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Magnesium in PDB 2ynd: Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor.

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor.

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

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor., PDB code: 2ynd 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) 59.60 / 1.89
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 (%) 16.768 / 22.316

Other elements in 2ynd:

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

Chlorine (Cl) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide Inhibitor. (pdb code 2ynd). 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 Pyrazole Sulphonamide Inhibitor., PDB code: 2ynd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 2ynd

Go back to Magnesium Binding Sites List in 2ynd
Magnesium binding site 1 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide 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 Pyrazole Sulphonamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1415

b:25.5
occ:1.00
O A:LEU169 2.8 15.7 1.0
O2A A:NHW1000 2.8 11.2 1.0
N A:LYS172 2.9 13.8 1.0
O4A A:NHW1000 3.0 14.4 1.0
N A:LEU174 3.1 13.6 1.0
N A:ARG173 3.4 13.4 1.0
N A:SER171 3.5 13.8 1.0
CA A:LYS172 3.5 14.6 1.0
CB A:LYS172 3.5 15.8 1.0
C A:LYS172 3.6 15.4 1.0
CB A:LEU174 3.7 15.4 1.0
C A:ARG170 3.8 14.0 1.0
P1A A:NHW1000 3.8 12.0 1.0
O1A A:NHW1000 3.9 10.9 1.0
C A:LEU169 3.9 13.8 1.0
CA A:ARG170 3.9 14.3 1.0
CA A:LEU174 3.9 14.8 1.0
C A:SER171 4.0 13.5 1.0
C A:ARG173 4.1 14.2 1.0
CG1 A:VAL165 4.1 13.3 1.0
P2A A:NHW1000 4.1 14.3 1.0
CA A:SER171 4.2 12.8 1.0
CG A:LEU174 4.2 16.9 1.0
CD1 A:LEU174 4.2 17.3 1.0
CA A:ARG173 4.2 13.0 1.0
O A:LYS172 4.3 16.6 1.0
N A:ARG170 4.4 13.3 1.0
O3A A:NHW1000 4.4 12.6 1.0
N A:ALA175 4.5 14.3 1.0
CG A:LYS172 4.5 17.6 1.0
O A:ARG170 4.5 14.3 1.0
O6A A:NHW1000 4.6 13.0 1.0
C A:LEU174 4.7 13.8 1.0
CB A:VAL165 4.9 13.5 1.0

Magnesium binding site 2 out of 3 in 2ynd

Go back to Magnesium Binding Sites List in 2ynd
Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide 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 Pyrazole Sulphonamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1414

b:24.8
occ:1.00
N B:LYS172 2.8 13.5 1.0
O B:LEU169 2.8 13.0 1.0
O2A B:NHW1000 3.0 13.6 1.0
O4A B:NHW1000 3.0 12.0 1.0
CA B:LYS172 3.3 14.4 1.0
N B:LEU174 3.3 15.7 1.0
CB B:LYS172 3.4 16.5 1.0
N B:ARG173 3.4 13.9 1.0
N B:SER171 3.4 14.8 1.0
C B:LYS172 3.5 13.1 1.0
CB B:LEU174 3.6 17.2 1.0
P1A B:NHW1000 3.7 13.9 1.0
C B:ARG170 3.7 14.7 1.0
C B:SER171 3.9 14.4 1.0
C B:LEU169 3.9 14.6 1.0
O1A B:NHW1000 3.9 14.7 1.0
CD1 B:LEU174 3.9 19.0 1.0
CA B:ARG170 3.9 14.1 1.0
CA B:LEU174 4.0 15.6 1.0
CG B:LEU174 4.0 18.2 1.0
CG1 B:VAL165 4.1 16.3 1.0
CA B:SER171 4.1 14.2 1.0
P2A B:NHW1000 4.2 12.9 1.0
O3A B:NHW1000 4.3 12.9 1.0
CG B:LYS172 4.3 18.3 1.0
C B:ARG173 4.3 15.3 1.0
N B:ARG170 4.4 14.9 1.0
CA B:ARG173 4.4 14.2 1.0
O B:LYS172 4.4 12.6 1.0
O B:ARG170 4.4 14.8 1.0
N B:ALA175 4.5 14.4 1.0
O6A B:NHW1000 4.6 12.5 1.0
C B:LEU174 4.8 15.3 1.0
CB B:VAL165 4.9 17.5 1.0
CD B:LYS172 4.9 22.5 1.0
CG2 B:VAL165 5.0 16.6 1.0

Magnesium binding site 3 out of 3 in 2ynd

Go back to Magnesium Binding Sites List in 2ynd
Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyrazole Sulphonamide 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 Pyrazole Sulphonamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1414

b:22.6
occ:1.00
O C:LEU169 2.7 18.4 1.0
N C:LYS172 2.8 15.3 1.0
O2A C:NHW1000 2.9 15.5 1.0
O4A C:NHW1000 3.0 16.2 1.0
N C:LEU174 3.2 13.7 1.0
N C:SER171 3.4 15.9 1.0
CA C:LYS172 3.4 15.3 1.0
N C:ARG173 3.5 14.2 1.0
CB C:LYS172 3.5 16.0 1.0
C C:LYS172 3.6 15.7 1.0
C C:ARG170 3.7 17.1 1.0
CB C:LEU174 3.7 13.8 1.0
P1A C:NHW1000 3.8 15.4 1.0
C C:SER171 3.8 16.2 1.0
C C:LEU169 3.9 18.4 1.0
CA C:ARG170 3.9 16.6 1.0
CD1 C:LEU174 4.0 15.6 1.0
CA C:SER171 4.0 15.1 1.0
O1A C:NHW1000 4.0 15.4 1.0
CA C:LEU174 4.0 12.7 1.0
CG1 C:VAL165 4.1 13.7 1.0
CG C:LEU174 4.1 15.9 1.0
C C:ARG173 4.2 13.2 1.0
P2A C:NHW1000 4.2 17.2 1.0
O C:ARG170 4.3 15.7 1.0
CA C:ARG173 4.4 15.0 1.0
CG C:LYS172 4.4 19.0 1.0
N C:ARG170 4.4 16.1 1.0
O3A C:NHW1000 4.4 15.8 1.0
O C:LYS172 4.5 14.6 1.0
N C:ALA175 4.6 12.0 1.0
O6A C:NHW1000 4.7 14.4 1.0
CD C:LYS172 4.8 20.2 1.0
C C:LEU174 4.9 11.7 1.0
CB C:VAL165 4.9 13.3 1.0
O C:SER171 5.0 16.7 1.0
CG2 C:VAL165 5.0 11.9 1.0

Reference:

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
Page generated: Mon Dec 14 07:49:11 2020

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