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Magnesium in PDB 4caf: Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A)

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A)

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A):
2.3.1.97;

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A), PDB code: 4caf was solved by M.D.Rackham, J.A.Brannigan, K.Rangachari, 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) 100.19 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.460, 121.100, 178.380, 90.00, 90.00, 90.00
R / Rfree (%) 15.961 / 20.495

Other elements in 4caf:

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A) 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 Benzothiophene Inhibitor (Compound 34A) (pdb code 4caf). 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 Benzothiophene Inhibitor (Compound 34A), PDB code: 4caf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4caf

Go back to Magnesium Binding Sites List in 4caf
Magnesium binding site 1 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A)


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 Benzothiophene Inhibitor (Compound 34A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1415

b:21.7
occ:1.00
 O A:LEU169 2.8 13.5 1.0
N A:LYS172 2.8 13.8 1.0
O2A A:NHW1422 2.9 12.0 1.0
O4A A:NHW1422 3.0 13.3 1.0
N A:LEU174 3.2 12.9 1.0
N A:ARG173 3.4 11.9 1.0
CA A:LYS172 3.5 14.9 1.0
N A:SER171 3.5 13.9 1.0
CB A:LEU174 3.5 16.8 1.0
CB A:LYS172 3.5 15.6 1.0
C A:LYS172 3.6 13.8 1.0
P1A A:NHW1422 3.7 12.5 1.0
C A:ARG170 3.8 14.4 1.0
C A:SER171 3.9 16.0 1.0
O1A A:NHW1422 3.9 13.0 1.0
CA A:LEU174 3.9 14.5 1.0
C A:LEU169 3.9 13.4 1.0
CA A:ARG170 3.9 13.5 1.0
CD1 A:LEU174 4.0 21.8 1.0
CG A:LEU174 4.0 21.1 1.0
P2A A:NHW1422 4.1 12.8 1.0
CA A:SER171 4.1 15.2 1.0
CG1 A:VAL165 4.1 10.4 1.0
C A:ARG173 4.2 14.0 1.0
CA A:ARG173 4.2 11.6 1.0
O3A A:NHW1422 4.3 12.1 1.0
N A:ALA175 4.4 11.8 1.0
CG A:LYS172 4.4 18.3 1.0
N A:ARG170 4.4 12.4 1.0
O A:LYS172 4.5 15.0 1.0
O A:ARG170 4.6 13.3 1.0
O6A A:NHW1422 4.6 12.5 1.0
C A:LEU174 4.7 12.8 1.0
CG2 A:VAL165 4.8 10.2 1.0
CB A:VAL165 4.9 10.5 1.0

Magnesium binding site 2 out of 3 in 4caf

Go back to Magnesium Binding Sites List in 4caf
Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A)


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 Benzothiophene Inhibitor (Compound 34A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1414

b:22.5
occ:1.00
 O2A B:NHW1422 2.8 12.8 1.0
O B:LEU169 2.9 15.5 1.0
N B:LYS172 2.9 13.5 1.0
O4A B:NHW1422 3.0 12.6 1.0
N B:LEU174 3.2 11.9 1.0
CB B:LEU174 3.4 14.6 1.0
N B:ARG173 3.4 13.5 1.0
CA B:LYS172 3.5 15.2 1.0
N B:SER171 3.5 14.0 1.0
CB B:LYS172 3.6 16.1 1.0
C B:LYS172 3.6 14.6 1.0
P1A B:NHW1422 3.7 12.6 1.0
C B:ARG170 3.9 16.2 1.0
CA B:LEU174 3.9 12.0 1.0
CG B:LEU174 3.9 15.2 1.0
O1A B:NHW1422 3.9 13.3 1.0
CD1 B:LEU174 3.9 16.0 1.0
C B:SER171 4.0 15.0 1.0
CA B:ARG170 4.0 16.0 1.0
C B:LEU169 4.0 14.6 1.0
CG1 B:VAL165 4.1 11.2 1.0
CA B:SER171 4.1 13.8 1.0
P2A B:NHW1422 4.1 12.1 1.0
C B:ARG173 4.2 13.5 1.0
CA B:ARG173 4.3 13.2 1.0
N B:ALA175 4.3 12.6 1.0
O3A B:NHW1422 4.4 12.8 1.0
O B:LYS172 4.4 13.0 1.0
CG B:LYS172 4.5 18.5 1.0
N B:ARG170 4.5 13.9 1.0
O6A B:NHW1422 4.6 11.4 1.0
O B:ARG170 4.6 15.8 1.0
C B:LEU174 4.6 13.6 1.0
CG2 B:VAL165 4.8 11.1 1.0
CB B:VAL165 4.8 12.0 1.0

Magnesium binding site 3 out of 3 in 4caf

Go back to Magnesium Binding Sites List in 4caf
Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 34A)


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 Benzothiophene Inhibitor (Compound 34A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1413

b:22.9
occ:1.00
 O C:LEU169 2.7 14.8 1.0
N C:LYS172 2.9 16.2 1.0
O4A C:NHW1422 3.0 12.6 1.0
O2A C:NHW1422 3.0 14.8 1.0
N C:LEU174 3.2 11.9 1.0
N C:ARG173 3.4 14.2 1.0
N C:SER171 3.5 17.6 1.0
CA C:LYS172 3.5 16.2 1.0
CB C:LEU174 3.5 14.5 1.0
C C:LYS172 3.5 18.2 1.0
CB C:LYS172 3.6 17.6 1.0
C C:ARG170 3.8 15.6 1.0
P1A C:NHW1422 3.8 13.7 1.0
C C:LEU169 3.8 14.3 1.0
CG C:LEU174 3.9 17.8 1.0
CA C:LEU174 3.9 13.1 1.0
CA C:ARG170 3.9 14.4 1.0
O1A C:NHW1422 3.9 13.8 1.0
C C:SER171 4.0 18.4 1.0
CD1 C:LEU174 4.1 17.8 1.0
CG1 C:VAL165 4.1 12.6 1.0
P2A C:NHW1422 4.1 13.7 1.0
CA C:SER171 4.2 18.2 1.0
C C:ARG173 4.2 14.5 1.0
CA C:ARG173 4.3 15.2 1.0
O C:LYS172 4.4 17.2 1.0
O3A C:NHW1422 4.4 12.6 1.0
N C:ARG170 4.4 13.3 1.0
N C:ALA175 4.4 12.5 1.0
CG C:LYS172 4.5 21.1 1.0
O C:ARG170 4.5 16.5 1.0
O6A C:NHW1422 4.6 11.8 1.0
C C:LEU174 4.7 12.6 1.0
CB C:VAL165 4.8 13.4 1.0
CG2 C:VAL165 4.9 13.3 1.0

Reference:

M.D.Rackham, J.A.Brannigan, K.Rangachari, S.Meister, A.J.Wilkinson, A.A.Holder, R.J.Leatherbarrow, E.W.Tate. Design and Synthesis of High Affinity Inhibitors of Plasmodium Falciparum and Plasmodium Vivax N- Myristoyltransferases Directed By Ligand Efficiency Dependent Lipophilicity (Lelp). J.Med.Chem. V. 57 2773 2014.
ISSN: ISSN 0022-2623
PubMed: 24641010
DOI: 10.1021/JM500066B
Page generated: Mon Dec 14 09:17:07 2020

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