved by T.O.Olaleye, J.A.Brannigan, V.Goncalves, S.M.Roberts, R.J.Leatherbarrow, A.J.Wilkinson, E.W.Tate, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.97 / 1.38
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.330, 121.430, 178.740, 90.00, 90.00, 90.00
R / Rfree (%)	21.987 / 25.989

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

Chlorine

(Cl)

5 atoms

The binding sites of Magnesium atom in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Peptidomimetic Inhibitor (pdb code 4c68). 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 Peptidomimetic Inhibitor, PDB code: 4c68:
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 Peptidomimetic 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 Peptidomimetic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1413 b:21.2 occ:1.00 O2A A:NHW1411 2.7 9.4 1.0 O4A A:NHW1411 2.8 9.7 1.0 N A:LYS172 2.9 12.3 1.0 O A:LEU169 3.0 13.4 1.0 N A:LEU174 3.1 9.8 1.0 N A:ARG173 3.3 10.6 1.0 N A:SER171 3.4 12.3 1.0 CA A:LYS172 3.5 11.7 1.0 C A:LYS172 3.5 10.5 1.0 P1A A:NHW1411 3.6 9.2 1.0 CB A:LYS172 3.6 11.7 1.0 CB A:LEU174 3.7 12.1 1.0 O1A A:NHW1411 3.8 9.9 1.0 C A:ARG170 3.8 12.4 1.0 CA A:LEU174 3.9 11.2 1.0 C A:SER171 3.9 11.3 1.0 CA A:ARG170 3.9 10.8 1.0 CG A:LEU174 4.0 12.5 1.0 CA A:SER171 4.0 11.2 1.0 CD1 A:LEU174 4.0 13.8 1.0 C A:LEU169 4.1 10.9 1.0 P2A A:NHW1411 4.1 10.1 1.0 C A:ARG173 4.1 11.5 1.0 CA A:ARG173 4.1 9.7 1.0 CG1 A:VAL165 4.1 9.2 1.0 O3A A:NHW1411 4.2 8.6 1.0 N A:ALA175 4.4 9.5 1.0 O A:LYS172 4.5 12.2 1.0 N A:ARG170 4.5 10.6 1.0 O6A A:NHW1411 4.6 8.3 1.0 CG A:LYS172 4.6 14.2 1.0 C A:LEU174 4.6 11.3 1.0 O A:ARG170 4.7 13.7 1.0 CG2 A:VAL165 4.7 8.8 1.0 CB A:VAL165 4.8 9.0 1.0

Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Peptidomimetic 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 Peptidomimetic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1413 b:21.7 occ:1.00 O B:LEU169 2.7 12.4 1.0 N B:LYS172 2.9 11.3 1.0 O2A B:NHW1411 3.0 10.9 1.0 O4A B:NHW1411 3.2 10.5 1.0 N B:LEU174 3.2 10.2 1.0 CB B:LEU174 3.3 10.4 1.0 CB B:LYS172 3.4 11.4 1.0 CA B:LYS172 3.4 11.4 1.0 N B:ARG173 3.5 10.9 1.0 N B:SER171 3.6 11.3 1.0 C B:LYS172 3.6 11.2 1.0 CD1 B:LEU174 3.8 14.7 1.0 CA B:LEU174 3.9 9.6 1.0 CG B:LEU174 3.9 10.7 1.0 P1A B:NHW1411 3.9 9.3 1.0 C B:ARG170 3.9 10.0 1.0 C B:LEU169 3.9 12.4 1.0 C B:SER171 4.0 11.6 1.0 CA B:ARG170 4.0 10.0 1.0 CG1 B:VAL165 4.0 8.8 1.0 O1A B:NHW1411 4.0 10.7 1.0 CA B:SER171 4.2 11.9 1.0 C B:ARG173 4.2 10.4 1.0 P2A B:NHW1411 4.3 9.3 1.0 CG B:LYS172 4.4 12.3 1.0 CA B:ARG173 4.4 10.0 1.0 O3A B:NHW1411 4.4 10.6 1.0 O B:LYS172 4.4 12.3 1.0 N B:ARG170 4.4 10.4 1.0 N B:ALA175 4.4 8.1 1.0 C B:LEU174 4.7 9.1 1.0 O6A B:NHW1411 4.7 9.3 1.0 O B:ARG170 4.7 10.3 1.0 CG2 B:VAL165 4.7 8.3 1.0 CB B:VAL165 4.8 8.0 1.0

Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Peptidomimetic 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 Peptidomimetic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1415 b:21.9 occ:1.00 O C:LEU169 2.9 12.4 1.0 O2A C:NHW1411 2.9 10.3 1.0 O4A C:NHW1411 2.9 11.0 1.0 N C:LYS172 3.0 14.2 1.0 N C:LEU174 3.3 10.0 1.0 N C:SER171 3.4 12.7 1.0 N C:ARG173 3.5 11.4 1.0 CA C:LYS172 3.5 12.1 1.0 C C:LYS172 3.6 11.6 1.0 CB C:LEU174 3.6 13.4 1.0 CB C:LYS172 3.7 13.0 1.0 C C:ARG170 3.7 12.2 1.0 P1A C:NHW1411 3.8 10.0 1.0 CG C:LEU174 3.9 14.0 1.0 O1A C:NHW1411 3.9 12.9 1.0 CA C:ARG170 3.9 12.2 1.0 CA C:LEU174 3.9 10.3 1.0 C C:SER171 4.0 14.5 1.0 C C:LEU169 4.0 11.9 1.0 CA C:SER171 4.1 14.9 1.0 CD1 C:LEU174 4.1 13.9 1.0 CG1 C:VAL165 4.1 11.2 1.0 P2A C:NHW1411 4.1 11.4 1.0 C C:ARG173 4.2 10.2 1.0 O C:LYS172 4.3 13.2 1.0 CA C:ARG173 4.3 11.3 1.0 O3A C:NHW1411 4.3 9.7 1.0 N C:ALA175 4.4 9.5 1.0 N C:ARG170 4.5 12.5 1.0 O C:ARG170 4.5 12.3 1.0 CG C:LYS172 4.5 16.0 1.0 O6A C:NHW1411 4.6 10.7 1.0 C C:LEU174 4.7 9.8 1.0 CB C:VAL165 4.8 11.4 1.0 CG2 C:VAL165 4.8 10.9 1.0

T.O.Olaleye, J.A.Brannigan, S.M.Roberts, R.J.Leatherbarrow, A.J.Wilkinson, E.W.Tate. Peptidomimetic Inhibitors of N-Myristoyltransferase From Human Malaria and Leishmaniasis Parasites. Org.Biomol.Chem. V. 12 8132 2014.
ISSN: ISSN 1477-0520
PubMed: 25230674
DOI: 10.1039/C4OB01669F