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Fluorine in PDB 1jkh: Crystal Structure of Y181C Mutant Hiv-1 Reverse Transcriptase in Complex with Dmp-266(Efavirenz)

Enzymatic activity of Crystal Structure of Y181C Mutant Hiv-1 Reverse Transcriptase in Complex with Dmp-266(Efavirenz)

All present enzymatic activity of Crystal Structure of Y181C Mutant Hiv-1 Reverse Transcriptase in Complex with Dmp-266(Efavirenz):
2.7.7.49;

Protein crystallography data

The structure of Crystal Structure of Y181C Mutant Hiv-1 Reverse Transcriptase in Complex with Dmp-266(Efavirenz), PDB code: 1jkh was solved by J.Ren, C.Nichols, L.Bird, P.Chamberlain, K.Weaver, S.Short, D.I.Stuart, D.K.Stammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.68 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 138.500, 109.000, 73.200, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 30.3

Other elements in 1jkh:

The structure of Crystal Structure of Y181C Mutant Hiv-1 Reverse Transcriptase in Complex with Dmp-266(Efavirenz) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Y181C Mutant Hiv-1 Reverse Transcriptase in Complex with Dmp-266(Efavirenz) (pdb code 1jkh). 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 Y181C Mutant Hiv-1 Reverse Transcriptase in Complex with Dmp-266(Efavirenz), PDB code: 1jkh:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 1jkh

Go back to Fluorine Binding Sites List in 1jkh
Fluorine binding site 1 out of 3 in the Crystal Structure of Y181C Mutant Hiv-1 Reverse Transcriptase in Complex with Dmp-266(Efavirenz)


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 Y181C Mutant Hiv-1 Reverse Transcriptase in Complex with Dmp-266(Efavirenz) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F999

b:55.3
occ:1.00
 F1 A:EFZ999 0.0 55.3 1.0
C13 A:EFZ999 1.3 60.0 1.0
F2 A:EFZ999 2.1 64.3 1.0
F3 A:EFZ999 2.1 70.6 1.0
C7 A:EFZ999 2.4 59.6 1.0
O2 A:EFZ999 2.8 65.0 1.0
C8 A:EFZ999 2.8 61.1 1.0
O A:TYR188 3.1 61.0 1.0
CG1 A:VAL179 3.6 43.7 1.0
C9 A:EFZ999 3.6 68.7 1.0
O A:VAL179 3.7 53.7 1.0
C14 A:EFZ999 3.7 55.5 1.0
C6 A:EFZ999 3.8 46.5 1.0
C A:TYR188 3.8 55.3 1.0
CB A:CYS181 3.9 58.2 1.0
N A:GLY190 3.9 46.9 1.0
CB A:TYR188 4.0 51.8 1.0
CB A:VAL179 4.2 42.0 1.0
C A:VAL179 4.2 53.7 1.0
N A:CYS181 4.2 61.9 1.0
O1 A:EFZ999 4.3 48.9 1.0
N A:EFZ999 4.4 48.5 1.0
N A:VAL189 4.5 54.9 1.0
C A:VAL189 4.5 47.2 1.0
CA A:VAL189 4.5 49.1 1.0
C1 A:EFZ999 4.6 42.8 1.0
CA A:GLY190 4.6 46.8 1.0
CA A:TYR188 4.6 50.4 1.0
C5 A:EFZ999 4.6 38.1 1.0
CA A:CYS181 4.7 55.5 1.0
C A:ILE180 4.7 59.4 1.0
N A:ILE180 4.8 51.2 1.0
CA A:ILE180 4.8 51.6 1.0
CA A:VAL179 4.9 52.7 1.0

Fluorine binding site 2 out of 3 in 1jkh

Go back to Fluorine Binding Sites List in 1jkh
Fluorine binding site 2 out of 3 in the Crystal Structure of Y181C Mutant Hiv-1 Reverse Transcriptase in Complex with Dmp-266(Efavirenz)


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 Y181C Mutant Hiv-1 Reverse Transcriptase in Complex with Dmp-266(Efavirenz) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F999

b:64.3
occ:1.00
 F2 A:EFZ999 0.0 64.3 1.0
C13 A:EFZ999 1.3 60.0 1.0
F1 A:EFZ999 2.1 55.3 1.0
F3 A:EFZ999 2.1 70.6 1.0
C7 A:EFZ999 2.4 59.6 1.0
C8 A:EFZ999 2.9 61.1 1.0
C6 A:EFZ999 3.0 46.5 1.0
C5 A:EFZ999 3.3 38.1 1.0
CG1 A:VAL106 3.5 43.4 1.0
CB A:TYR188 3.5 51.8 1.0
N A:GLY190 3.6 46.9 1.0
O A:TYR188 3.6 61.0 1.0
C9 A:EFZ999 3.6 68.7 1.0
C A:TYR188 3.6 55.3 1.0
O2 A:EFZ999 3.6 65.0 1.0
C A:VAL189 3.8 47.2 1.0
N A:VAL189 3.9 54.9 1.0
CA A:GLY190 3.9 46.8 1.0
C1 A:EFZ999 4.1 42.8 1.0
O A:VAL189 4.1 44.9 1.0
CA A:TYR188 4.1 50.4 1.0
CA A:VAL189 4.2 49.1 1.0
C4 A:EFZ999 4.4 41.7 1.0
C14 A:EFZ999 4.5 55.5 1.0
N A:EFZ999 4.6 48.5 1.0
CB A:VAL106 4.6 43.4 1.0
CG2 A:VAL106 4.6 37.8 1.0
CG A:TYR188 4.7 60.9 1.0
O A:VAL179 4.8 53.7 1.0
CD2 A:TYR188 4.8 57.7 1.0
O A:THR107 4.9 57.4 1.0

Fluorine binding site 3 out of 3 in 1jkh

Go back to Fluorine Binding Sites List in 1jkh
Fluorine binding site 3 out of 3 in the Crystal Structure of Y181C Mutant Hiv-1 Reverse Transcriptase in Complex with Dmp-266(Efavirenz)


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 Y181C Mutant Hiv-1 Reverse Transcriptase in Complex with Dmp-266(Efavirenz) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F999

b:70.6
occ:1.00
 F3 A:EFZ999 0.0 70.6 1.0
C13 A:EFZ999 1.3 60.0 1.0
F2 A:EFZ999 2.1 64.3 1.0
F1 A:EFZ999 2.1 55.3 1.0
C7 A:EFZ999 2.4 59.6 1.0
O2 A:EFZ999 2.9 65.0 1.0
C6 A:EFZ999 2.9 46.5 1.0
C14 A:EFZ999 3.1 55.5 1.0
N A:EFZ999 3.2 48.5 1.0
CA A:GLY190 3.3 46.8 1.0
C1 A:EFZ999 3.3 42.8 1.0
N A:GLY190 3.4 46.9 1.0
C8 A:EFZ999 3.7 61.1 1.0
CG A:LYS103 3.8 38.3 1.0
O1 A:EFZ999 3.9 48.9 1.0
C5 A:EFZ999 3.9 38.1 1.0
CB A:VAL179 4.2 42.0 1.0
CG1 A:VAL179 4.2 43.7 1.0
C A:GLY190 4.2 47.5 1.0
C A:VAL189 4.2 47.2 1.0
O A:VAL179 4.3 53.7 1.0
C2 A:EFZ999 4.4 31.3 1.0
CE A:LYS103 4.5 45.8 1.0
O A:GLY190 4.6 47.1 1.0
O A:TYR188 4.7 61.0 1.0
CD A:LYS103 4.7 42.1 1.0
C9 A:EFZ999 4.7 68.7 1.0
CB A:LYS103 4.8 39.1 1.0
CG1 A:VAL106 4.8 43.4 1.0
C4 A:EFZ999 4.8 41.7 1.0
O A:VAL189 4.8 44.9 1.0
CG2 A:VAL106 4.9 37.8 1.0
CA A:VAL189 5.0 49.1 1.0
C A:VAL179 5.0 53.7 1.0

Reference:

J.Ren, C.Nichols, L.Bird, P.Chamberlain, K.Weaver, S.Short, D.I.Stuart, D.K.Stammers. Structural Mechanisms of Drug Resistance For Mutations at Codons 181 and 188 in Hiv-1 Reverse Transcriptase and the Improved Resilience of Second Generation Non-Nucleoside Inhibitors. J.Mol.Biol. V. 312 795 2001.
ISSN: ISSN 0022-2836
PubMed: 11575933
DOI: 10.1006/JMBI.2001.4988
Page generated: Sun Dec 13 11:30:30 2020

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