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Fluorine in PDB 4b6p: Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid

Enzymatic activity of Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid

All present enzymatic activity of Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid:
4.2.1.10;

Protein crystallography data

The structure of Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid, PDB code: 4b6p was solved by J.M.Otero, A.L.Llamas-Saiz, E.Lence, L.Tizon, A.Peon, V.F.V.Prazeres, H.Lamb, A.R.Hawkins, C.Gonzalez-Bello, M.J.Van Raaij, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.64 / 2.30
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 126.270, 126.270, 126.270, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 22.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid (pdb code 4b6p). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid, PDB code: 4b6p:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 4b6p

Go back to Fluorine Binding Sites List in 4b6p
Fluorine binding site 1 out of 5 in the Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1145

b:22.5
occ:1.00
 FAK A:2HN1145 0.0 22.5 1.0
CAT A:2HN1145 1.3 20.7 1.0
CAR A:2HN1145 2.3 21.2 1.0
CAU A:2HN1145 2.4 18.6 1.0
FAI A:2HN1145 2.7 22.2 1.0
CAL A:2HN1145 2.9 18.3 1.0
CD1 A:LEU13 3.3 9.2 1.0
CAX A:2HN1145 3.6 16.2 1.0
CAP A:2HN1145 3.6 22.3 1.0
CAS A:2HN1145 3.6 19.6 1.0
OAC A:2HN1145 3.8 14.8 1.0
CD1 A:TYR24 3.8 34.3 1.0
CD1 A:ILE102 3.9 12.5 1.0
CE1 A:TYR24 4.0 35.1 1.0
CG A:TYR24 4.0 37.2 1.0
CAN A:2HN1145 4.0 14.8 1.0
CAQ A:2HN1145 4.1 20.9 1.0
CD1 A:LEU16 4.1 22.6 1.0
CD2 A:LEU13 4.2 15.2 1.0
CZ A:TYR24 4.3 35.3 1.0
CD2 A:TYR24 4.3 36.7 1.0
CG A:LEU13 4.4 15.8 1.0
OAA A:2HN1145 4.4 14.9 1.0
CAY A:2HN1145 4.5 15.0 1.0
CE2 A:TYR24 4.5 35.7 1.0
CB A:ILE102 4.5 13.3 1.0
CB A:TYR24 4.6 40.6 1.0
CG1 A:ILE102 4.6 11.4 1.0
FAG A:2HN1145 4.7 27.0 1.0
CAO A:2HN1145 4.7 15.3 1.0
FAJ A:2HN1145 4.8 20.5 1.0
OAB A:2HN1145 4.9 16.5 1.0

Fluorine binding site 2 out of 5 in 4b6p

Go back to Fluorine Binding Sites List in 4b6p
Fluorine binding site 2 out of 5 in the Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1145

b:22.2
occ:1.00
 FAI A:2HN1145 0.0 22.2 1.0
CAR A:2HN1145 1.3 21.2 1.0
CAT A:2HN1145 2.4 20.7 1.0
CAP A:2HN1145 2.4 22.3 1.0
FAK A:2HN1145 2.7 22.5 1.0
FAG A:2HN1145 2.8 27.0 1.0
O A:ASN12 3.4 13.5 1.0
CD1 A:LEU16 3.5 22.6 1.0
CA A:LEU16 3.5 24.9 1.0
N A:LEU16 3.5 22.6 1.0
CAQ A:2HN1145 3.6 20.9 1.0
CAU A:2HN1145 3.6 18.6 1.0
CB A:LEU16 3.7 24.8 1.0
CA A:LEU13 4.0 14.3 1.0
CD1 A:LEU13 4.0 9.2 1.0
CAS A:2HN1145 4.1 19.6 1.0
CG A:LEU16 4.2 24.3 1.0
C A:ARG15 4.2 20.4 1.0
C A:ASN12 4.3 13.9 1.0
CD2 A:TYR24 4.3 36.7 1.0
O A:LEU13 4.4 14.2 1.0
CD A:ARG19 4.4 46.7 1.0
C A:LEU13 4.5 14.1 1.0
N A:LEU13 4.5 14.1 1.0
CE2 A:TYR24 4.6 35.7 1.0
CG A:TYR24 4.6 37.2 1.0
FAH A:2HN1145 4.7 19.4 1.0
O A:ARG15 4.7 21.4 1.0
CG A:LEU13 4.8 15.8 1.0
CD2 A:LEU13 4.9 15.2 1.0
CAL A:2HN1145 4.9 18.3 1.0
CD2 A:LEU16 4.9 23.7 1.0
CB A:LEU13 4.9 14.3 1.0
N A:ARG15 5.0 16.6 1.0
CA A:ARG15 5.0 17.7 1.0
C A:LEU16 5.0 27.5 1.0
CB A:ARG15 5.0 16.7 1.0
CB A:TYR24 5.0 40.6 1.0

Fluorine binding site 3 out of 5 in 4b6p

Go back to Fluorine Binding Sites List in 4b6p
Fluorine binding site 3 out of 5 in the Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1145

b:27.0
occ:1.00
 FAG A:2HN1145 0.0 27.0 1.0
CAP A:2HN1145 1.3 22.3 1.0
CAQ A:2HN1145 2.2 20.9 1.0
CAR A:2HN1145 2.4 21.2 1.0
FAH A:2HN1145 2.5 19.4 1.0
O A:ASN12 2.7 13.5 1.0
FAI A:2HN1145 2.8 22.2 1.0
CD A:ARG19 2.9 46.7 1.0
NH1 A:ARG19 3.0 46.5 1.0
NE A:ARG19 3.3 44.9 1.0
CZ A:ARG19 3.4 45.7 1.0
CAS A:2HN1145 3.5 19.6 1.0
CB A:ARG15 3.6 16.7 1.0
CAT A:2HN1145 3.6 20.7 1.0
C A:ASN12 3.7 13.9 1.0
CB A:ASN12 3.7 13.4 1.0
CAU A:2HN1145 4.1 18.6 1.0
CA A:ASN12 4.2 13.7 1.0
CG A:ARG19 4.3 47.4 1.0
C A:ARG15 4.3 20.4 1.0
CG A:ARG15 4.4 15.7 1.0
NH2 A:ARG19 4.4 44.5 1.0
CA A:ARG15 4.4 17.7 1.0
N A:LEU16 4.5 22.6 1.0
FAJ A:2HN1145 4.6 20.5 1.0
O A:ARG15 4.6 21.4 1.0
FAK A:2HN1145 4.7 22.5 1.0
N A:LEU13 4.7 14.1 1.0
CE2 A:TYR24 4.7 35.7 1.0
CG A:ASN12 4.7 12.9 1.0
N A:ARG15 4.8 16.6 1.0

Fluorine binding site 4 out of 5 in 4b6p

Go back to Fluorine Binding Sites List in 4b6p
Fluorine binding site 4 out of 5 in the Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1145

b:19.4
occ:1.00
 FAH A:2HN1145 0.0 19.4 1.0
CAQ A:2HN1145 1.3 20.9 1.0
CAP A:2HN1145 2.3 22.3 1.0
CAS A:2HN1145 2.4 19.6 1.0
FAG A:2HN1145 2.5 27.0 1.0
FAJ A:2HN1145 2.7 20.5 1.0
NH1 A:ARG19 2.9 46.5 1.0
CZ A:ARG19 3.0 45.7 1.0
NH2 A:ARG19 3.3 44.5 1.0
CB A:ASN12 3.5 13.4 1.0
NE A:ARG19 3.6 44.9 1.0
CAR A:2HN1145 3.6 21.2 1.0
CAU A:2HN1145 3.6 18.6 1.0
CG A:ASN12 4.0 12.9 1.0
CAT A:2HN1145 4.1 20.7 1.0
CD A:ARG19 4.1 46.7 1.0
O A:HOH2046 4.4 31.7 1.0
ND2 A:ASN12 4.4 11.9 1.0
O A:ASN12 4.4 13.5 1.0
OH A:TYR24 4.6 34.9 1.0
OD1 A:ASN12 4.6 14.9 1.0
OAB A:2HN1145 4.6 16.5 1.0
FAI A:2HN1145 4.7 22.2 1.0
CA A:ASN12 4.8 13.7 1.0
CE2 A:TYR24 4.8 35.7 1.0
CAL A:2HN1145 4.9 18.3 1.0
C A:ASN12 4.9 13.9 1.0
O A:HOH2003 4.9 13.0 1.0
CZ A:TYR24 5.0 35.3 1.0

Fluorine binding site 5 out of 5 in 4b6p

Go back to Fluorine Binding Sites List in 4b6p
Fluorine binding site 5 out of 5 in the Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By (2S)-2-Perfluorobenzyl-3-Dehydroquinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1145

b:20.5
occ:1.00
 FAJ A:2HN1145 0.0 20.5 1.0
CAS A:2HN1145 1.4 19.6 1.0
CAQ A:2HN1145 2.3 20.9 1.0
CAU A:2HN1145 2.4 18.6 1.0
FAH A:2HN1145 2.7 19.4 1.0
CAL A:2HN1145 2.9 18.3 1.0
CAO A:2HN1145 3.0 15.3 1.0
OAB A:2HN1145 3.0 16.5 1.0
OH A:TYR24 3.3 34.9 1.0
CAW A:2HN1145 3.3 15.5 1.0
O A:HOH2046 3.5 31.7 1.0
CAX A:2HN1145 3.6 16.2 1.0
CAP A:2HN1145 3.6 22.3 1.0
CAT A:2HN1145 3.7 20.7 1.0
OAE A:2HN1145 3.8 13.7 1.0
CZ A:TYR24 4.1 35.3 1.0
CAR A:2HN1145 4.1 21.2 1.0
O A:HOH2003 4.4 13.0 1.0
FAG A:2HN1145 4.6 27.0 1.0
NH1 A:ARG108 4.6 22.4 1.0
NH1 A:ARG112 4.7 17.0 1.0
CE2 A:TYR24 4.7 35.7 1.0
CAV A:2HN1145 4.7 15.2 1.0
NH2 A:ARG108 4.8 27.3 1.0
CE1 A:TYR24 4.8 35.1 1.0
CAY A:2HN1145 4.8 15.0 1.0
FAK A:2HN1145 4.8 22.5 1.0
CAM A:2HN1145 4.9 13.3 1.0
NH2 A:ARG19 5.0 44.5 1.0

Reference:

E.Lence, L.Tizon, J.M.Otero, A.Peon, V.F.Prazeres, A.L.Llamas-Saiz, G.C.Fox, M.J.Van Raaij, H.Lamb, A.R.Hawkins, C.Gonzalez-Bello. Mechanistic Basis of the Inhibition of Type II Dehydroquinase By (2S)- and (2R)-2-Benzyl-3-Dehydroquinic Acids. Acs Chem. Biol. V. 8 568 2013.
ISSN: ESSN 1554-8937
PubMed: 23198883
DOI: 10.1021/CB300493S
Page generated: Thu Aug 1 00:06:39 2024

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