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Magnesium in PDB 5g1z: Plasmodium Vivax N-Myristoyltransferase in Complex with A Quinoline Inhibitor (Compound 1)

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Quinoline Inhibitor (Compound 1)

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Quinoline Inhibitor (Compound 1):
2.3.1.97;

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Quinoline Inhibitor (Compound 1), PDB code: 5g1z was solved by V.Goncalves, J.A.Brannigan, A.Laporte, A.S.Bell, S.M.Roberts, A.J.Wilkinson, R.J.Leatherbarrow, E.W.Tate, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.45 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.400, 118.900, 175.300, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 18.7

Other elements in 5g1z:

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Quinoline Inhibitor (Compound 1) 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 Quinoline Inhibitor (Compound 1) (pdb code 5g1z). 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 Quinoline Inhibitor (Compound 1), PDB code: 5g1z:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5g1z

Go back to Magnesium Binding Sites List in 5g1z
Magnesium binding site 1 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Quinoline Inhibitor (Compound 1)


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 Quinoline Inhibitor (Compound 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1412

b:23.9
occ:1.00
 O A:LEU169 2.8 16.4 1.0
N A:LYS172 2.9 15.3 1.0
O1A A:NHW1000 3.0 13.4 1.0
O4A A:NHW1000 3.0 14.0 1.0
N A:LEU174 3.1 13.8 1.0
N A:ARG173 3.4 13.6 1.0
CA A:LYS172 3.5 15.8 1.0
N A:SER171 3.5 15.6 1.0
CB A:LEU174 3.5 16.0 1.0
CB A:LYS172 3.5 16.2 1.0
C A:LYS172 3.6 15.2 1.0
P1A A:NHW1000 3.8 13.6 1.0
C A:ARG170 3.8 15.8 1.0
CG A:LEU174 3.9 18.2 1.0
CA A:LEU174 3.9 14.3 1.0
C A:SER171 3.9 16.4 1.0
C A:LEU169 4.0 14.4 1.0
CA A:ARG170 4.0 14.4 1.0
O2A A:NHW1000 4.0 13.4 1.0
CD1 A:LEU174 4.0 20.8 1.0
CG1 A:VAL165 4.1 14.4 1.0
C A:ARG173 4.1 15.0 1.0
P2A A:NHW1000 4.2 13.9 1.0
CA A:SER171 4.2 16.1 1.0
CA A:ARG173 4.2 15.4 1.0
N A:ALA175 4.3 12.3 1.0
O3A A:NHW1000 4.4 13.8 1.0
N A:ARG170 4.4 13.8 1.0
CG A:LYS172 4.4 19.2 1.0
O A:LYS172 4.4 16.6 1.0
O A:ARG170 4.6 18.2 1.0
C A:LEU174 4.6 13.3 1.0
O6A A:NHW1000 4.7 12.9 1.0
CB A:VAL165 4.8 11.0 1.0
CG2 A:VAL165 4.9 14.1 1.0

Magnesium binding site 2 out of 3 in 5g1z

Go back to Magnesium Binding Sites List in 5g1z
Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Quinoline Inhibitor (Compound 1)


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 Quinoline Inhibitor (Compound 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1412

b:22.6
occ:1.00
 O B:LEU169 2.8 16.6 1.0
N B:LYS172 2.9 14.3 1.0
O4A B:NHW1000 3.0 15.1 1.0
O1A B:NHW1000 3.0 14.0 1.0
N B:LEU174 3.2 13.3 1.0
N B:ARG173 3.5 14.7 1.0
CA B:LYS172 3.5 18.3 1.0
N B:SER171 3.5 15.9 1.0
CB B:LEU174 3.6 15.8 1.0
CB B:LYS172 3.6 19.6 1.0
C B:LYS172 3.6 16.7 1.0
P1A B:NHW1000 3.8 14.6 1.0
C B:ARG170 3.8 16.8 1.0
CA B:LEU174 3.9 15.2 1.0
CG B:LEU174 3.9 19.6 1.0
C B:LEU169 4.0 15.6 1.0
CA B:ARG170 4.0 15.3 1.0
C B:SER171 4.0 18.5 1.0
O2A B:NHW1000 4.0 15.5 1.0
CG1 B:VAL165 4.0 15.8 1.0
CD1 B:LEU174 4.1 23.5 1.0
P2A B:NHW1000 4.1 15.0 1.0
C B:ARG173 4.2 14.4 1.0
CA B:SER171 4.2 16.4 1.0
CA B:ARG173 4.3 15.9 1.0
N B:ALA175 4.3 13.1 1.0
O3A B:NHW1000 4.4 15.2 1.0
N B:ARG170 4.4 16.1 1.0
O B:LYS172 4.4 17.2 1.0
CG B:LYS172 4.5 22.7 1.0
O B:ARG170 4.6 18.7 1.0
C B:LEU174 4.6 13.6 1.0
O6A B:NHW1000 4.6 14.0 1.0
CG2 B:VAL165 4.8 13.0 1.0
CB B:VAL165 4.9 14.6 1.0

Magnesium binding site 3 out of 3 in 5g1z

Go back to Magnesium Binding Sites List in 5g1z
Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Quinoline Inhibitor (Compound 1)


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 Quinoline Inhibitor (Compound 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1413

b:21.8
occ:1.00
 O C:LEU169 2.8 16.7 1.0
N C:LYS172 2.9 16.1 1.0
O2A C:NHW1000 2.9 14.9 1.0
O4A C:NHW1000 3.0 13.5 1.0
N C:LEU174 3.1 13.6 1.0
N C:ARG173 3.4 15.1 1.0
N C:SER171 3.4 14.9 1.0
CA C:LYS172 3.5 16.3 1.0
CB C:LYS172 3.6 16.9 1.0
C C:LYS172 3.6 16.6 1.0
CB C:LEU174 3.6 14.7 1.0
P1A C:NHW1000 3.7 13.1 1.0
C C:ARG170 3.8 15.5 1.0
CG C:LEU174 3.9 17.3 1.0
CA C:LEU174 3.9 13.9 1.0
C C:LEU169 3.9 13.8 1.0
O1A C:NHW1000 3.9 14.2 1.0
C C:SER171 3.9 17.3 1.0
CA C:ARG170 3.9 14.4 1.0
CD1 C:LEU174 4.0 19.4 1.0
CA C:SER171 4.1 15.5 1.0
C C:ARG173 4.1 16.1 1.0
P2A C:NHW1000 4.1 14.1 1.0
CG1 C:VAL165 4.1 13.5 1.0
CA C:ARG173 4.2 14.9 1.0
O3A C:NHW1000 4.3 14.5 1.0
CG C:LYS172 4.4 19.4 1.0
N C:ALA175 4.4 11.6 1.0
N C:ARG170 4.4 13.8 1.0
O C:LYS172 4.5 16.0 1.0
O C:ARG170 4.6 18.6 1.0
C C:LEU174 4.6 13.3 1.0
O6A C:NHW1000 4.7 13.6 1.0
CG2 C:VAL165 4.9 13.9 1.0
CB C:VAL165 4.9 12.3 1.0

Reference:

V.Goncalves, J.A.Brannigan, A.Laporte, A.S.Bell, S.M.Roberts, A.J.Wilkinson, R.J.Leatherbarrow, E.W.Tate. Structure-Guided Optimization of Quinoline Inhibitors of Plasmodium N-Myristoyltransferase. Medchemcomm V. 8 191 2017.
ISSN: ISSN 2040-2503
PubMed: 28626547
DOI: 10.1039/C6MD00531D
Page generated: Mon Dec 14 20:20:16 2020

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