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Chlorine in PDB 2yne: Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor

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

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

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor, PDB code: 2yne was solved by M.H.Wright, B.Clough, M.D.Rackham, J.A.Brannigan, M.Grainger, A.R.Bottrill, W.P.Heal, M.Broncel, R.A.Serwa, D.Mann, R.J.Leatherbarrow, A.J.Wilkinson, A.A.Holder, E.W.Tate, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.83 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.620, 121.850, 179.160, 90.00, 90.00, 90.00
R / Rfree (%) 17.347 / 21.814

Other elements in 2yne:

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

Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor (pdb code 2yne). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor, PDB code: 2yne:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2yne

Go back to Chlorine Binding Sites List in 2yne
Chlorine binding site 1 out of 4 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1413

b:36.4
occ:1.00
 N A:SER328 3.3 19.2 1.0
N A:THR329 3.4 14.8 1.0
CA A:TYR327 3.8 17.8 1.0
O A:THR329 3.8 15.4 1.0
OG A:SER328 3.9 27.4 1.0
CD1 A:TYR327 4.0 15.7 1.0
C A:TYR327 4.1 19.2 1.0
CB A:THR329 4.1 15.9 1.0
CB A:TYR327 4.1 16.6 1.0
CA A:THR329 4.2 13.9 1.0
CA A:SER328 4.3 18.6 1.0
C A:SER328 4.3 15.5 1.0
NZ A:LYS220 4.4 11.8 1.0
O A:HOH2313 4.5 25.9 1.0
C A:THR329 4.5 15.3 1.0
CG A:TYR327 4.5 14.9 1.0
OG1 A:THR329 4.6 17.6 1.0
CB A:SER328 4.7 21.8 1.0
O A:LYS326 4.9 19.0 1.0

Chlorine binding site 2 out of 4 in 2yne

Go back to Chlorine Binding Sites List in 2yne
Chlorine binding site 2 out of 4 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1414

b:13.0
occ:1.00
 NZ A:LYS180 3.3 13.2 1.0
CE1 A:TYR65 3.7 13.0 1.0
CD A:LYS180 3.8 14.1 1.0
CE A:LYS180 4.0 12.2 1.0
OH A:TYR65 4.4 14.2 1.0
CZ A:TYR65 4.6 13.3 1.0
CD1 A:TYR65 4.6 13.1 1.0

Chlorine binding site 3 out of 4 in 2yne

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1412

b:13.5
occ:1.00
 O B:HOH2064 3.1 16.9 1.0
NZ B:LYS180 3.3 12.1 1.0
O B:HOH2065 3.7 10.1 1.0
CE2 B:TYR65 3.8 11.9 1.0
CD B:LYS180 3.9 10.7 1.0
CE B:LYS180 4.0 9.4 1.0
OH B:TYR65 4.4 11.8 1.0
CZ B:TYR65 4.6 12.6 1.0
CD2 B:TYR65 4.7 10.5 1.0

Chlorine binding site 4 out of 4 in 2yne

Go back to Chlorine Binding Sites List in 2yne
Chlorine binding site 4 out of 4 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Benzothiophene Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1412

b:14.1
occ:1.00
 O C:HOH2059 3.2 17.2 1.0
NZ C:LYS180 3.3 17.5 1.0
O C:HOH2041 3.8 14.7 1.0
CE2 C:TYR65 3.8 12.0 1.0
CD C:LYS180 3.9 13.8 1.0
CE C:LYS180 4.0 13.6 1.0
OH C:TYR65 4.5 12.7 1.0
CD2 C:TYR65 4.7 11.6 1.0
CZ C:TYR65 4.7 12.4 1.0

Reference:

M.H.Wright, B.Clough, M.D.Rackham, K.Rangachari, J.A.Brannigan, M.Grainger, D.K.Moss, A.R.Bottrill, W.P.Heal, M.Broncel, R.A.Serwa, D.Brady, D.Mann, R.J.Leatherbarrow, R.Tewari, A.J.Wilkinson, A.A.Holder, E.W.Tate. Validation of N-Myristoyltransferase As An Antimalarial Drug Target Using An Integrated Chemical Biology Approach. Nat.Chem. V. 6 112 2014.
ISSN: ISSN 1755-4330
PubMed: 24451586
DOI: 10.1038/NCHEM.1836
Page generated: Sat Jul 20 15:11:28 2024

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