Magnesium in PDB 4b10: Plasmodium Vivax N-Myristoyltransferase with A Non- Hydrolysable Co-Factor

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase with A Non- Hydrolysable Co-Factor:
2.3.1.97;

The structure of Plasmodium Vivax N-Myristoyltransferase with A Non- Hydrolysable Co-Factor, PDB code: 4b10 was solved by Z.Yu, J.A.Brannigan, D.K.Moss, A.M.Brzozowski, A.J.Wilkinson, A.A.Holder, E.W.Tate, R.J.Leatherbarrow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.83 / 1.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.370, 119.060, 176.400, 90.00, 90.00, 90.00
R / Rfree (%)	18.811 / 23.83

The structure of Plasmodium Vivax N-Myristoyltransferase with A Non- Hydrolysable Co-Factor also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Plasmodium Vivax N-Myristoyltransferase with A Non- Hydrolysable Co-Factor (pdb code 4b10). 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 with A Non- Hydrolysable Co-Factor, PDB code: 4b10:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Plasmodium Vivax N-Myristoyltransferase with A Non- Hydrolysable Co-Factor


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 with A Non- Hydrolysable Co-Factor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1412 b:16.2 occ:1.00 O A:LEU169 2.7 10.7 1.0 N A:LYS172 2.9 10.6 1.0 O2A A:NHW1000 3.0 7.3 1.0 O4A A:NHW1000 3.0 9.1 1.0 N A:LEU174 3.2 9.2 1.0 N A:ARG173 3.5 9.5 1.0 CB A:LYS172 3.5 11.1 1.0 N A:SER171 3.5 12.4 1.0 CA A:LYS172 3.5 10.9 1.0 CB A:LEU174 3.6 11.3 1.0 C A:LYS172 3.6 11.0 1.0 C A:ARG170 3.9 12.0 1.0 C A:LEU169 3.9 11.2 1.0 CA A:LEU174 3.9 10.0 1.0 CD1 A:LEU174 3.9 14.7 1.0 CG1 A:VAL165 3.9 7.0 1.0 P1A A:NHW1000 3.9 8.4 1.0 O1A A:NHW1000 3.9 9.9 1.0 CA A:ARG170 4.0 11.0 1.0 CG A:LEU174 4.0 13.4 1.0 C A:SER171 4.1 12.2 1.0 C A:ARG173 4.2 9.8 1.0 P2A A:NHW1000 4.2 9.1 1.0 CA A:SER171 4.2 12.3 1.0 CA A:ARG173 4.4 9.0 1.0 CG A:LYS172 4.4 12.1 1.0 O3A A:NHW1000 4.4 8.7 1.0 N A:ARG170 4.4 10.5 1.0 N A:ALA175 4.4 8.0 1.0 O A:LYS172 4.4 11.5 1.0 O A:ARG170 4.6 12.9 1.0 C A:LEU174 4.7 8.8 1.0 CB A:VAL165 4.7 7.6 1.0 CG2 A:VAL165 4.7 7.9 1.0 O6A A:NHW1000 4.8 9.2 1.0 CD A:LYS172 4.9 11.3 1.0

Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase with A Non- Hydrolysable Co-Factor


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 with A Non- Hydrolysable Co-Factor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1413 b:19.9 occ:1.00 O B:LEU169 2.7 11.8 1.0 O2A B:NHW1000 2.9 10.1 1.0 O4A B:NHW1000 2.9 9.1 1.0 N B:LYS172 2.9 12.2 1.0 N B:LEU174 3.2 9.8 1.0 N B:SER171 3.5 12.5 1.0 N B:ARG173 3.5 11.7 1.0 CA B:LYS172 3.5 13.3 1.0 CB B:LEU174 3.5 11.5 1.0 CB B:LYS172 3.6 15.6 1.0 C B:LYS172 3.6 12.1 1.0 P1A B:NHW1000 3.7 10.0 1.0 C B:ARG170 3.8 13.9 1.0 O1A B:NHW1000 3.8 10.7 1.0 CD1 B:LEU174 3.8 13.7 1.0 C B:LEU169 3.9 12.4 1.0 CA B:LEU174 3.9 9.9 1.0 CA B:ARG170 4.0 12.3 1.0 CG B:LEU174 4.0 12.4 1.0 C B:SER171 4.0 13.8 1.0 CG1 B:VAL165 4.1 10.6 1.0 P2A B:NHW1000 4.1 10.7 1.0 CA B:SER171 4.1 13.6 1.0 O3A B:NHW1000 4.3 9.6 1.0 C B:ARG173 4.3 10.5 1.0 CA B:ARG173 4.4 10.8 1.0 N B:ARG170 4.4 12.3 1.0 N B:ALA175 4.4 8.2 1.0 CG B:LYS172 4.5 16.8 1.0 O B:LYS172 4.5 13.4 1.0 O B:ARG170 4.5 15.4 1.0 O6A B:NHW1000 4.6 11.0 1.0 CG2 B:VAL165 4.7 9.8 1.0 C B:LEU174 4.7 9.4 1.0 CB B:VAL165 4.8 10.7 1.0

Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase with A Non- Hydrolysable Co-Factor


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 with A Non- Hydrolysable Co-Factor within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1412 b:19.4 occ:1.00 O C:LEU169 2.7 15.1 1.0 N C:LYS172 2.9 12.3 1.0 O2A C:NHW1000 2.9 9.7 1.0 O4A C:NHW1000 3.0 10.1 1.0 N C:LEU174 3.2 9.3 1.0 N C:SER171 3.4 13.3 1.0 CA C:LYS172 3.4 13.0 1.0 N C:ARG173 3.5 9.7 1.0 CB C:LEU174 3.5 10.8 1.0 CB C:LYS172 3.5 13.0 1.0 C C:LYS172 3.5 11.1 1.0 C C:ARG170 3.7 13.1 1.0 P1A C:NHW1000 3.8 10.3 1.0 C C:LEU169 3.8 12.8 1.0 CA C:ARG170 3.8 12.6 1.0 CG C:LEU174 3.8 12.0 1.0 CD1 C:LEU174 3.9 12.3 1.0 CA C:LEU174 3.9 9.1 1.0 C C:SER171 4.0 14.7 1.0 O1A C:NHW1000 4.0 11.0 1.0 CG1 C:VAL165 4.1 10.0 1.0 CA C:SER171 4.1 13.9 1.0 C C:ARG173 4.2 9.4 1.0 P2A C:NHW1000 4.2 9.1 1.0 N C:ARG170 4.3 12.0 1.0 CA C:ARG173 4.3 9.1 1.0 O C:LYS172 4.4 12.5 1.0 CG C:LYS172 4.4 15.6 1.0 N C:ALA175 4.4 7.4 1.0 O3A C:NHW1000 4.4 10.0 1.0 O C:ARG170 4.5 15.6 1.0 O6A C:NHW1000 4.7 9.1 1.0 C C:LEU174 4.7 7.9 1.0 CB C:VAL165 4.9 9.1 1.0 CG2 C:VAL165 4.9 9.6 1.0 CD C:LYS172 5.0 18.0 1.0

Z.Yu, J.A.Brannigan, D.K.Moss, A.M.Brzozowski, A.J.Wilkinson, A.A.Holder, E.W.Tate, R.J.Leatherbarrow. Design and Synthesis of Inhibitors of Plasmodium Falciparum N-Myristoyltransferase, A Promising Target For Anti- Malarial Drug Discovery. J.Med.Chem. V. 55 8879 2012.
ISSN: ISSN 0022-2623
PubMed: 23035716
DOI: 10.1021/JM301160H