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Magnesium in PDB 4ufw: Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22):
2.3.1.97;

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22), PDB code: 4ufw 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) 100.73 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.520, 121.910, 178.800, 90.00, 90.00, 90.00
R / Rfree (%) 21.444 / 26.101

Other elements in 4ufw:

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22) 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 22) (pdb code 4ufw). 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 22), PDB code: 4ufw:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4ufw

Go back to Magnesium Binding Sites List in 4ufw
Magnesium binding site 1 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)


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 22) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1413

b:22.1
occ:1.00
 O2A A:NHW1000 2.7 11.2 1.0
O4A A:NHW1000 2.8 11.4 1.0
O A:LEU169 2.9 15.4 1.0
N A:LYS172 3.0 15.3 1.0
N A:LEU174 3.2 12.6 1.0
N A:SER171 3.3 14.0 1.0
N A:ARG173 3.4 12.5 1.0
CA A:LYS172 3.6 14.7 1.0
C A:LYS172 3.6 13.7 1.0
P1A A:NHW1000 3.6 13.1 1.0
CB A:LEU174 3.7 15.0 1.0
CB A:LYS172 3.7 15.6 1.0
C A:ARG170 3.8 15.6 1.0
O1A A:NHW1000 3.8 13.7 1.0
CA A:ARG170 3.9 12.8 1.0
CA A:LEU174 3.9 12.7 1.0
C A:LEU169 4.0 14.9 1.0
C A:SER171 4.0 16.8 1.0
P2A A:NHW1000 4.0 13.4 1.0
CA A:SER171 4.1 13.9 1.0
CG A:LEU174 4.1 18.0 1.0
CG1 A:VAL165 4.1 9.0 1.0
C A:ARG173 4.2 14.0 1.0
O3A A:NHW1000 4.2 11.7 1.0
CD1 A:LEU174 4.3 20.0 1.0
CA A:ARG173 4.3 13.3 1.0
N A:ALA175 4.4 11.0 1.0
N A:ARG170 4.4 13.1 1.0
O A:LYS172 4.5 15.2 1.0
O6A A:NHW1000 4.5 13.0 1.0
CG A:LYS172 4.6 17.9 1.0
O A:ARG170 4.7 15.0 1.0
C A:LEU174 4.7 11.6 1.0
CG2 A:VAL165 4.7 10.5 1.0
CB A:VAL165 4.8 9.5 1.0

Magnesium binding site 2 out of 3 in 4ufw

Go back to Magnesium Binding Sites List in 4ufw
Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)


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 22) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1412

b:27.4
occ:1.00
 O B:LEU169 2.7 14.9 1.0
O2A B:NHW1000 2.8 12.4 1.0
N B:LYS172 2.9 16.2 1.0
O5A B:NHW1000 3.1 13.8 1.0
N B:LEU174 3.2 12.9 1.0
N B:ARG173 3.5 16.9 1.0
CB B:LEU174 3.5 14.1 1.0
CA B:LYS172 3.5 15.0 1.0
CB B:LYS172 3.6 15.1 1.0
N B:SER171 3.6 13.8 1.0
C B:LYS172 3.6 16.4 1.0
P1A B:NHW1000 3.8 11.8 1.0
CG B:LEU174 3.8 15.5 1.0
CD1 B:LEU174 3.9 17.3 1.0
C B:LEU169 3.9 14.2 1.0
CG1 B:VAL165 3.9 14.7 1.0
CA B:LEU174 3.9 14.0 1.0
C B:ARG170 3.9 16.4 1.0
CA B:ARG170 4.0 14.1 1.0
C B:SER171 4.0 16.3 1.0
O1A B:NHW1000 4.1 14.6 1.0
CA B:SER171 4.2 17.0 1.0
P2A B:NHW1000 4.2 12.5 1.0
C B:ARG173 4.3 14.7 1.0
O B:LYS172 4.4 18.1 1.0
N B:ARG170 4.4 13.4 1.0
N B:ALA175 4.4 13.0 1.0
CA B:ARG173 4.4 12.5 1.0
O3A B:NHW1000 4.4 13.1 1.0
CG B:LYS172 4.5 15.6 1.0
O6A B:NHW1000 4.7 11.8 1.0
O B:ARG170 4.7 17.0 1.0
CG2 B:VAL165 4.7 13.3 1.0
C B:LEU174 4.7 14.2 1.0
CB B:VAL165 4.8 12.8 1.0

Magnesium binding site 3 out of 3 in 4ufw

Go back to Magnesium Binding Sites List in 4ufw
Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)


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 22) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1412

b:22.4
occ:1.00
 O C:LEU169 2.9 12.8 1.0
N C:LYS172 2.9 16.7 1.0
O2A C:NHW1000 3.0 12.9 1.0
O4A C:NHW1000 3.0 12.2 1.0
N C:LEU174 3.1 12.1 1.0
N C:ARG173 3.3 14.0 1.0
CA C:LYS172 3.5 15.9 1.0
C C:LYS172 3.5 14.6 1.0
N C:SER171 3.5 18.5 1.0
CB C:LEU174 3.6 13.4 1.0
CB C:LYS172 3.7 17.8 1.0
P1A C:NHW1000 3.7 12.5 1.0
O1A C:NHW1000 3.7 14.6 1.0
C C:ARG170 3.8 14.8 1.0
CA C:LEU174 3.8 12.2 1.0
CG C:LEU174 3.9 14.4 1.0
C C:SER171 4.0 17.7 1.0
CA C:ARG170 4.0 14.5 1.0
C C:LEU169 4.0 14.0 1.0
C C:ARG173 4.1 12.4 1.0
CG1 C:VAL165 4.1 13.0 1.0
CA C:SER171 4.1 16.8 1.0
P2A C:NHW1000 4.1 13.8 1.0
CA C:ARG173 4.2 12.9 1.0
CD1 C:LEU174 4.2 13.7 1.0
O3A C:NHW1000 4.3 12.7 1.0
N C:ALA175 4.3 11.7 1.0
O C:LYS172 4.4 14.8 1.0
O C:ARG170 4.5 15.1 1.0
N C:ARG170 4.5 13.7 1.0
O6A C:NHW1000 4.5 12.6 1.0
C C:LEU174 4.6 13.2 1.0
CG C:LYS172 4.7 20.4 1.0
CB C:VAL165 4.9 13.5 1.0
CG2 C:VAL165 4.9 14.3 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 04:42:20 2024

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