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Fluorine in PDB 6mb0: Crystal Structure of N-Myristoyl Transferase (Nmt) G386E Mutant From Plasmodium Vivax in Complex with Inhibitor Imp-1002

Enzymatic activity of Crystal Structure of N-Myristoyl Transferase (Nmt) G386E Mutant From Plasmodium Vivax in Complex with Inhibitor Imp-1002

All present enzymatic activity of Crystal Structure of N-Myristoyl Transferase (Nmt) G386E Mutant From Plasmodium Vivax in Complex with Inhibitor Imp-1002:
2.3.1.97;

Protein crystallography data

The structure of Crystal Structure of N-Myristoyl Transferase (Nmt) G386E Mutant From Plasmodium Vivax in Complex with Inhibitor Imp-1002, PDB code: 6mb0 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.440, 121.190, 178.250, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 17.8

Other elements in 6mb0:

The structure of Crystal Structure of N-Myristoyl Transferase (Nmt) G386E Mutant From Plasmodium Vivax in Complex with Inhibitor Imp-1002 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of N-Myristoyl Transferase (Nmt) G386E Mutant From Plasmodium Vivax in Complex with Inhibitor Imp-1002 (pdb code 6mb0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of N-Myristoyl Transferase (Nmt) G386E Mutant From Plasmodium Vivax in Complex with Inhibitor Imp-1002, PDB code: 6mb0:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6mb0

Go back to Fluorine Binding Sites List in 6mb0
Fluorine binding site 1 out of 3 in the Crystal Structure of N-Myristoyl Transferase (Nmt) G386E Mutant From Plasmodium Vivax in Complex with Inhibitor Imp-1002


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of N-Myristoyl Transferase (Nmt) G386E Mutant From Plasmodium Vivax in Complex with Inhibitor Imp-1002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:11.2
occ:1.00
 F19 A:JCY502 0.0 11.2 1.0
C18 A:JCY502 1.4 10.5 1.0
C17 A:JCY502 2.3 9.1 1.0
C20 A:JCY502 2.4 10.5 1.0
N A:ALA366 3.3 7.7 1.0
CB A:ASN365 3.3 10.3 1.0
CB A:TYR211 3.5 9.7 0.4
C A:ASN365 3.5 11.1 1.0
C A:ALA366 3.6 9.9 1.0
C16 A:JCY502 3.6 9.8 1.0
CB A:TYR211 3.6 9.7 0.6
C21 A:JCY502 3.6 9.5 1.0
CA A:ALA366 3.7 7.0 1.0
O A:ALA366 3.7 9.7 1.0
CD2 A:TYR334 3.7 10.6 1.0
CE2 A:TYR334 3.8 10.1 1.0
CD1 A:TYR211 3.8 10.1 0.6
O A:HOH713 3.9 17.0 1.0
CA A:ASN365 4.0 7.5 1.0
O A:ASN365 4.0 11.1 1.0
N A:LEU367 4.0 7.2 1.0
CG A:TYR211 4.1 9.9 0.6
C15 A:JCY502 4.1 10.3 1.0
CG A:LEU367 4.3 8.7 1.0
CG A:ASN365 4.4 12.9 1.0
CG A:TYR211 4.4 12.6 0.4
CD2 A:LEU367 4.4 11.3 1.0
O A:HOH856 4.5 20.4 1.0
CA A:TYR211 4.6 10.2 0.6
CA A:TYR211 4.6 9.9 0.4
O A:TYR212 4.6 9.8 1.0
O22 A:JCY502 4.8 9.3 1.0
CA A:LEU367 4.8 6.7 1.0
ND2 A:ASN365 4.8 15.0 1.0
CG A:TYR334 4.9 6.4 1.0
CE1 A:TYR211 4.9 13.1 0.6
N A:TYR212 4.9 8.8 1.0
CD2 A:TYR211 4.9 18.8 0.4
C23 A:JCY502 5.0 9.7 1.0
CZ A:TYR334 5.0 8.7 1.0

Fluorine binding site 2 out of 3 in 6mb0

Go back to Fluorine Binding Sites List in 6mb0
Fluorine binding site 2 out of 3 in the Crystal Structure of N-Myristoyl Transferase (Nmt) G386E Mutant From Plasmodium Vivax in Complex with Inhibitor Imp-1002


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of N-Myristoyl Transferase (Nmt) G386E Mutant From Plasmodium Vivax in Complex with Inhibitor Imp-1002 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:11.5
occ:1.00
 F19 B:JCY503 0.0 11.5 1.0
C18 B:JCY503 1.4 11.4 1.0
C20 B:JCY503 2.4 9.3 1.0
C17 B:JCY503 2.4 11.5 1.0
N B:ALA366 3.2 8.5 1.0
CB B:ASN365 3.4 8.7 1.0
C B:ASN365 3.5 10.2 1.0
C B:ALA366 3.5 9.3 1.0
CB B:TYR211 3.5 10.3 0.4
C16 B:JCY503 3.6 10.3 1.0
O B:ALA366 3.6 8.7 1.0
C21 B:JCY503 3.6 10.3 1.0
CB B:TYR211 3.6 9.6 0.6
CA B:ALA366 3.7 6.7 1.0
CD2 B:TYR334 3.8 9.2 1.0
CE2 B:TYR334 3.9 11.3 1.0
O B:HOH680 3.9 17.9 1.0
CD2 B:TYR211 3.9 10.3 0.6
O B:ASN365 3.9 10.9 1.0
CA B:ASN365 4.0 6.9 1.0
N B:LEU367 4.0 6.3 1.0
C15 B:JCY503 4.1 11.5 1.0
CG B:TYR211 4.1 7.3 0.6
CG B:LEU367 4.3 6.8 1.0
CG B:ASN365 4.4 12.6 1.0
CG B:TYR211 4.4 11.9 0.4
CD2 B:LEU367 4.4 8.4 1.0
O B:HOH793 4.5 18.7 1.0
O B:TYR212 4.5 10.3 1.0
CA B:TYR211 4.6 7.2 0.6
CA B:TYR211 4.6 7.7 0.4
CA B:LEU367 4.7 7.2 1.0
O22 B:JCY503 4.8 11.2 1.0
ND2 B:ASN365 4.8 13.1 1.0
N B:TYR212 4.9 7.8 1.0
CG B:TYR334 4.9 6.6 1.0
C23 B:JCY503 5.0 9.8 1.0
CD2 B:TYR211 5.0 16.0 0.4
CE2 B:TYR211 5.0 12.1 0.6
CZ B:TYR334 5.0 10.5 1.0

Fluorine binding site 3 out of 3 in 6mb0

Go back to Fluorine Binding Sites List in 6mb0
Fluorine binding site 3 out of 3 in the Crystal Structure of N-Myristoyl Transferase (Nmt) G386E Mutant From Plasmodium Vivax in Complex with Inhibitor Imp-1002


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of N-Myristoyl Transferase (Nmt) G386E Mutant From Plasmodium Vivax in Complex with Inhibitor Imp-1002 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:11.5
occ:1.00
 F19 C:JCY502 0.0 11.5 1.0
C18 C:JCY502 1.4 8.7 1.0
C17 C:JCY502 2.4 11.0 1.0
C20 C:JCY502 2.4 9.5 1.0
N C:ALA366 3.1 7.7 1.0
CB C:ASN365 3.3 12.1 1.0
C C:ASN365 3.4 9.6 1.0
C C:ALA366 3.5 9.7 1.0
CB C:TYR211 3.6 10.8 0.5
CA C:ALA366 3.6 7.4 1.0
O C:ALA366 3.6 10.3 1.0
C16 C:JCY502 3.6 11.0 1.0
CB C:TYR211 3.6 11.8 0.5
C21 C:JCY502 3.6 10.8 1.0
O C:HOH765 3.8 17.5 1.0
CA C:ASN365 3.8 8.3 1.0
O C:ASN365 3.9 10.3 1.0
CD2 C:TYR334 3.9 9.1 1.0
N C:LEU367 4.0 10.5 1.0
CE2 C:TYR334 4.0 13.6 1.0
C15 C:JCY502 4.1 10.8 1.0
CD1 C:TYR211 4.2 20.9 0.5
CG C:TYR211 4.3 16.6 0.5
CG C:LEU367 4.3 9.0 1.0
O C:TYR212 4.3 11.1 1.0
CG C:ASN365 4.3 15.9 1.0
CA C:TYR211 4.5 10.8 0.5
CA C:TYR211 4.5 10.8 0.5
CG C:TYR211 4.6 9.3 0.5
CD2 C:LEU367 4.6 9.1 1.0
O C:HOH700 4.6 18.6 1.0
N C:TYR212 4.7 10.6 1.0
CA C:LEU367 4.8 6.9 1.0
O22 C:JCY502 4.8 12.7 1.0
ND2 C:ASN365 4.9 20.0 1.0

Reference:

A.C.Schlott, S.Mayclin, A.R.Reers, O.Coburn-Flynn, A.S.Bell, J.Green, E.Knuepfer, D.Charter, R.Bonnert, B.Campo, J.Burrows, S.Lyons-Abbott, B.L.Staker, C.W.Chung, P.J.Myler, D.A.Fidock, E.W.Tate, A.A.Holder. Structure-Guided Identification of Resistance Breaking Antimalarial N‐Myristoyltransferase Inhibitors. Cell Chem Biol V. 26 991 2019.
ISSN: ESSN 2451-9456
PubMed: 31080074
DOI: 10.1016/J.CHEMBIOL.2019.03.015
Page generated: Tue Jul 15 13:07:35 2025

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