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Magnesium in PDB 4cae: Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 20B)

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 20B)

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 20B):
2.3.1.97;

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 20B), PDB code: 4cae 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) 100.22 / 1.46
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.501, 121.054, 178.677, 90.00, 90.00, 90.00
R / Rfree (%) 21.492 / 25.426

Other elements in 4cae:

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 20B) also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 20B) (pdb code 4cae). 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 20B), PDB code: 4cae:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4cae

Go back to Magnesium Binding Sites List in 4cae
Magnesium binding site 1 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 20B)


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 20B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1411

b:22.0
occ:1.00
 O A:LEU169 2.8 14.4 1.0
N A:LYS172 2.9 16.5 1.0
O4A A:NHW1422 2.9 12.7 1.0
O2A A:NHW1422 2.9 14.9 1.0
N A:LEU174 3.3 14.3 1.0
N A:SER171 3.4 12.6 1.0
N A:ARG173 3.4 14.2 1.0
CA A:LYS172 3.5 15.4 1.0
C A:LYS172 3.6 14.8 1.0
CB A:LEU174 3.7 15.6 1.0
C A:ARG170 3.7 14.3 1.0
P1A A:NHW1422 3.8 14.5 1.0
CB A:LYS172 3.8 16.5 1.0
CA A:ARG170 3.9 12.5 1.0
C A:LEU169 3.9 13.1 1.0
CG A:LEU174 3.9 17.0 1.0
O1A A:NHW1422 3.9 15.9 1.0
CD1 A:LEU174 3.9 18.2 1.0
C A:SER171 3.9 16.9 1.0
CA A:LEU174 4.0 13.6 1.0
CG1 A:VAL165 4.0 13.3 1.0
P2A A:NHW1422 4.1 12.6 1.0
CA A:SER171 4.1 15.7 1.0
C A:ARG173 4.2 14.8 1.0
CA A:ARG173 4.3 15.3 1.0
O3A A:NHW1422 4.3 13.2 1.0
N A:ARG170 4.4 12.3 1.0
N A:ALA175 4.4 12.4 1.0
O A:ARG170 4.5 15.7 1.0
O A:LYS172 4.5 14.1 1.0
O6A A:NHW1422 4.6 13.3 1.0
CG A:LYS172 4.7 19.4 1.0
CB A:VAL165 4.8 14.0 1.0
C A:LEU174 4.8 13.0 1.0
CG2 A:VAL165 4.8 13.6 1.0

Magnesium binding site 2 out of 3 in 4cae

Go back to Magnesium Binding Sites List in 4cae
Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 20B)


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 20B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1412

b:21.5
occ:1.00
 O B:LEU169 2.8 14.2 1.0
N B:LYS172 2.8 13.1 1.0
O2A B:NHW1422 2.9 10.8 1.0
O4A B:NHW1422 2.9 10.6 1.0
N B:LEU174 3.2 11.5 1.0
N B:SER171 3.4 12.6 1.0
CA B:LYS172 3.5 13.8 1.0
N B:ARG173 3.5 12.8 1.0
CB B:LYS172 3.5 15.4 1.0
CB B:LEU174 3.6 12.3 1.0
C B:LYS172 3.7 13.0 1.0
P1A B:NHW1422 3.8 11.2 1.0
C B:ARG170 3.8 13.6 1.0
C B:SER171 3.9 15.0 1.0
C B:LEU169 3.9 13.2 1.0
CG B:LEU174 3.9 13.7 1.0
CA B:ARG170 3.9 13.3 1.0
CA B:LEU174 3.9 11.2 1.0
CG1 B:VAL165 3.9 11.8 1.0
O1A B:NHW1422 4.0 11.0 1.0
CD1 B:LEU174 4.0 14.6 1.0
P2A B:NHW1422 4.1 10.5 1.0
CA B:SER171 4.1 15.0 1.0
C B:ARG173 4.2 11.7 1.0
CA B:ARG173 4.3 13.9 1.0
O3A B:NHW1422 4.4 10.5 1.0
N B:ARG170 4.4 12.7 1.0
N B:ALA175 4.5 10.4 1.0
CG B:LYS172 4.5 16.8 1.0
O B:LYS172 4.5 12.4 1.0
O6A B:NHW1422 4.6 10.0 1.0
O B:ARG170 4.6 13.4 1.0
C B:LEU174 4.7 11.2 1.0
CB B:VAL165 4.8 10.9 1.0
CG2 B:VAL165 4.8 11.6 1.0

Magnesium binding site 3 out of 3 in 4cae

Go back to Magnesium Binding Sites List in 4cae
Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (Compound 20B)


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 20B) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1411

b:20.1
occ:1.00
 O C:LEU169 2.9 11.1 1.0
O2A C:NHW1422 2.9 12.5 1.0
N C:LYS172 3.0 16.1 1.0
O4A C:NHW1422 3.0 11.1 1.0
N C:LEU174 3.2 11.4 1.0
N C:ARG173 3.4 12.2 1.0
CB C:LEU174 3.5 11.7 1.0
CA C:LYS172 3.5 13.7 1.0
N C:SER171 3.6 15.0 1.0
C C:LYS172 3.6 14.3 1.0
CB C:LYS172 3.6 15.5 1.0
P1A C:NHW1422 3.7 10.9 1.0
O1A C:NHW1422 3.8 12.9 1.0
CG C:LEU174 3.8 13.6 1.0
C C:ARG170 3.8 12.9 1.0
CA C:LEU174 3.9 11.0 1.0
C C:LEU169 4.0 11.5 1.0
CA C:ARG170 4.0 12.6 1.0
C C:SER171 4.0 16.0 1.0
P2A C:NHW1422 4.1 11.2 1.0
CG1 C:VAL165 4.1 9.5 1.0
CD1 C:LEU174 4.1 14.0 1.0
C C:ARG173 4.2 12.5 1.0
CA C:SER171 4.2 15.2 1.0
O3A C:NHW1422 4.3 11.6 1.0
CA C:ARG173 4.3 13.0 1.0
N C:ALA175 4.3 9.8 1.0
O C:LYS172 4.4 15.6 1.0
CG C:LYS172 4.4 16.9 1.0
N C:ARG170 4.4 10.2 1.0
O6A C:NHW1422 4.6 10.3 1.0
O C:ARG170 4.6 13.3 1.0
C C:LEU174 4.6 10.6 1.0
CB C:VAL165 4.8 9.4 1.0
CG2 C:VAL165 4.9 10.1 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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