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Fluorine in PDB 6ook: Ctx-M-14 Beta Lactamase with Compound 3

Enzymatic activity of Ctx-M-14 Beta Lactamase with Compound 3

All present enzymatic activity of Ctx-M-14 Beta Lactamase with Compound 3:
3.5.2.6;

Protein crystallography data

The structure of Ctx-M-14 Beta Lactamase with Compound 3, PDB code: 6ook was solved by M.Kemp, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.27 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.003, 106.725, 47.736, 90.00, 101.73, 90.00
R / Rfree (%) 12.2 / 15.4

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Ctx-M-14 Beta Lactamase with Compound 3 (pdb code 6ook). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Ctx-M-14 Beta Lactamase with Compound 3, PDB code: 6ook:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 6ook

Go back to Fluorine Binding Sites List in 6ook
Fluorine binding site 1 out of 12 in the Ctx-M-14 Beta Lactamase with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ctx-M-14 Beta Lactamase with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:24.9
occ:0.87
 F07 A:MZV301 0.0 24.9 0.9
C06 A:MZV301 1.4 25.5 0.9
F08 A:MZV301 2.2 24.7 0.9
F09 A:MZV301 2.2 25.6 0.9
C05 A:MZV301 2.4 28.4 0.9
C10 A:MZV301 2.9 25.9 0.9
N25 A:MZV302 3.0 11.9 1.0
CG2 A:THR216 3.3 11.2 1.0
N24 A:MZV302 3.3 11.2 1.0
CB A:THR216 3.3 9.8 1.0
N26 A:MZV302 3.4 10.9 1.0
O A:HOH557 3.5 15.6 1.0
C04 A:MZV301 3.5 22.4 0.9
OG1 A:THR235 3.7 9.5 1.0
C23 A:MZV302 3.8 11.4 1.0
N27 A:MZV302 3.8 10.1 1.0
OG1 A:THR216 3.9 10.1 1.0
C11 A:MZV301 4.2 27.7 0.9
CB A:SER130 4.3 10.5 1.0
O A:HOH532 4.5 13.0 1.0
C03 A:MZV301 4.6 28.5 0.9
CA A:THR216 4.6 9.5 1.0
OG A:SER130 4.7 15.0 1.0
C22 A:MZV302 4.8 10.7 1.0
O A:THR216 4.8 10.6 1.0
CB A:THR235 4.8 9.6 1.0
C18 A:MZV301 4.9 39.2 0.9
C28 A:MZV302 5.0 11.7 1.0

Fluorine binding site 2 out of 12 in 6ook

Go back to Fluorine Binding Sites List in 6ook
Fluorine binding site 2 out of 12 in the Ctx-M-14 Beta Lactamase with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ctx-M-14 Beta Lactamase with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:24.7
occ:0.87
 F08 A:MZV301 0.0 24.7 0.9
C06 A:MZV301 1.4 25.5 0.9
F09 A:MZV301 2.2 25.6 0.9
F07 A:MZV301 2.2 24.9 0.9
C05 A:MZV301 2.3 28.4 0.9
C04 A:MZV301 2.6 22.4 0.9
CE2 A:TYR105 3.4 12.8 1.0
CB A:SER130 3.4 10.5 1.0
N24 A:MZV302 3.6 11.2 1.0
C10 A:MZV301 3.6 25.9 0.9
O A:TYR129 3.7 10.6 1.0
C28 A:MZV302 3.7 11.7 1.0
CZ A:TYR105 3.8 15.9 1.0
OH A:TYR105 3.8 19.2 1.0
C23 A:MZV302 3.8 11.4 1.0
O A:HOH423 3.9 17.8 1.0
C03 A:MZV301 4.0 28.5 0.9
CG2 A:THR216 4.0 11.2 1.0
OG A:SER130 4.1 15.0 1.0
C22 A:MZV302 4.1 10.7 1.0
CD2 A:TYR105 4.1 11.9 1.0
N25 A:MZV302 4.1 11.9 1.0
N27 A:MZV302 4.5 10.1 1.0
CA A:SER130 4.6 8.9 1.0
C A:TYR129 4.6 9.4 1.0
O A:SER130 4.6 9.9 1.0
N26 A:MZV302 4.6 10.9 1.0
C11 A:MZV301 4.7 27.7 0.9
C29 A:MZV302 4.7 11.4 1.0
CE1 A:TYR105 4.8 16.4 1.0
CB A:THR216 4.8 9.8 1.0
C18 A:MZV301 4.8 39.2 0.9
O01 A:MZV301 4.9 40.3 0.9
C02 A:MZV301 4.9 21.5 0.9
C A:SER130 4.9 8.7 1.0
N A:SER130 5.0 9.0 1.0

Fluorine binding site 3 out of 12 in 6ook

Go back to Fluorine Binding Sites List in 6ook
Fluorine binding site 3 out of 12 in the Ctx-M-14 Beta Lactamase with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ctx-M-14 Beta Lactamase with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:25.6
occ:0.87
 F09 A:MZV301 0.0 25.6 0.9
C06 A:MZV301 1.4 25.5 0.9
F08 A:MZV301 2.2 24.7 0.9
F07 A:MZV301 2.2 24.9 0.9
C05 A:MZV301 2.3 28.4 0.9
C10 A:MZV301 2.9 25.9 0.9
C04 A:MZV301 3.3 22.4 0.9
CG2 A:THR216 3.6 11.2 1.0
OH A:TYR105 3.8 19.2 1.0
O A:HOH423 3.9 17.8 1.0
CB A:THR216 4.1 9.8 1.0
C11 A:MZV301 4.2 27.7 0.9
CZ A:TYR105 4.4 15.9 1.0
C03 A:MZV301 4.4 28.5 0.9
O A:HOH557 4.6 15.6 1.0
CE2 A:TYR105 4.6 12.8 1.0
O A:HOH470 4.8 22.5 1.0
C18 A:MZV301 4.8 39.2 0.9
O A:TYR129 4.9 10.6 1.0

Fluorine binding site 4 out of 12 in 6ook

Go back to Fluorine Binding Sites List in 6ook
Fluorine binding site 4 out of 12 in the Ctx-M-14 Beta Lactamase with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ctx-M-14 Beta Lactamase with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:17.2
occ:0.96
 F07 A:MZV302 0.0 17.2 1.0
C06 A:MZV302 1.4 18.8 1.0
F08 A:MZV302 2.2 17.0 1.0
F09 A:MZV302 2.2 22.5 1.0
C05 A:MZV302 2.3 16.4 1.0
C04 A:MZV302 3.0 13.8 1.0
O A:PRO167 3.1 11.3 1.0
N A:THR171 3.1 10.3 1.0
C A:ASN170 3.2 10.9 1.0
C10 A:MZV302 3.3 16.3 1.0
CG2 A:THR171 3.4 11.5 1.0
CA A:THR171 3.5 10.9 1.0
O A:ASN170 3.6 10.9 1.0
CA A:ASN170 3.8 10.5 1.0
CB A:ASN170 3.8 11.2 1.0
CA A:THR168 3.8 10.5 1.0
N A:ASN170 3.8 10.7 1.0
O A:THR168 3.9 11.4 1.0
C A:PRO167 4.0 10.6 1.0
C A:THR168 4.0 10.5 1.0
CB A:THR171 4.0 10.7 1.0
C03 A:MZV302 4.3 12.9 1.0
N A:THR168 4.4 10.4 1.0
C11 A:MZV302 4.5 16.6 1.0
C A:THR171 4.8 11.5 1.0
C18 A:MZV302 4.9 12.8 1.0
ND2 A:ASN170 4.9 12.0 1.0
N A:LEU169 4.9 9.7 1.0
CG A:ASN170 4.9 10.7 1.0
CB A:THR168 4.9 11.2 1.0
OG1 A:THR171 4.9 10.9 1.0
C A:LEU169 5.0 9.9 1.0

Fluorine binding site 5 out of 12 in 6ook

Go back to Fluorine Binding Sites List in 6ook
Fluorine binding site 5 out of 12 in the Ctx-M-14 Beta Lactamase with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Ctx-M-14 Beta Lactamase with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:17.0
occ:0.96
 F08 A:MZV302 0.0 17.0 1.0
C06 A:MZV302 1.4 18.8 1.0
F07 A:MZV302 2.2 17.2 1.0
F09 A:MZV302 2.2 22.5 1.0
C05 A:MZV302 2.4 16.4 1.0
C04 A:MZV302 2.8 13.8 1.0
O A:PRO167 3.2 11.3 1.0
C A:PRO167 3.5 10.6 1.0
C10 A:MZV302 3.6 16.3 1.0
CB A:PRO167 3.6 11.6 1.0
CG A:PRO167 3.8 12.4 1.0
CA A:THR168 4.0 10.5 1.0
N A:THR168 4.0 10.4 1.0
C03 A:MZV302 4.1 12.9 1.0
CA A:PRO167 4.2 12.1 1.0
O A:HOH635 4.5 45.8 1.0
C11 A:MZV302 4.7 16.6 1.0
CG2 A:THR168 4.7 13.3 1.0
CG2 A:THR171 4.8 11.5 1.0
C A:THR168 4.9 10.5 1.0
CB A:THR168 4.9 11.2 1.0
C18 A:MZV302 4.9 12.8 1.0
ND2 A:ASN104 5.0 14.4 1.0
O01 A:MZV302 5.0 13.2 1.0

Fluorine binding site 6 out of 12 in 6ook

Go back to Fluorine Binding Sites List in 6ook
Fluorine binding site 6 out of 12 in the Ctx-M-14 Beta Lactamase with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Ctx-M-14 Beta Lactamase with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:22.5
occ:0.96
 F09 A:MZV302 0.0 22.5 1.0
C06 A:MZV302 1.4 18.8 1.0
F07 A:MZV302 2.2 17.2 1.0
F08 A:MZV302 2.2 17.0 1.0
C05 A:MZV302 2.3 16.4 1.0
C10 A:MZV302 2.7 16.3 1.0
C04 A:MZV302 3.6 13.8 1.0
CG2 A:THR171 4.0 11.5 1.0
C11 A:MZV302 4.1 16.6 1.0
CA A:THR171 4.5 10.9 1.0
C03 A:MZV302 4.7 12.9 1.0
N A:THR171 4.8 10.3 1.0
C17 A:MZV302 4.9 20.5 1.0
CB A:THR171 4.9 10.7 1.0
O A:HOH459 4.9 15.8 1.0
O A:PRO167 4.9 11.3 1.0
C18 A:MZV302 4.9 12.8 1.0
O A:ASN170 5.0 10.9 1.0
C A:ASN170 5.0 10.9 1.0

Fluorine binding site 7 out of 12 in 6ook

Go back to Fluorine Binding Sites List in 6ook
Fluorine binding site 7 out of 12 in the Ctx-M-14 Beta Lactamase with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Ctx-M-14 Beta Lactamase with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:18.6
occ:0.95
 F07 B:MZV301 0.0 18.6 0.9
C06 B:MZV301 1.4 20.8 0.9
F08 B:MZV301 2.2 19.4 0.9
F09 B:MZV301 2.2 24.7 0.9
C05 B:MZV301 2.4 16.8 0.9
C04 B:MZV301 2.8 13.5 0.9
O B:PRO167 3.1 12.0 1.0
CB B:PRO167 3.5 13.0 1.0
C B:PRO167 3.5 12.0 1.0
C10 B:MZV301 3.6 17.9 0.9
CG B:PRO167 3.9 14.0 1.0
CA B:THR168 4.0 12.3 1.0
N B:THR168 4.0 11.5 1.0
C03 B:MZV301 4.1 14.8 0.9
CA B:PRO167 4.2 11.6 1.0
C11 B:MZV301 4.7 18.3 0.9
CG2 B:THR168 4.7 14.7 1.0
CG2 B:THR171 4.8 15.2 1.0
C B:THR168 4.9 12.3 1.0
O01 B:MZV301 4.9 12.5 0.9
C18 B:MZV301 4.9 14.8 0.9
CB B:THR168 5.0 12.8 1.0
ND2 B:ASN104 5.0 15.9 1.0

Fluorine binding site 8 out of 12 in 6ook

Go back to Fluorine Binding Sites List in 6ook
Fluorine binding site 8 out of 12 in the Ctx-M-14 Beta Lactamase with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Ctx-M-14 Beta Lactamase with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:19.4
occ:0.95
 F08 B:MZV301 0.0 19.4 0.9
C06 B:MZV301 1.4 20.8 0.9
F07 B:MZV301 2.2 18.6 0.9
F09 B:MZV301 2.2 24.7 0.9
C05 B:MZV301 2.3 16.8 0.9
C04 B:MZV301 3.0 13.5 0.9
O B:PRO167 3.1 12.0 1.0
N B:THR171 3.1 12.8 1.0
C B:ASN170 3.2 13.7 1.0
C10 B:MZV301 3.3 17.9 0.9
CG2 B:THR171 3.4 15.2 1.0
CA B:THR171 3.5 14.4 1.0
O B:ASN170 3.6 13.6 1.0
CB B:ASN170 3.7 13.4 1.0
CA B:ASN170 3.7 12.6 1.0
N B:ASN170 3.8 12.5 1.0
CA B:THR168 3.8 12.3 1.0
O B:THR168 3.9 12.6 1.0
C B:PRO167 4.0 12.0 1.0
C B:THR168 4.0 12.3 1.0
CB B:THR171 4.0 15.2 1.0
C03 B:MZV301 4.3 14.8 0.9
N B:THR168 4.4 11.5 1.0
C11 B:MZV301 4.5 18.3 0.9
ND2 B:ASN170 4.8 12.6 1.0
CG B:ASN170 4.8 12.2 1.0
C B:THR171 4.9 15.5 1.0
N B:LEU169 4.9 11.6 1.0
C18 B:MZV301 4.9 14.8 0.9
CB B:THR168 4.9 12.8 1.0
OG1 B:THR171 5.0 16.1 1.0
C B:LEU169 5.0 12.2 1.0

Fluorine binding site 9 out of 12 in 6ook

Go back to Fluorine Binding Sites List in 6ook
Fluorine binding site 9 out of 12 in the Ctx-M-14 Beta Lactamase with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Ctx-M-14 Beta Lactamase with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:24.7
occ:0.95
 F09 B:MZV301 0.0 24.7 0.9
C06 B:MZV301 1.4 20.8 0.9
F08 B:MZV301 2.2 19.4 0.9
F07 B:MZV301 2.2 18.6 0.9
C05 B:MZV301 2.4 16.8 0.9
C10 B:MZV301 2.8 17.9 0.9
O B:HOH524 3.1 43.5 1.0
C04 B:MZV301 3.6 13.5 0.9
CG2 B:THR171 4.0 15.2 1.0
C11 B:MZV301 4.2 18.3 0.9
CA B:THR171 4.6 14.4 1.0
C03 B:MZV301 4.7 14.8 0.9
O B:PRO167 4.8 12.0 1.0
N B:THR171 4.8 12.8 1.0
CB B:THR171 4.9 15.2 1.0
OD2 B:ASP240 4.9 25.9 1.0
C17 B:MZV301 4.9 27.6 0.9
C18 B:MZV301 5.0 14.8 0.9

Fluorine binding site 10 out of 12 in 6ook

Go back to Fluorine Binding Sites List in 6ook
Fluorine binding site 10 out of 12 in the Ctx-M-14 Beta Lactamase with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Ctx-M-14 Beta Lactamase with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:25.5
occ:0.86
 F07 B:MZV302 0.0 25.5 0.9
C06 B:MZV302 1.4 19.8 0.9
F08 B:MZV302 2.2 23.5 0.9
F09 B:MZV302 2.2 27.2 0.9
C05 B:MZV302 2.3 18.7 0.9
C04 B:MZV302 2.9 21.0 0.9
C10 B:MZV302 3.4 19.2 0.9
O B:HOH640 3.6 28.8 1.0
CG2 B:THR216 3.6 11.3 1.0
OH B:TYR105 3.7 18.5 1.0
O B:HOH417 3.8 17.9 1.0
CB B:THR216 4.2 11.3 1.0
C03 B:MZV302 4.2 28.0 0.9
CZ B:TYR105 4.4 16.3 1.0
O B:HOH469 4.4 16.9 1.0
C11 B:MZV302 4.5 26.6 0.9
CE2 B:TYR105 4.6 13.8 1.0
C18 B:MZV302 4.8 21.6 0.9
O B:TYR129 5.0 11.6 1.0
O B:HOH460 5.0 20.0 1.0

Reference:

K.Defrees, M.T.Kemp, X.Elhilali-Pollard, X.Zhang, A.Mohamed, Y.Chen, A.R.Renslo. An Empirical Study of Amide-Heteroarene Pi-Stacking Interactions Using Reversible Inhibitors of A Bacterial Serine Hydrolase. Org Chem Front V. 6 1749 2019.
ISSN: ISSN 2052-4110
PubMed: 32774871
DOI: 10.1039/C9QO00342H
Page generated: Thu Aug 1 23:51:32 2024

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