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Chlorine in PDB 4ufw: Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22):
2.3.1.97;

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22), PDB code: 4ufw was solved by Z.Yu, J.A.Brannigan, K.Rangachari, W.P.Heal, 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) 100.73 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.520, 121.910, 178.800, 90.00, 90.00, 90.00
R / Rfree (%) 21.444 / 26.101

Other elements in 4ufw:

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22) 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 Pyridyl Inhibitor (Compound 22) (pdb code 4ufw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22), PDB code: 4ufw:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4ufw

Go back to Chlorine Binding Sites List in 4ufw
Chlorine binding site 1 out of 6 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)


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 Pyridyl Inhibitor (Compound 22) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1411

b:26.0
occ:1.00
 CL A:7Y61411 0.0 26.0 1.0
C12 A:7Y61411 1.8 25.3 1.0
C11 A:7Y61411 2.7 28.9 1.0
C13 A:7Y61411 2.7 28.9 1.0
O A:HOH2412 2.8 20.7 1.0
N A:ALA366 3.4 11.3 1.0
C A:ALA366 3.4 10.9 1.0
CA A:ALA366 3.6 10.1 1.0
CB A:ASN365 3.7 11.8 1.0
C A:ASN365 3.7 10.6 1.0
N A:LEU367 3.7 10.0 1.0
CG A:LEU367 3.7 11.3 1.0
CD2 A:TYR334 3.7 9.3 1.0
O A:HOH2393 3.8 32.9 1.0
O A:ALA366 3.8 12.2 1.0
C10 A:7Y61411 3.9 28.4 1.0
C14 A:7Y61411 4.0 29.3 1.0
O A:ASN365 4.0 12.4 1.0
CB A:TYR211 4.0 13.7 1.0
CE2 A:TYR334 4.2 10.3 1.0
CD2 A:LEU367 4.2 12.3 1.0
O A:HOH2281 4.3 15.8 0.5
CA A:ASN365 4.3 11.0 1.0
CD1 A:LEU367 4.4 13.6 1.0
C9 A:7Y61411 4.4 26.0 1.0
CA A:LEU367 4.4 10.5 1.0
CB A:LEU367 4.7 11.4 1.0
O A:HOH2411 4.8 11.1 1.0
CG A:TYR334 4.8 8.6 1.0
CG A:ASN365 4.9 12.2 1.0
O A:TYR212 5.0 14.1 1.0

Chlorine binding site 2 out of 6 in 4ufw

Go back to Chlorine Binding Sites List in 4ufw
Chlorine binding site 2 out of 6 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)


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 Pyridyl Inhibitor (Compound 22) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1414

b:13.6
occ:1.00
 O A:HOH2073 3.1 20.1 1.0
NZ A:LYS180 3.3 13.4 1.0
CE1 A:TYR65 3.8 11.0 1.0
CD A:LYS180 3.9 11.2 1.0
CE A:LYS180 4.1 12.3 1.0
OH A:TYR65 4.5 13.2 1.0
CZ A:TYR65 4.6 11.6 1.0
CD1 A:TYR65 4.6 10.3 1.0

Chlorine binding site 3 out of 6 in 4ufw

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Chlorine binding site 3 out of 6 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)


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 Pyridyl Inhibitor (Compound 22) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1411

b:24.2
occ:1.00
 CL B:7Y61411 0.0 24.2 1.0
C12 B:7Y61411 1.7 19.3 1.0
C13 B:7Y61411 2.7 24.8 1.0
C11 B:7Y61411 2.7 23.0 1.0
O B:HOH2356 2.7 22.8 1.0
C B:ALA366 3.5 10.1 1.0
N B:ALA366 3.6 9.0 1.0
CA B:ALA366 3.6 9.6 1.0
N B:LEU367 3.7 9.1 1.0
C B:ASN365 3.7 9.9 1.0
CD2 B:TYR334 3.7 11.0 1.0
CG B:LEU367 3.8 10.9 1.0
CB B:ASN365 3.8 11.2 1.0
O B:ALA366 3.8 9.8 1.0
C10 B:7Y61411 4.0 25.3 1.0
C14 B:7Y61411 4.0 23.6 1.0
O B:ASN365 4.0 9.9 1.0
CE2 B:TYR334 4.1 11.5 1.0
CB B:TYR211 4.1 13.3 1.0
CD2 B:LEU367 4.2 12.3 1.0
CA B:ASN365 4.4 10.2 1.0
C9 B:7Y61411 4.4 24.3 1.0
CD1 B:LEU367 4.5 13.4 1.0
CA B:LEU367 4.5 9.1 1.0
O B:HOH2234 4.6 14.7 0.5
CB B:LEU367 4.6 9.8 1.0
O B:HOH2357 4.8 9.7 1.0
CG B:TYR334 4.8 9.0 1.0
CG B:ASN365 5.0 15.6 1.0
O B:TYR212 5.0 10.5 1.0

Chlorine binding site 4 out of 6 in 4ufw

Go back to Chlorine Binding Sites List in 4ufw
Chlorine binding site 4 out of 6 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)


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 Pyridyl Inhibitor (Compound 22) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1413

b:13.5
occ:1.00
 NZ B:LYS180 3.5 11.3 1.0
CE2 B:TYR65 3.6 11.8 1.0
CD B:LYS180 4.0 9.2 1.0
CE B:LYS180 4.1 10.3 1.0
CD2 B:TYR65 4.5 10.4 1.0
CZ B:TYR65 4.5 12.3 1.0
OH B:TYR65 4.5 12.8 1.0

Chlorine binding site 5 out of 6 in 4ufw

Go back to Chlorine Binding Sites List in 4ufw
Chlorine binding site 5 out of 6 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)


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 Pyridyl Inhibitor (Compound 22) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1411

b:28.9
occ:1.00
 CL C:7Y61411 0.0 28.9 1.0
C12 C:7Y61411 1.8 25.6 1.0
C11 C:7Y61411 2.7 28.8 1.0
C13 C:7Y61411 2.7 26.2 1.0
O C:HOH2304 2.9 20.7 1.0
C C:ALA366 3.5 11.2 1.0
N C:ALA366 3.6 10.4 1.0
CA C:ALA366 3.7 11.5 1.0
CG C:LEU367 3.7 10.9 1.0
CD2 C:TYR334 3.8 13.4 1.0
C C:ASN365 3.8 12.1 1.0
O C:ALA366 3.8 13.4 1.0
CB C:ASN365 3.8 15.7 1.0
N C:LEU367 3.9 12.2 1.0
C10 C:7Y61411 3.9 30.7 1.0
CD2 C:LEU367 4.0 11.6 1.0
O C:HOH2292 4.0 24.4 1.0
C14 C:7Y61411 4.0 28.2 1.0
O C:ASN365 4.0 13.5 1.0
CB C:TYR211 4.1 15.3 1.0
CE2 C:TYR334 4.3 13.8 1.0
CA C:ASN365 4.4 12.1 1.0
C9 C:7Y61411 4.4 29.1 1.0
O C:HOH2206 4.5 12.0 0.5
CA C:LEU367 4.5 10.9 1.0
CD1 C:LEU367 4.6 14.1 1.0
CB C:LEU367 4.6 11.5 1.0
O C:HOH2303 4.8 15.8 1.0
CG C:TYR334 4.9 11.1 1.0
CG C:ASN365 5.0 19.8 1.0

Chlorine binding site 6 out of 6 in 4ufw

Go back to Chlorine Binding Sites List in 4ufw
Chlorine binding site 6 out of 6 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1413

b:13.8
occ:1.00
 NZ C:LYS180 3.2 12.1 1.0
CE2 C:TYR65 3.7 12.8 1.0
CD C:LYS180 3.9 11.0 1.0
CE C:LYS180 4.0 11.3 1.0
OH C:TYR65 4.5 15.4 1.0
CD2 C:TYR65 4.5 12.8 1.0
CZ C:TYR65 4.6 13.3 1.0

Reference:

Z.Yu, J.A.Brannigan, K.Rangachari, W.P.Heal, A.J.Wilkinson, A.A.Holder, R.J.Leatherbarrow, E.W.Tate. Discovery of Pyridyl-Based Inhibitors of Plasmodium Falciparum N-Myristoyltransferase Medchemcomm V. 6 1767 2015.
ISSN: ISSN 2040-2503
PubMed: 26962430
DOI: 10.1039/C5MD00242G
Page generated: Fri Jul 26 02:14:38 2024

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