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Chlorine in PDB 6nxg: Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A

Enzymatic activity of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A

All present enzymatic activity of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A:
2.3.1.97;

Protein crystallography data

The structure of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A, PDB code: 6nxg was solved by B.L.Staker, S.Mayclin, Seattle Structural Genomics Center Forinfectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.29 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.420, 119.030, 175.350, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 17.4

Other elements in 6nxg:

The structure of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A (pdb code 6nxg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A, PDB code: 6nxg:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 6nxg

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Chlorine binding site 1 out of 5 in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:8.8
occ:1.00
 NZ A:LYS180 3.3 7.9 1.0
CE1 A:TYR65 3.8 9.1 1.0
CD A:LYS180 3.9 7.5 1.0
CE A:LYS180 4.1 7.6 1.0
OH A:TYR65 4.5 8.9 1.0
CD1 A:TYR65 4.6 9.3 1.0
CZ A:TYR65 4.6 8.8 1.0

Chlorine binding site 2 out of 5 in 6nxg

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Chlorine binding site 2 out of 5 in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:15.6
occ:1.00
 CL A:L7Y504 0.0 15.6 1.0
C02 A:L7Y504 1.8 15.0 1.0
C07 A:L7Y504 2.7 15.1 1.0
C03 A:L7Y504 2.7 15.1 1.0
N A:ALA366 3.5 7.3 1.0
C A:ALA366 3.6 7.1 1.0
CB A:TYR211 3.7 10.2 1.0
CB A:ASN365 3.7 7.9 1.0
CD2 A:TYR334 3.7 7.6 1.0
O A:HOH742 3.7 9.8 1.0
O A:ALA366 3.8 7.4 1.0
CA A:ALA366 3.8 7.2 1.0
C A:ASN365 3.8 7.4 1.0
CE2 A:TYR334 3.8 7.9 1.0
O A:HOH602 3.9 20.8 1.0
N A:LEU367 3.9 6.9 1.0
C06 A:L7Y504 4.0 15.4 1.0
O A:HOH850 4.0 13.2 1.0
CG A:LEU367 4.0 6.8 1.0
C04 A:L7Y504 4.0 15.4 1.0
CD2 A:LEU367 4.3 7.0 1.0
O A:ASN365 4.3 7.4 1.0
CA A:ASN365 4.3 7.7 1.0
C05 A:L7Y504 4.5 15.8 1.0
CA A:TYR211 4.6 9.5 1.0
CA A:LEU367 4.7 6.9 1.0
CG A:TYR211 4.7 11.1 1.0
CG A:ASN365 4.7 8.4 1.0
O A:TYR212 4.8 9.1 1.0
CG A:TYR334 4.8 7.2 1.0
CB A:LEU367 4.9 6.9 1.0
CD1 A:LEU367 4.9 6.8 1.0

Chlorine binding site 3 out of 5 in 6nxg

Go back to Chlorine Binding Sites List in 6nxg
Chlorine binding site 3 out of 5 in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:9.2
occ:1.00
 NZ B:LYS180 3.4 8.5 1.0
CE1 B:TYR65 3.8 9.5 1.0
CD B:LYS180 4.0 7.9 1.0
CE B:LYS180 4.1 8.2 1.0
OH B:TYR65 4.4 9.4 1.0
CZ B:TYR65 4.6 9.4 1.0
CD1 B:TYR65 4.6 9.7 1.0

Chlorine binding site 4 out of 5 in 6nxg

Go back to Chlorine Binding Sites List in 6nxg
Chlorine binding site 4 out of 5 in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:13.8
occ:1.00
 CL B:L7Y503 0.0 13.8 1.0
C02 B:L7Y503 1.8 14.0 1.0
C07 B:L7Y503 2.7 13.9 1.0
C03 B:L7Y503 2.7 13.8 1.0
N B:ALA366 3.5 7.4 1.0
C B:ALA366 3.5 7.0 1.0
CB B:TYR211 3.6 10.4 1.0
CB B:ASN365 3.7 8.3 1.0
O B:ALA366 3.7 7.0 1.0
O B:HOH779 3.7 10.2 1.0
CD2 B:TYR334 3.8 8.7 1.0
CA B:ALA366 3.8 7.1 1.0
C B:ASN365 3.9 7.6 1.0
O B:HOH601 3.9 18.9 1.0
N B:LEU367 3.9 6.8 1.0
CE2 B:TYR334 3.9 9.2 1.0
C06 B:L7Y503 4.0 14.4 1.0
C04 B:L7Y503 4.0 14.2 1.0
CG B:LEU367 4.0 6.8 1.0
O B:HOH879 4.1 12.0 1.0
CD2 B:LEU367 4.3 6.9 1.0
CA B:ASN365 4.3 8.0 1.0
O B:ASN365 4.4 7.8 1.0
C05 B:L7Y503 4.5 14.6 1.0
CA B:TYR211 4.5 9.9 1.0
CG B:TYR211 4.6 11.1 1.0
CA B:LEU367 4.7 6.9 1.0
CG B:ASN365 4.7 9.0 1.0
O B:TYR212 4.7 9.3 1.0
CG B:TYR334 4.9 8.4 1.0
CD1 B:LEU367 4.9 6.7 1.0
CB B:LEU367 4.9 6.7 1.0

Chlorine binding site 5 out of 5 in 6nxg

Go back to Chlorine Binding Sites List in 6nxg
Chlorine binding site 5 out of 5 in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl503

b:9.6
occ:1.00
 O C:HOH636 3.1 10.7 1.0
NH2 C:ARG358 3.3 9.6 1.0
O C:HOH815 3.3 10.2 1.0
N C:LEU248 3.3 9.1 1.0
CA C:THR247 3.6 9.4 1.0
O C:HOH907 3.9 10.8 1.0
CG2 C:THR247 4.0 9.6 1.0
C C:THR247 4.0 9.2 1.0
CB C:LEU248 4.1 8.9 1.0
O C:ASP246 4.1 9.7 1.0
CG C:LEU248 4.1 8.7 1.0
CZ C:ARG358 4.2 9.4 1.0
NH1 C:ARG358 4.2 9.1 1.0
CD1 C:LEU248 4.3 8.7 1.0
CB C:THR247 4.3 9.6 1.0
CA C:LEU248 4.3 9.0 1.0
N C:THR247 4.6 9.6 1.0
OG1 C:THR247 4.7 9.7 1.0
C C:ASP246 4.8 9.8 1.0
O C:LEU248 4.9 9.3 1.0

Reference:

A.Harupa, L.De Las Heras, G.Colmenarejo, S.Lyons-Abbott, A.Reers, I.Caballero Hernandez, C.W.Chung, D.Charter, P.J.Myler, R.M.Fernandez-Menendez, F.Calderon, S.Palomo, B.Rodriguez, M.Berlanga, E.Herreros-Aviles, B.L.Staker, E.Fernandez Alvaro, A.Kaushansky. Identification of Selective Inhibitors of Plasmodium N-Myristoyltransferase By High-Throughput Screening. J.Med.Chem. 2019.
ISSN: ISSN 0022-2623
PubMed: 31850752
DOI: 10.1021/ACS.JMEDCHEM.9B01343
Page generated: Mon Jul 29 12:19:35 2024

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