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Magnesium in PDB 4b13: Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 25)

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 25)

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 25):
2.3.1.97;

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 25), PDB code: 4b13 was solved by Z.Yu, J.A.Brannigan, D.K.Moss, A.M.Brzozowski, 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) 37.51 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.320, 119.130, 178.460, 90.00, 90.00, 90.00
R / Rfree (%) 23.758 / 29.113

Other elements in 4b13:

The structure of Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 25) 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 Benzofuran Inhibitor (Compound 25) (pdb code 4b13). 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 Benzofuran Inhibitor (Compound 25), PDB code: 4b13:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4b13

Go back to Magnesium Binding Sites List in 4b13
Magnesium binding site 1 out of 3 in the Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 25)


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 Benzofuran Inhibitor (Compound 25) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1414

b:20.5
occ:1.00
 N A:LYS172 2.8 13.1 1.0
O2A A:NHW1412 2.9 14.8 1.0
O A:LEU169 2.9 13.8 1.0
O4A A:NHW1412 3.1 13.9 1.0
N A:LEU174 3.2 13.4 1.0
N A:SER171 3.4 12.6 1.0
N A:ARG173 3.4 11.2 1.0
CB A:LEU174 3.4 13.7 1.0
CA A:LYS172 3.5 12.2 1.0
CB A:LYS172 3.5 13.5 1.0
C A:LYS172 3.6 12.8 1.0
P1A A:NHW1412 3.8 12.8 1.0
CD1 A:LEU174 3.8 17.6 1.0
CG A:LEU174 3.8 16.9 1.0
C A:ARG170 3.8 11.7 1.0
O1A A:NHW1412 3.8 15.2 1.0
CA A:LEU174 3.8 12.1 1.0
C A:SER171 3.9 13.0 1.0
CA A:ARG170 3.9 11.0 1.0
C A:LEU169 4.0 12.4 1.0
CG1 A:VAL165 4.1 9.8 1.0
CA A:SER171 4.1 12.9 1.0
C A:ARG173 4.2 12.4 1.0
P2A A:NHW1412 4.2 12.8 1.0
CA A:ARG173 4.3 12.5 1.0
N A:ALA175 4.4 9.6 1.0
O3A A:NHW1412 4.4 12.7 1.0
CG A:LYS172 4.4 14.3 1.0
N A:ARG170 4.5 13.1 1.0
O A:LYS172 4.5 12.7 1.0
C A:LEU174 4.6 10.7 1.0
O A:ARG170 4.6 12.8 1.0
O6A A:NHW1412 4.7 10.9 1.0
CG2 A:VAL165 4.7 9.9 1.0
CB A:VAL165 4.8 9.9 1.0

Magnesium binding site 2 out of 3 in 4b13

Go back to Magnesium Binding Sites List in 4b13
Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 25)


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 Benzofuran Inhibitor (Compound 25) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1415

b:25.2
occ:1.00
 O1A B:NHW1412 2.8 13.5 1.0
O B:LEU169 2.8 17.8 1.0
N B:LYS172 2.8 16.3 1.0
O4A B:NHW1412 3.0 14.3 1.0
N B:LEU174 3.1 12.7 1.0
CB B:LEU174 3.4 14.7 1.0
N B:ARG173 3.4 13.4 1.0
CA B:LYS172 3.4 15.2 1.0
CB B:LYS172 3.5 17.6 1.0
N B:SER171 3.5 19.6 1.0
C B:LYS172 3.5 15.4 1.0
P1A B:NHW1412 3.6 13.3 1.0
CD1 B:LEU174 3.7 18.2 1.0
O2A B:NHW1412 3.7 16.4 1.0
CA B:LEU174 3.8 13.1 1.0
CG B:LEU174 3.8 15.4 1.0
C B:ARG170 3.9 19.7 1.0
C B:SER171 3.9 16.9 1.0
C B:LEU169 4.0 19.7 1.0
CG1 B:VAL165 4.0 12.1 1.0
CA B:ARG170 4.1 18.1 1.0
CA B:SER171 4.1 20.1 1.0
C B:ARG173 4.1 12.8 1.0
P2A B:NHW1412 4.1 14.6 1.0
CG B:LYS172 4.2 20.2 1.0
O3A B:NHW1412 4.2 14.1 1.0
CA B:ARG173 4.3 12.4 1.0
N B:ALA175 4.3 13.2 1.0
O B:LYS172 4.4 18.0 1.0
N B:ARG170 4.6 18.2 1.0
O B:ARG170 4.6 18.6 1.0
O6A B:NHW1412 4.6 12.8 1.0
C B:LEU174 4.6 12.9 1.0
CB B:VAL165 4.9 13.1 1.0
CG2 B:VAL165 4.9 12.2 1.0
O5X B:NHW1412 5.0 11.8 1.0

Magnesium binding site 3 out of 3 in 4b13

Go back to Magnesium Binding Sites List in 4b13
Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 25)


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 Benzofuran Inhibitor (Compound 25) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1414

b:20.8
occ:1.00
 O C:LEU169 2.8 14.5 1.0
N C:LYS172 2.8 16.4 1.0
O2A C:NHW1412 2.9 14.0 1.0
O4A C:NHW1412 3.0 14.2 1.0
N C:LEU174 3.1 11.7 1.0
N C:ARG173 3.4 13.9 1.0
CB C:LEU174 3.5 14.6 1.0
CA C:LYS172 3.5 17.1 1.0
CB C:LYS172 3.5 15.7 1.0
N C:SER171 3.5 15.1 1.0
C C:LYS172 3.6 16.1 1.0
P1A C:NHW1412 3.7 14.1 1.0
CA C:LEU174 3.8 12.0 1.0
C C:ARG170 3.8 15.2 1.0
O1A C:NHW1412 3.8 15.8 1.0
C C:SER171 3.9 16.9 1.0
C C:LEU169 3.9 12.8 1.0
CG C:LEU174 4.0 16.5 1.0
CA C:ARG170 4.0 13.9 1.0
CA C:SER171 4.1 17.2 1.0
CD1 C:LEU174 4.1 14.8 1.0
P2A C:NHW1412 4.1 13.4 1.0
C C:ARG173 4.1 11.9 1.0
CG1 C:VAL165 4.2 10.3 1.0
CA C:ARG173 4.3 13.5 1.0
N C:ALA175 4.3 10.1 1.0
O3A C:NHW1412 4.4 14.2 1.0
CG C:LYS172 4.4 19.1 1.0
O C:ARG170 4.4 16.2 1.0
O C:LYS172 4.5 17.1 1.0
N C:ARG170 4.5 12.3 1.0
O6A C:NHW1412 4.5 12.7 1.0
C C:LEU174 4.6 11.6 1.0
CG2 C:VAL165 4.8 10.6 1.0
CB C:VAL165 4.9 11.2 1.0

Reference:

Z.Yu, J.A.Brannigan, D.K.Moss, A.M.Brzozowski, A.J.Wilkinson, A.A.Holder, E.W.Tate, R.J.Leatherbarrow. Design and Synthesis of Inhibitors of Plasmodium Falciparum N-Myristoyltransferase, A Promising Target For Antimalarial Drug Discovery. J.Med.Chem. V. 55 8879 2012.
ISSN: ISSN 0022-2623
PubMed: 23035716
DOI: 10.1021/JM301160H
Page generated: Thu Aug 15 15:12:33 2024

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