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Magnesium in PDB 4ufx: Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19)

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19)

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19):
2.3.1.97;

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19), PDB code: 4ufx was solved by Z.Yu, J.A.Brannigan, K.Rangachari, W.P.Heal, 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) 98.32 / 1.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.328, 118.891, 174.895, 90.00, 90.00, 90.00
R / Rfree (%) 15.82 / 19.664

Other elements in 4ufx:

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19) also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19) (pdb code 4ufx). 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 Pyridyl Inhibitor (Compound 19), PDB code: 4ufx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4ufx

Go back to Magnesium Binding Sites List in 4ufx
Magnesium binding site 1 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19)


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 Pyridyl Inhibitor (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1412

b:18.8
occ:1.00
 O A:LEU169 2.8 10.6 1.0
O4A A:NHW1001 2.9 9.9 1.0
O2A A:NHW1001 2.9 8.5 1.0
N A:LYS172 2.9 11.1 1.0
N A:LEU174 3.3 9.4 1.0
N A:ARG173 3.4 10.4 1.0
N A:SER171 3.5 11.8 1.0
CB A:LEU174 3.5 10.9 1.0
CA A:LYS172 3.6 11.7 1.0
C A:LYS172 3.7 11.6 1.0
CB A:LYS172 3.7 13.2 1.0
P1A A:NHW1001 3.8 9.1 1.0
C A:ARG170 3.8 12.1 1.0
O1A A:NHW1001 3.9 9.3 1.0
C A:LEU169 3.9 10.1 1.0
CA A:LEU174 3.9 9.5 1.0
CG A:LEU174 4.0 15.2 1.0
CA A:ARG170 4.0 9.9 1.0
C A:SER171 4.0 11.9 1.0
CG1 A:VAL165 4.0 10.7 1.0
P2A A:NHW1001 4.1 9.7 1.0
CD1 A:LEU174 4.1 15.3 1.0
CA A:SER171 4.1 12.2 1.0
C A:ARG173 4.2 10.1 1.0
CA A:ARG173 4.3 10.7 1.0
O3A A:NHW1001 4.3 9.5 1.0
N A:ALA175 4.4 10.6 1.0
N A:ARG170 4.4 10.0 1.0
O A:LYS172 4.5 11.7 1.0
CG A:LYS172 4.5 17.9 1.0
O A:ARG170 4.6 12.8 1.0
O6A A:NHW1001 4.6 9.1 1.0
C A:LEU174 4.7 9.9 1.0
CG2 A:VAL165 4.7 9.8 1.0
CB A:VAL165 4.7 8.9 1.0

Magnesium binding site 2 out of 3 in 4ufx

Go back to Magnesium Binding Sites List in 4ufx
Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19)


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 Pyridyl Inhibitor (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1412

b:17.7
occ:1.00
 O B:LEU169 2.8 12.8 1.0
N B:LYS172 2.9 10.9 1.0
O2A B:NHW1001 2.9 9.8 1.0
O4A B:NHW1001 3.0 9.3 1.0
N B:LEU174 3.2 9.2 1.0
N B:ARG173 3.4 10.1 1.0
CA B:LYS172 3.4 10.4 1.0
CB B:LEU174 3.5 10.7 1.0
N B:SER171 3.5 11.5 1.0
C B:LYS172 3.5 10.4 1.0
CB B:LYS172 3.5 12.2 1.0
CG B:LEU174 3.8 12.4 1.0
C B:ARG170 3.8 11.4 1.0
P1A B:NHW1001 3.8 9.2 1.0
CA B:LEU174 3.9 9.5 1.0
CG1 B:VAL165 3.9 10.3 1.0
CD1 B:LEU174 4.0 15.0 1.0
C B:LEU169 4.0 11.0 1.0
C B:SER171 4.0 12.5 1.0
O1A B:NHW1001 4.0 9.1 1.0
CA B:ARG170 4.0 9.8 1.0
C B:ARG173 4.2 10.0 1.0
P2A B:NHW1001 4.2 9.9 1.0
CA B:SER171 4.2 12.0 1.0
CA B:ARG173 4.3 10.0 1.0
O B:LYS172 4.3 11.5 1.0
O3A B:NHW1001 4.4 9.5 1.0
CG B:LYS172 4.4 17.5 1.0
N B:ALA175 4.4 8.2 1.0
N B:ARG170 4.5 11.0 1.0
O B:ARG170 4.5 14.3 1.0
O6A B:NHW1001 4.7 9.8 1.0
C B:LEU174 4.7 9.0 1.0
CB B:VAL165 4.8 10.6 1.0
CG2 B:VAL165 4.8 10.3 1.0

Magnesium binding site 3 out of 3 in 4ufx

Go back to Magnesium Binding Sites List in 4ufx
Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 19)


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 Pyridyl Inhibitor (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1411

b:16.9
occ:1.00
 O C:LEU169 2.7 10.4 1.0
N C:LYS172 2.8 10.7 1.0
O2A C:NHW1001 2.9 9.2 1.0
O4A C:NHW1001 3.0 9.9 1.0
N C:LEU174 3.2 8.6 1.0
N C:ARG173 3.4 9.9 1.0
N C:SER171 3.4 10.3 1.0
CA C:LYS172 3.5 10.7 1.0
C C:LYS172 3.6 10.5 1.0
CB C:LYS172 3.6 12.4 1.0
CB C:LEU174 3.6 9.0 1.0
P1A C:NHW1001 3.8 8.9 1.0
C C:ARG170 3.8 10.7 1.0
CG C:LEU174 3.9 11.6 1.0
C C:SER171 3.9 10.9 1.0
C C:LEU169 3.9 9.8 1.0
CA C:LEU174 3.9 8.4 1.0
O1A C:NHW1001 4.0 9.8 1.0
CD1 C:LEU174 4.0 13.0 1.0
CA C:ARG170 4.0 10.3 1.0
CG1 C:VAL165 4.1 9.7 1.0
CA C:SER171 4.1 11.2 1.0
C C:ARG173 4.2 8.9 1.0
P2A C:NHW1001 4.2 8.9 1.0
CA C:ARG173 4.3 9.2 1.0
CG C:LYS172 4.4 15.1 1.0
O3A C:NHW1001 4.4 9.5 1.0
O C:LYS172 4.4 12.4 1.0
N C:ALA175 4.4 7.5 1.0
N C:ARG170 4.4 9.8 1.0
O C:ARG170 4.5 11.0 1.0
O6A C:NHW1001 4.6 8.1 1.0
C C:LEU174 4.7 7.8 1.0
CB C:VAL165 4.9 8.0 1.0
CG2 C:VAL165 4.9 8.3 1.0

Reference:

Z.Yu, J.A.Brannigan, K.Rangachari, W.P.Heal, A.J.Wilkinson, A.A.Holder, R.J.Leatherbarrow, E.W.Tate. Discovery of Pyridyl-Based Inhibitors of Plasmodium Falciparum N-Myristoyltransferase Medchemcomm V. 6 1767 2015.
ISSN: ISSN 2040-2503
PubMed: 26962430
DOI: 10.1039/C5MD00242G
Page generated: Tue Aug 20 04:43:02 2024

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