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Magnesium in PDB 4a95: Plasmodium Vivax N-Myristoyltransferase with Quinoline Inhibitor

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase with Quinoline Inhibitor

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase with Quinoline Inhibitor:
2.3.1.97;

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase with Quinoline Inhibitor, PDB code: 4a95 was solved by V.Goncalves, J.A.Brannigan, D.Whalley, K.H.Ansell, B.Saxty, A.A.Holder, A.J.Wilkinson, 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) 72.08 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.490, 121.560, 179.010, 90.00, 90.00, 90.00
R / Rfree (%) 18.649 / 23.596

Other elements in 4a95:

The structure of Plasmodium Vivax N-Myristoyltransferase with Quinoline 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 Quinoline Inhibitor (pdb code 4a95). 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 Quinoline Inhibitor, PDB code: 4a95:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4a95

Go back to Magnesium Binding Sites List in 4a95
Magnesium binding site 1 out of 3 in the Plasmodium Vivax N-Myristoyltransferase with Quinoline 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 Quinoline Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1412

b:20.4
occ:1.00
O A:LEU169 2.8 12.5 1.0
N A:LYS172 2.9 13.9 1.0
O2A A:NHW1001 2.9 10.8 1.0
O5A A:NHW1001 2.9 13.0 1.0
N A:LEU174 3.2 13.4 1.0
CB A:LEU174 3.4 15.7 1.0
N A:ARG173 3.4 14.2 1.0
N A:SER171 3.5 11.9 1.0
CA A:LYS172 3.5 12.9 1.0
C A:LYS172 3.6 13.7 1.0
CB A:LYS172 3.6 13.2 1.0
C A:ARG170 3.8 13.5 1.0
P1A A:NHW1001 3.8 11.8 1.0
CA A:LEU174 3.9 12.7 1.0
CA A:ARG170 3.9 13.1 1.0
C A:SER171 3.9 13.2 1.0
O1A A:NHW1001 3.9 13.7 1.0
C A:LEU169 4.0 13.2 1.0
CG A:LEU174 4.0 18.1 1.0
CG1 A:VAL165 4.0 13.1 1.0
P2A A:NHW1001 4.1 13.3 1.0
CA A:SER171 4.1 14.2 1.0
CD1 A:LEU174 4.1 18.6 1.0
C A:ARG173 4.2 14.4 1.0
CA A:ARG173 4.3 12.4 1.0
O3A A:NHW1001 4.3 12.3 1.0
N A:ALA175 4.4 11.3 1.0
N A:ARG170 4.4 12.5 1.0
CG A:LYS172 4.5 15.4 1.0
O A:LYS172 4.5 13.9 1.0
O6A A:NHW1001 4.6 14.0 1.0
O A:ARG170 4.6 13.7 1.0
C A:LEU174 4.6 12.0 1.0
CG2 A:VAL165 4.7 9.9 1.0
CB A:VAL165 4.7 11.5 1.0

Magnesium binding site 2 out of 3 in 4a95

Go back to Magnesium Binding Sites List in 4a95
Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase with Quinoline 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 Quinoline Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1413

b:20.3
occ:1.00
O B:LEU169 2.8 17.2 1.0
O1A B:NHW1001 2.8 13.1 1.0
O4A B:NHW1001 2.9 11.6 1.0
N B:LYS172 3.1 15.0 1.0
N B:LEU174 3.2 12.7 1.0
CB B:LEU174 3.4 15.1 1.0
N B:ARG173 3.5 14.0 1.0
N B:SER171 3.6 13.7 1.0
CB B:LYS172 3.6 17.3 1.0
CA B:LYS172 3.7 16.0 1.0
P1A B:NHW1001 3.7 12.8 1.0
C B:LYS172 3.8 15.6 1.0
CG B:LEU174 3.8 14.8 1.0
CG1 B:VAL165 3.8 15.4 1.0
CA B:LEU174 3.9 12.5 1.0
C B:ARG170 3.9 15.2 1.0
CD1 B:LEU174 3.9 15.9 1.0
C B:LEU169 3.9 15.8 1.0
O2A B:NHW1001 3.9 14.5 1.0
CA B:ARG170 4.0 14.5 1.0
P2A B:NHW1001 4.1 13.1 1.0
C B:SER171 4.1 16.2 1.0
CA B:SER171 4.2 15.7 1.0
C B:ARG173 4.3 12.3 1.0
O3A B:NHW1001 4.3 12.7 1.0
N B:ALA175 4.3 11.5 1.0
CA B:ARG173 4.4 12.5 1.0
N B:ARG170 4.4 14.1 1.0
O6A B:NHW1001 4.5 12.4 1.0
CG B:LYS172 4.6 18.3 1.0
O B:LYS172 4.6 17.9 1.0
C B:LEU174 4.6 12.1 1.0
O B:ARG170 4.6 16.5 1.0
CB B:VAL165 4.7 13.6 1.0
CG2 B:VAL165 4.8 14.6 1.0

Magnesium binding site 3 out of 3 in 4a95

Go back to Magnesium Binding Sites List in 4a95
Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase with Quinoline 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 Quinoline Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1412

b:21.4
occ:1.00
O C:LEU169 2.7 16.1 1.0
O1A C:NHW1001 2.9 12.7 1.0
O4A C:NHW1001 2.9 11.0 1.0
N C:LYS172 2.9 14.4 1.0
N C:LEU174 3.2 13.2 1.0
N C:SER171 3.4 16.1 1.0
N C:ARG173 3.5 14.4 1.0
CA C:LYS172 3.5 15.6 1.0
CB C:LEU174 3.5 13.1 1.0
C C:LYS172 3.6 13.7 1.0
CB C:LYS172 3.7 15.4 1.0
P1A C:NHW1001 3.8 12.5 1.0
C C:ARG170 3.8 16.8 1.0
C C:LEU169 3.8 15.3 1.0
CA C:ARG170 3.9 15.5 1.0
O2A C:NHW1001 3.9 13.3 1.0
CA C:LEU174 3.9 13.6 1.0
CG C:LEU174 4.0 15.4 1.0
C C:SER171 4.0 17.7 1.0
CG1 C:VAL165 4.0 13.9 1.0
P2A C:NHW1001 4.1 12.4 1.0
CA C:SER171 4.1 16.8 1.0
CD1 C:LEU174 4.1 16.3 1.0
C C:ARG173 4.2 13.8 1.0
O3A C:NHW1001 4.3 13.1 1.0
CA C:ARG173 4.3 13.6 1.0
N C:ALA175 4.3 11.7 1.0
N C:ARG170 4.4 15.4 1.0
CG C:LYS172 4.4 17.1 1.0
O C:LYS172 4.4 15.7 1.0
O6A C:NHW1001 4.5 11.9 1.0
O C:ARG170 4.6 16.9 1.0
C C:LEU174 4.7 13.1 1.0
CB C:VAL165 4.9 14.8 1.0
CG2 C:VAL165 4.9 12.5 1.0

Reference:

V.Goncalves, J.A.Brannigan, D.Whalley, K.H.Ansell, B.Saxty, A.A.Holder, A.J.Wilkinson, E.W.Tate, R.J.Leatherbarrow. Discovery of Plasmodium Vivax N-Myristoyltransferase Inhibitors: Screening, Synthesis, and Structural Characterization of Their Binding Mode. J.Med.Chem. V. 55 3578 2012.
ISSN: ISSN 0022-2623
PubMed: 22439843
DOI: 10.1021/JM300040P
Page generated: Mon Dec 14 09:06:58 2020

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