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Magnesium in PDB 4bbh: Plasmodium Vivax N-Myristoyltransferase with A Bound Benzothiophene Inhibitor

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase with A Bound Benzothiophene Inhibitor

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase with A Bound Benzothiophene Inhibitor:
2.3.1.97;

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase with A Bound Benzothiophene Inhibitor, PDB code: 4bbh was solved by M.D.Rackham, J.A.Brannigan, D.K.Moss, Z.Yu, 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) 72.07 / 1.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.470, 121.870, 178.340, 90.00, 90.00, 90.00
R / Rfree (%) 21.444 / 26.443

Other elements in 4bbh:

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

Magnesium binding site 1 out of 3 in 4bbh

Go back to Magnesium Binding Sites List in 4bbh
Magnesium binding site 1 out of 3 in the Plasmodium Vivax N-Myristoyltransferase with A Bound Benzothiophene Inhibitor


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 with A Bound Benzothiophene Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1413

b:19.5
occ:1.00
O2A A:NHW1000 2.7 9.3 1.0
O4A A:NHW1000 2.9 11.1 1.0
O A:LEU169 2.9 12.0 1.0
N A:LYS172 2.9 11.7 1.0
N A:LEU174 3.2 10.0 1.0
CB A:LEU174 3.4 12.4 1.0
N A:ARG173 3.5 11.1 1.0
N A:SER171 3.5 11.8 1.0
CA A:LYS172 3.5 11.5 1.0
C A:LYS172 3.6 11.2 1.0
P1A A:NHW1000 3.6 11.0 1.0
O1A A:NHW1000 3.8 10.3 1.0
CA A:LEU174 3.8 11.2 1.0
C A:ARG170 3.9 11.6 1.0
CB A:LYS172 3.9 12.7 1.0
CG A:LEU174 3.9 15.2 1.0
P2A A:NHW1000 4.0 10.9 1.0
C A:SER171 4.0 13.0 1.0
CA A:ARG170 4.0 10.7 1.0
C A:LEU169 4.0 11.5 1.0
CD1 A:LEU174 4.1 16.3 1.0
CG1 A:VAL165 4.1 6.9 1.0
CA A:SER171 4.2 12.5 1.0
C A:ARG173 4.2 10.4 1.0
N A:ALA175 4.2 10.3 1.0
O3A A:NHW1000 4.3 11.1 1.0
CA A:ARG173 4.3 10.8 1.0
O A:LYS172 4.3 9.9 1.0
O6A A:NHW1000 4.4 11.9 1.0
N A:ARG170 4.5 11.0 1.0
C A:LEU174 4.6 10.4 1.0
O A:ARG170 4.6 12.9 1.0
CG2 A:VAL165 4.7 7.1 1.0
CB A:VAL165 4.8 7.5 1.0
CG A:LYS172 4.8 12.9 1.0

Magnesium binding site 2 out of 3 in 4bbh

Go back to Magnesium Binding Sites List in 4bbh
Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase with A Bound Benzothiophene Inhibitor


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 with A Bound Benzothiophene Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1412

b:22.6
occ:1.00
O B:LEU169 2.7 12.7 1.0
O2A B:NHW1000 2.9 9.1 1.0
N B:LYS172 2.9 11.8 1.0
O4A B:NHW1000 3.2 10.8 1.0
N B:LEU174 3.2 10.0 1.0
CB B:LEU174 3.4 9.9 1.0
N B:ARG173 3.4 12.0 1.0
CA B:LYS172 3.5 12.6 1.0
CB B:LYS172 3.5 13.6 1.0
N B:SER171 3.6 11.1 1.0
C B:LYS172 3.6 12.0 1.0
P1A B:NHW1000 3.8 9.8 1.0
CD1 B:LEU174 3.8 11.6 1.0
CG B:LEU174 3.8 10.7 1.0
C B:LEU169 3.9 11.8 1.0
C B:ARG170 3.9 12.3 1.0
CA B:LEU174 3.9 9.2 1.0
C B:SER171 4.0 12.2 1.0
O1A B:NHW1000 4.0 9.6 1.0
CG1 B:VAL165 4.0 9.2 1.0
CA B:ARG170 4.0 11.5 1.0
CA B:SER171 4.1 12.9 1.0
C B:ARG173 4.2 11.2 1.0
O B:LYS172 4.3 13.9 1.0
P2A B:NHW1000 4.3 10.3 1.0
CA B:ARG173 4.3 11.1 1.0
O3A B:NHW1000 4.3 10.3 1.0
CG B:LYS172 4.4 14.9 1.0
N B:ALA175 4.4 9.0 1.0
N B:ARG170 4.4 11.6 1.0
O6A B:NHW1000 4.6 8.7 1.0
O B:ARG170 4.7 13.6 1.0
C B:LEU174 4.7 9.1 1.0
CB B:VAL165 4.9 8.3 1.0
CG2 B:VAL165 4.9 8.5 1.0
CD B:LYS172 5.0 16.3 1.0

Magnesium binding site 3 out of 3 in 4bbh

Go back to Magnesium Binding Sites List in 4bbh
Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase with A Bound Benzothiophene Inhibitor


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 with A Bound Benzothiophene Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1412

b:16.6
occ:1.00
N C:LYS172 2.8 13.9 1.0
O C:LEU169 2.8 8.8 1.0
O2A C:NHW1000 3.1 10.8 1.0
O4A C:NHW1000 3.1 9.3 1.0
N C:LEU174 3.1 8.1 1.0
N C:ARG173 3.3 11.2 1.0
CA C:LYS172 3.4 14.0 1.0
C C:LYS172 3.4 13.1 1.0
N C:SER171 3.5 13.3 1.0
CB C:LYS172 3.6 14.4 1.0
CB C:LEU174 3.7 9.4 1.0
O1A C:NHW1000 3.8 11.7 1.0
P1A C:NHW1000 3.8 9.3 1.0
C C:ARG170 3.8 11.9 1.0
C C:SER171 3.9 14.3 1.0
CA C:LEU174 3.9 8.8 1.0
C C:LEU169 4.0 9.5 1.0
CA C:ARG170 4.0 10.7 1.0
CG C:LEU174 4.0 9.5 1.0
C C:ARG173 4.1 9.6 1.0
CD1 C:LEU174 4.1 10.2 1.0
CA C:SER171 4.1 14.5 1.0
CA C:ARG173 4.1 10.2 1.0
P2A C:NHW1000 4.1 9.0 1.0
O C:LYS172 4.2 14.8 1.0
CG1 C:VAL165 4.3 9.4 1.0
O3A C:NHW1000 4.3 10.0 1.0
N C:ALA175 4.4 8.4 1.0
N C:ARG170 4.5 10.4 1.0
O C:ARG170 4.5 13.4 1.0
CG C:LYS172 4.6 16.6 1.0
O6A C:NHW1000 4.7 8.6 1.0
C C:LEU174 4.7 8.3 1.0
CB C:VAL165 5.0 9.2 1.0
CG2 C:VAL165 5.0 8.9 1.0
O C:SER171 5.0 15.7 1.0

Reference:

M.D.Rackham, J.A.Brannigan, D.K.Moss, Z.Yu, A.J.Wilkinson, A.A.Holder, E.W.Tate, R.J.Leatherbarrow. Discovery of Novel and Ligand-Efficient Inhibitors of Plasmodium Falciparum and Plasmodium Vivax N- Myristoyltransferase. J.Med.Chem. V. 56 371 2013.
ISSN: ISSN 0022-2623
PubMed: 23170970
DOI: 10.1021/JM301474T
Page generated: Mon Dec 14 09:11:28 2020

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