Atomistry » Magnesium » PDB 4ava-4b2q » 4b11
Atomistry »
  Magnesium »
    PDB 4ava-4b2q »
      4b11 »

Magnesium in PDB 4b11: Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 13)

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 13)

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 13):
2.3.1.97;

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 13), PDB code: 4b11 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) 70.72 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.340, 119.030, 175.470, 90.00, 90.00, 90.00
R / Rfree (%) 17.055 / 21.878

Other elements in 4b11:

The structure of Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 13) 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 with A Bound Benzofuran Inhibitor (Compound 13) (pdb code 4b11). 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 13), PDB code: 4b11:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4b11

Go back to Magnesium Binding Sites List in 4b11
Magnesium binding site 1 out of 3 in the Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 13)


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 13) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1413

b:18.8
occ:1.00
 O A:LEU169 2.8 13.2 1.0
N A:LYS172 2.9 12.3 1.0
O2A A:NHW1000 3.0 8.4 1.0
O4A A:NHW1000 3.0 11.2 1.0
N A:LEU174 3.1 13.3 1.0
N A:ARG173 3.4 12.3 1.0
CB A:LEU174 3.5 13.4 1.0
N A:SER171 3.5 12.7 1.0
CA A:LYS172 3.6 12.7 1.0
CB A:LYS172 3.6 14.9 1.0
C A:LYS172 3.6 14.0 1.0
CA A:LEU174 3.8 12.8 1.0
P1A A:NHW1000 3.8 10.7 1.0
CG A:LEU174 3.9 17.1 1.0
CG1 A:VAL165 3.9 12.5 1.0
CD1 A:LEU174 3.9 16.6 1.0
C A:ARG170 3.9 13.3 1.0
C A:LEU169 3.9 11.9 1.0
C A:SER171 4.0 13.4 1.0
O1A A:NHW1000 4.0 12.9 1.0
CA A:ARG170 4.0 14.2 1.0
C A:ARG173 4.2 13.3 1.0
CA A:SER171 4.2 14.6 1.0
P2A A:NHW1000 4.2 11.8 1.0
CA A:ARG173 4.3 13.2 1.0
N A:ALA175 4.3 10.5 1.0
O3A A:NHW1000 4.4 11.5 1.0
CG A:LYS172 4.4 15.3 1.0
O A:LYS172 4.4 14.5 1.0
N A:ARG170 4.5 12.2 1.0
C A:LEU174 4.6 11.8 1.0
O A:ARG170 4.7 15.0 1.0
O6A A:NHW1000 4.7 11.8 1.0
CB A:VAL165 4.7 11.7 1.0
CG2 A:VAL165 4.8 11.8 1.0

Magnesium binding site 2 out of 3 in 4b11

Go back to Magnesium Binding Sites List in 4b11
Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 13)


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

b:21.3
occ:1.00
 O B:LEU169 2.8 14.5 1.0
O1A B:NHW1000 2.9 12.4 1.0
N B:LYS172 3.0 13.4 1.0
O4A B:NHW1000 3.0 9.9 1.0
N B:LEU174 3.2 12.4 1.0
CB B:LEU174 3.5 14.0 1.0
CA B:LYS172 3.5 13.8 1.0
N B:ARG173 3.5 13.8 1.0
N B:SER171 3.5 13.8 1.0
CB B:LYS172 3.6 17.5 1.0
C B:LYS172 3.6 12.6 1.0
P1A B:NHW1000 3.8 11.4 1.0
C B:ARG170 3.8 13.6 1.0
CA B:LEU174 3.9 12.3 1.0
C B:LEU169 3.9 12.7 1.0
CG B:LEU174 3.9 15.0 1.0
CA B:ARG170 3.9 11.5 1.0
CG1 B:VAL165 3.9 13.1 1.0
CD1 B:LEU174 4.0 16.6 1.0
O2A B:NHW1000 4.0 13.7 1.0
C B:SER171 4.0 15.6 1.0
P2A B:NHW1000 4.1 11.9 1.0
CA B:SER171 4.2 15.5 1.0
C B:ARG173 4.3 12.3 1.0
O3A B:NHW1000 4.3 12.4 1.0
CG B:LYS172 4.4 17.6 1.0
N B:ALA175 4.4 10.6 1.0
CA B:ARG173 4.4 13.3 1.0
N B:ARG170 4.4 12.2 1.0
O B:LYS172 4.5 12.5 1.0
O B:ARG170 4.5 15.0 1.0
O6A B:NHW1000 4.6 13.3 1.0
C B:LEU174 4.7 12.1 1.0
CB B:VAL165 4.7 13.4 1.0
CG2 B:VAL165 4.8 12.9 1.0
CD B:LYS172 5.0 24.6 1.0

Magnesium binding site 3 out of 3 in 4b11

Go back to Magnesium Binding Sites List in 4b11
Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase with A Bound Benzofuran Inhibitor (Compound 13)


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

b:20.0
occ:1.00
 O C:LEU169 2.8 13.7 1.0
O1A C:NHW1000 2.9 12.3 1.0
N C:LYS172 2.9 14.4 1.0
O4A C:NHW1000 3.0 11.9 1.0
N C:LEU174 3.2 11.4 1.0
N C:SER171 3.5 13.7 1.0
N C:ARG173 3.5 10.4 1.0
CA C:LYS172 3.5 13.0 1.0
CB C:LEU174 3.6 13.3 1.0
C C:LYS172 3.6 10.6 1.0
CB C:LYS172 3.6 13.5 1.0
P1A C:NHW1000 3.7 11.7 1.0
C C:ARG170 3.8 13.0 1.0
O2A C:NHW1000 3.9 13.3 1.0
CA C:LEU174 3.9 13.0 1.0
C C:LEU169 3.9 12.9 1.0
C C:SER171 4.0 15.6 1.0
CA C:ARG170 4.0 12.7 1.0
CG C:LEU174 4.0 14.8 1.0
CD1 C:LEU174 4.1 15.5 1.0
CG1 C:VAL165 4.1 13.4 1.0
CA C:SER171 4.1 15.8 1.0
C C:ARG173 4.2 11.2 1.0
P2A C:NHW1000 4.2 11.9 1.0
CA C:ARG173 4.3 10.0 1.0
O3A C:NHW1000 4.3 12.3 1.0
N C:ALA175 4.4 9.2 1.0
CG C:LYS172 4.4 14.4 1.0
N C:ARG170 4.4 12.2 1.0
O C:LYS172 4.5 11.6 1.0
O C:ARG170 4.6 14.7 1.0
C C:LEU174 4.6 10.0 1.0
O6A C:NHW1000 4.6 11.7 1.0
CG2 C:VAL165 4.8 11.4 1.0
CB C:VAL165 4.8 12.2 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 Anti- Malarial Drug Discovery. J.Med.Chem. V. 55 8879 2012.
ISSN: ISSN 0022-2623
PubMed: 23035716
DOI: 10.1021/JM301160H
Page generated: Thu Aug 15 15:12:07 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy