Magnesium in PDB 2ync: Plasmodium Vivax N-Myristoyltransferase in Complex with YNC12-Coa Thioester.

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with YNC12-Coa Thioester.:
2.3.1.97;

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with YNC12-Coa Thioester., PDB code: 2ync 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)	98.74 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.450, 119.050, 176.730, 90.00, 90.00, 90.00
R / Rfree (%)	15.93 / 20.263

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with YNC12-Coa Thioester. 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 YNC12-Coa Thioester. (pdb code 2ync). 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 YNC12-Coa Thioester., PDB code: 2ync:
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 YNC12-Coa Thioester.


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 YNC12-Coa Thioester. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1412 b:19.9 occ:1.00 O A:LEU169 2.8 11.7 1.0 N A:LYS172 2.9 12.7 1.0 O15 A:YNC1000 3.0 10.4 1.0 O8 A:YNC1000 3.0 10.4 1.0 N A:LEU174 3.2 9.9 1.0 N A:ARG173 3.4 11.0 1.0 CA A:LYS172 3.5 12.6 1.0 N A:SER171 3.5 12.4 1.0 CB A:LEU174 3.5 12.4 1.0 CB A:LYS172 3.6 13.7 1.0 C A:LYS172 3.6 13.9 1.0 C A:ARG170 3.8 12.7 1.0 P1 A:YNC1000 3.8 9.9 1.0 C A:SER171 3.9 13.3 1.0 C A:LEU169 3.9 11.2 1.0 CA A:LEU174 3.9 9.9 1.0 CG1 A:VAL165 4.0 10.5 1.0 CA A:ARG170 4.0 11.6 1.0 O6 A:YNC1000 4.0 9.7 1.0 CG A:LEU174 4.1 14.6 1.0 CA A:SER171 4.1 12.6 1.0 P2 A:YNC1000 4.1 11.6 1.0 C A:ARG173 4.2 11.1 1.0 CD1 A:LEU174 4.2 15.1 1.0 CA A:ARG173 4.3 10.3 1.0 N A:ALA175 4.4 8.7 1.0 N A:ARG170 4.4 11.8 1.0 O A:LYS172 4.4 13.8 1.0 O7 A:YNC1000 4.5 10.6 1.0 CG A:LYS172 4.5 15.3 1.0 O A:ARG170 4.6 13.3 1.0 O9 A:YNC1000 4.6 10.0 1.0 C A:LEU174 4.7 8.9 1.0 CB A:VAL165 4.7 8.4 1.0 CG2 A:VAL165 4.8 9.7 1.0

Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with YNC12-Coa Thioester.


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 YNC12-Coa Thioester. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1411 b:20.9 occ:1.00 O B:LEU169 2.7 11.1 1.0 O8 B:YNC1000 2.9 12.5 1.0 N B:LYS172 2.9 11.7 1.0 O15 B:YNC1000 2.9 10.3 1.0 N B:LEU174 3.3 10.2 1.0 N B:SER171 3.5 11.9 1.0 CB B:LEU174 3.5 11.6 1.0 CA B:LYS172 3.5 12.2 1.0 N B:ARG173 3.5 11.1 1.0 CB B:LYS172 3.6 15.6 1.0 C B:LYS172 3.7 11.3 1.0 C B:ARG170 3.8 12.2 1.0 P1 B:YNC1000 3.8 10.1 1.0 CG1 B:VAL165 3.9 9.0 1.0 CG B:LEU174 3.9 13.0 1.0 C B:LEU169 3.9 11.0 1.0 CA B:LEU174 3.9 10.6 1.0 C B:SER171 4.0 12.9 1.0 CA B:ARG170 4.0 10.6 1.0 O6 B:YNC1000 4.0 11.6 1.0 CD1 B:LEU174 4.0 12.9 1.0 P2 B:YNC1000 4.1 11.1 1.0 CA B:SER171 4.2 12.5 1.0 C B:ARG173 4.3 12.3 1.0 O7 B:YNC1000 4.4 10.6 1.0 CA B:ARG173 4.4 12.2 1.0 CG B:LYS172 4.4 17.7 1.0 N B:ALA175 4.4 8.8 1.0 O B:ARG170 4.4 13.9 1.0 N B:ARG170 4.4 10.7 1.0 O B:LYS172 4.5 9.9 1.0 O9 B:YNC1000 4.6 11.1 1.0 C B:LEU174 4.7 9.3 1.0 CB B:VAL165 4.8 9.5 1.0 CG2 B:VAL165 4.8 10.0 1.0 CD B:LYS172 4.9 25.9 1.0

Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with YNC12-Coa Thioester.


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 YNC12-Coa Thioester. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1411 b:19.4 occ:1.00 O C:LEU169 2.8 11.8 1.0 N C:LYS172 2.8 11.0 1.0 O15 C:YNC1000 3.0 9.7 1.0 O8 C:YNC1000 3.1 10.3 1.0 N C:LEU174 3.2 10.6 1.0 N C:SER171 3.4 12.4 1.0 CA C:LYS172 3.4 11.0 1.0 N C:ARG173 3.5 10.4 1.0 CB C:LYS172 3.5 11.8 1.0 C C:LYS172 3.6 10.4 1.0 CB C:LEU174 3.6 10.8 1.0 C C:ARG170 3.8 12.4 1.0 P1 C:YNC1000 3.8 10.7 1.0 C C:SER171 3.9 13.3 1.0 CD1 C:LEU174 3.9 13.1 1.0 C C:LEU169 3.9 11.9 1.0 CG C:LEU174 4.0 13.3 1.0 CA C:LEU174 4.0 10.3 1.0 CA C:ARG170 4.0 11.5 1.0 CG1 C:VAL165 4.1 10.9 1.0 O6 C:YNC1000 4.1 10.7 1.0 CA C:SER171 4.1 13.8 1.0 C C:ARG173 4.2 12.0 1.0 P2 C:YNC1000 4.2 11.3 1.0 CA C:ARG173 4.3 10.5 1.0 O7 C:YNC1000 4.3 11.0 1.0 CG C:LYS172 4.4 14.7 1.0 N C:ALA175 4.4 8.5 1.0 O C:LYS172 4.5 9.0 1.0 N C:ARG170 4.5 11.2 1.0 O C:ARG170 4.5 12.3 1.0 O9 C:YNC1000 4.7 9.8 1.0 C C:LEU174 4.7 9.6 1.0 CG2 C:VAL165 4.8 10.1 1.0 CB C:VAL165 4.8 8.9 1.0 CD C:LYS172 5.0 16.6 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