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Magnesium in PDB 4ufv: Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 18)

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 18)

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 18):
2.3.1.97;

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 18), PDB code: 4ufv 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) 98.88 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.480, 118.990, 177.740, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23.715

Other elements in 4ufv:

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 18) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 18) (pdb code 4ufv). 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 18), PDB code: 4ufv:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4ufv

Go back to Magnesium Binding Sites List in 4ufv
Magnesium binding site 1 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 18)


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 18) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1411

b:15.1
occ:1.00
 O2A A:NHW1000 2.8 8.3 1.0
O A:LEU169 2.9 8.9 1.0
N A:LYS172 2.9 10.2 1.0
O4A A:NHW1000 3.0 7.9 1.0
N A:LEU174 3.1 9.4 1.0
N A:ARG173 3.4 9.0 1.0
CA A:LYS172 3.5 10.3 1.0
N A:SER171 3.5 10.0 1.0
CB A:LEU174 3.6 11.9 1.0
CB A:LYS172 3.6 10.3 1.0
C A:LYS172 3.6 10.6 1.0
P1A A:NHW1000 3.7 8.2 1.0
O1A A:NHW1000 3.8 8.1 1.0
C A:ARG170 3.8 9.4 1.0
CA A:LEU174 3.9 9.6 1.0
C A:SER171 3.9 10.6 1.0
CA A:ARG170 4.0 8.6 1.0
C A:LEU169 4.0 8.9 1.0
P2A A:NHW1000 4.1 7.1 1.0
CA A:SER171 4.1 10.1 1.0
CG A:LEU174 4.1 15.3 1.0
C A:ARG173 4.1 9.5 1.0
CG1 A:VAL165 4.2 5.9 1.0
O3A A:NHW1000 4.3 7.7 1.0
CA A:ARG173 4.3 9.4 1.0
N A:ALA175 4.3 7.4 1.0
N A:ARG170 4.5 9.3 1.0
O6A A:NHW1000 4.5 7.2 1.0
O A:LYS172 4.5 9.6 1.0
CD1 A:LEU174 4.6 15.7 1.0
C A:LEU174 4.6 8.6 1.0
CG A:LYS172 4.6 10.4 1.0
O A:ARG170 4.6 10.0 1.0
CB A:VAL165 4.8 5.8 1.0
CG2 A:VAL165 4.8 5.9 1.0

Magnesium binding site 2 out of 3 in 4ufv

Go back to Magnesium Binding Sites List in 4ufv
Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 18)


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

b:22.9
occ:1.00
 O2A B:NHW1000 2.8 10.0 1.0
N B:LYS172 2.9 11.3 1.0
O B:LEU169 2.9 13.1 1.0
O4A B:NHW1000 3.0 7.0 1.0
N B:LEU174 3.0 7.8 1.0
CB B:LEU174 3.3 9.3 1.0
N B:ARG173 3.4 8.7 1.0
CA B:LYS172 3.4 11.7 1.0
C B:LYS172 3.5 10.0 1.0
CB B:LYS172 3.5 14.4 1.0
N B:SER171 3.7 11.2 1.0
CA B:LEU174 3.7 7.7 1.0
P1A B:NHW1000 3.7 9.3 1.0
CG B:LEU174 3.8 10.1 1.0
O1A B:NHW1000 4.0 10.2 1.0
C B:ARG170 4.0 10.8 1.0
CD1 B:LEU174 4.0 11.0 1.0
C B:SER171 4.0 11.2 1.0
C B:ARG173 4.1 8.0 1.0
C B:LEU169 4.1 12.2 1.0
CG1 B:VAL165 4.1 7.4 1.0
CA B:ARG170 4.1 10.3 1.0
CA B:ARG173 4.2 8.3 1.0
P2A B:NHW1000 4.2 9.2 1.0
N B:ALA175 4.3 7.1 1.0
CA B:SER171 4.3 11.7 1.0
O B:LYS172 4.3 9.6 1.0
O3A B:NHW1000 4.4 8.8 1.0
CG B:LYS172 4.5 15.9 1.0
C B:LEU174 4.5 7.8 1.0
N B:ARG170 4.6 10.8 1.0
O6A B:NHW1000 4.6 7.4 1.0
O B:ARG170 4.7 10.8 1.0
CG2 B:VAL165 4.7 7.8 1.0
CB B:VAL165 4.8 7.4 1.0

Magnesium binding site 3 out of 3 in 4ufv

Go back to Magnesium Binding Sites List in 4ufv
Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 18)


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 18) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1411

b:16.6
occ:1.00
 O C:LEU169 2.7 10.3 1.0
N C:LYS172 2.9 9.3 1.0
O2A C:NHW1000 3.1 8.4 1.0
O4A C:NHW1000 3.1 8.7 1.0
N C:LEU174 3.2 7.6 1.0
CB C:LYS172 3.4 10.8 1.0
CB C:LEU174 3.4 8.5 1.0
CA C:LYS172 3.4 10.7 1.0
N C:SER171 3.5 10.3 1.0
N C:ARG173 3.6 8.6 1.0
C C:LYS172 3.6 9.4 1.0
C C:ARG170 3.7 9.7 1.0
CG C:LEU174 3.8 9.4 1.0
C C:LEU169 3.8 10.3 1.0
CA C:ARG170 3.8 9.5 1.0
CD1 C:LEU174 3.8 9.2 1.0
CA C:LEU174 3.9 8.2 1.0
P1A C:NHW1000 4.0 9.5 1.0
CG1 C:VAL165 4.0 7.7 1.0
C C:SER171 4.0 10.5 1.0
O1A C:NHW1000 4.1 8.4 1.0
CA C:SER171 4.2 10.6 1.0
P2A C:NHW1000 4.3 8.6 1.0
C C:ARG173 4.3 8.2 1.0
N C:ARG170 4.3 10.1 1.0
CA C:ARG173 4.4 7.8 1.0
N C:ALA175 4.4 7.3 1.0
O C:LYS172 4.4 9.8 1.0
O C:ARG170 4.5 11.1 1.0
CG C:LYS172 4.5 12.8 1.0
O3A C:NHW1000 4.6 8.9 1.0
C C:LEU174 4.7 7.5 1.0
O6A C:NHW1000 4.7 8.1 1.0
CB C:VAL165 4.8 7.3 1.0
CG2 C:VAL165 4.8 7.1 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: Mon Dec 14 19:37:04 2020

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