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Chlorine in PDB 4c68: Plasmodium Vivax N-Myristoyltransferase in Complex with A Peptidomimetic Inhibitor

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

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

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Peptidomimetic Inhibitor, PDB code: 4c68 was solved by T.O.Olaleye, J.A.Brannigan, V.Goncalves, S.M.Roberts, R.J.Leatherbarrow, A.J.Wilkinson, E.W.Tate, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.97 / 1.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.330, 121.430, 178.740, 90.00, 90.00, 90.00
R / Rfree (%) 21.987 / 25.989

Other elements in 4c68:

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Peptidomimetic 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 Peptidomimetic Inhibitor (pdb code 4c68). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Peptidomimetic Inhibitor, PDB code: 4c68:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4c68

Go back to Chlorine Binding Sites List in 4c68
Chlorine binding site 1 out of 5 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Peptidomimetic 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 Peptidomimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1412

b:9.0
occ:1.00
 O A:HOH2334 3.2 9.4 1.0
NH2 A:ARG358 3.2 10.1 1.0
O A:HOH2328 3.3 9.8 1.0
N A:LEU248 3.3 10.5 1.0
CA A:THR247 3.6 9.3 1.0
CG A:LEU248 3.9 8.1 1.0
C A:THR247 3.9 9.1 1.0
O A:HOH2432 4.0 11.3 1.0
CD1 A:LEU248 4.0 8.1 1.0
O A:ASP246 4.0 11.7 1.0
CG2 A:THR247 4.1 9.3 1.0
CB A:LEU248 4.1 10.2 1.0
CZ A:ARG358 4.2 9.1 1.0
CB A:THR247 4.3 9.7 1.0
CA A:LEU248 4.3 9.8 1.0
NH1 A:ARG358 4.3 7.7 1.0
N A:THR247 4.6 8.8 1.0
OG1 A:THR247 4.6 10.4 1.0
C A:ASP246 4.7 9.2 1.0
O A:LEU248 4.9 11.9 1.0

Chlorine binding site 2 out of 5 in 4c68

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Chlorine binding site 2 out of 5 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Peptidomimetic 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 Peptidomimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1412

b:9.3
occ:1.00
 O B:HOH2313 3.3 11.0 1.0
N B:LEU248 3.3 7.8 1.0
NH2 B:ARG358 3.4 8.7 1.0
CA B:THR247 3.7 8.5 1.0
C B:THR247 4.0 7.2 1.0
CB B:LEU248 4.1 8.0 1.0
O B:ASP246 4.1 9.9 1.0
CG2 B:THR247 4.1 9.6 1.0
CG B:LEU248 4.2 8.7 1.0
CD1 B:LEU248 4.3 7.6 1.0
CA B:LEU248 4.3 8.4 1.0
CZ B:ARG358 4.3 9.5 1.0
NH1 B:ARG358 4.3 9.2 1.0
CB B:THR247 4.4 9.6 1.0
OG1 B:THR247 4.7 7.9 1.0
N B:THR247 4.7 7.8 1.0
C B:ASP246 4.8 6.7 1.0

Chlorine binding site 3 out of 5 in 4c68

Go back to Chlorine Binding Sites List in 4c68
Chlorine binding site 3 out of 5 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Peptidomimetic 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 Peptidomimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1412

b:10.5
occ:1.00
 O C:HOH2234 3.1 13.0 1.0
NH2 C:ARG358 3.2 10.2 1.0
N C:LEU248 3.3 9.2 1.0
O C:HOH2230 3.3 13.3 1.0
CA C:THR247 3.6 9.1 1.0
O C:HOH2324 3.8 13.1 1.0
C C:THR247 3.9 10.0 1.0
O C:ASP246 4.1 10.6 1.0
CG2 C:THR247 4.1 8.6 1.0
CG C:LEU248 4.2 9.9 1.0
CB C:LEU248 4.2 9.8 1.0
CZ C:ARG358 4.2 9.6 1.0
CD1 C:LEU248 4.3 11.3 1.0
CB C:THR247 4.3 9.6 1.0
NH1 C:ARG358 4.3 10.7 1.0
CA C:LEU248 4.3 8.5 1.0
OG1 C:THR247 4.6 10.8 1.0
N C:THR247 4.6 9.1 1.0
C C:ASP246 4.7 10.3 1.0
O C:LEU248 5.0 10.3 1.0

Chlorine binding site 4 out of 5 in 4c68

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Chlorine binding site 4 out of 5 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Peptidomimetic 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 Peptidomimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1413

b:41.9
occ:1.00
 O C:HOH2320 3.1 16.1 1.0
NH1 C:ARG214 3.3 14.7 0.5
OE1 C:GLN350 3.5 19.7 1.0
CG C:GLN350 3.5 15.0 1.0
O C:HOH2223 3.7 18.6 1.0
NH2 C:ARG214 3.8 15.3 0.5
NH2 C:ARG214 3.8 22.1 0.5
CD C:GLN350 3.9 14.8 1.0
CZ C:ARG214 4.0 14.3 0.5
CD2 C:LEU379 4.3 21.7 1.0
CZ C:ARG214 4.6 19.9 0.5
CB C:VAL244 4.6 18.6 1.0
O C:HOH2224 4.6 10.7 1.0
CB C:GLN350 4.7 11.6 1.0
CG2 C:ILE353 4.8 12.2 1.0
CA C:GLN350 5.0 10.2 1.0
CG1 C:VAL244 5.0 23.8 1.0

Chlorine binding site 5 out of 5 in 4c68

Go back to Chlorine Binding Sites List in 4c68
Chlorine binding site 5 out of 5 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Peptidomimetic Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Peptidomimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1414

b:54.8
occ:1.00
 N C:SER215 2.9 13.7 1.0
O C:LYS380 3.0 19.7 1.0
O C:HIS213 3.5 18.9 1.0
OG C:SER215 3.5 23.5 1.0
CA C:ARG214 3.5 13.0 0.5
CA C:ARG214 3.5 12.4 0.5
C C:ARG214 3.7 13.7 1.0
CB C:SER215 3.7 17.2 1.0
CD C:ARG214 3.8 17.8 0.5
CA C:SER215 3.9 15.5 1.0
C C:LYS380 4.1 19.2 1.0
N C:GLY382 4.1 20.6 1.0
CD C:ARG214 4.2 14.7 0.5
C C:HIS213 4.2 15.2 1.0
N C:ARG214 4.3 13.6 1.0
CE2 C:TYR242 4.4 65.7 0.5
CG C:ARG214 4.4 16.1 0.5
CA C:PHE381 4.5 20.2 1.0
CB C:ARG214 4.5 14.9 0.5
NE C:ARG214 4.6 19.8 0.5
C C:PHE381 4.6 22.1 1.0
CB C:ARG214 4.7 13.5 0.5
CD2 C:TYR242 4.7 75.9 0.5
CZ C:TYR242 4.7 63.5 0.5
O C:SER215 4.7 17.0 1.0
N C:PHE381 4.8 19.7 1.0
C C:SER215 4.8 14.7 1.0
NE C:ARG214 4.9 15.9 0.5
O C:ARG214 4.9 13.5 1.0
CG C:ARG214 4.9 12.8 0.5

Reference:

T.O.Olaleye, J.A.Brannigan, S.M.Roberts, R.J.Leatherbarrow, A.J.Wilkinson, E.W.Tate. Peptidomimetic Inhibitors of N-Myristoyltransferase From Human Malaria and Leishmaniasis Parasites. Org.Biomol.Chem. V. 12 8132 2014.
ISSN: ISSN 1477-0520
PubMed: 25230674
DOI: 10.1039/C4OB01669F
Page generated: Sat Dec 12 10:28:30 2020

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