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Fluorine in PDB 3g30: Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30)

Enzymatic activity of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30)

All present enzymatic activity of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30):
3.5.2.6;

Protein crystallography data

The structure of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30), PDB code: 3g30 was solved by Y.Chen, B.K.Shoichet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.43 / 1.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 41.803, 41.803, 230.542, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 24.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30) (pdb code 3g30). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30), PDB code: 3g30:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3g30

Go back to Fluorine Binding Sites List in 3g30
Fluorine binding site 1 out of 6 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:25.3
occ:0.50
 F11 A:G301 0.0 25.3 0.5
C11 A:G301 1.4 24.9 0.5
C12 A:G301 2.4 24.4 0.5
C10 A:G301 2.4 25.5 0.5
OD1 A:ASP240 3.5 26.8 1.0
CB A:ASN170 3.6 17.0 1.0
C13 A:G301 3.6 25.9 0.5
C9 A:G301 3.7 24.7 0.5
CG A:ASP240 4.0 23.7 1.0
O A:ASN170 4.0 16.9 1.0
C14 A:G301 4.2 24.7 0.5
OD2 A:ASP240 4.2 26.7 1.0
N A:ASP240 4.2 15.8 1.0
C A:ASN170 4.4 17.6 1.0
CA A:GLY238 4.5 16.4 1.0
CG A:ASN170 4.6 18.9 1.0
O A:PRO167 4.6 19.1 1.0
C A:GLY238 4.6 15.2 1.0
CA A:ASN170 4.7 16.3 1.0
ND2 A:ASN170 4.7 20.6 1.0
N5 A:G301 4.8 25.0 0.5
CB A:ASP240 4.9 17.6 1.0
O15 A:G301 4.9 25.9 0.5

Fluorine binding site 2 out of 6 in 3g30

Go back to Fluorine Binding Sites List in 3g30
Fluorine binding site 2 out of 6 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:26.3
occ:0.50
 F14 A:G301 0.0 26.3 0.5
C14 A:G301 1.3 24.7 0.5
OG A:SER237 2.3 20.3 0.5
C13 A:G301 2.4 25.9 0.5
C9 A:G301 2.4 24.7 0.5
N5 A:G301 2.8 25.0 0.5
CB A:SER237 3.2 18.6 0.5
CB A:SER237 3.2 19.0 0.5
O7 A:G301 3.4 24.7 0.5
C12 A:G301 3.6 24.4 0.5
C A:SER237 3.7 18.0 1.0
C10 A:G301 3.7 25.5 0.5
O A:SER237 3.8 16.9 1.0
O A:HOH337 3.9 53.9 1.0
C4 A:G301 4.0 25.1 0.5
N A:GLY238 4.0 16.3 1.0
CA A:SER237 4.0 17.8 0.5
CA A:SER237 4.1 18.0 0.5
C11 A:G301 4.1 24.9 0.5
O A:HOH317 4.2 27.2 1.0
OG A:SER237 4.3 18.5 0.5
CA A:GLY238 4.4 16.4 1.0
C6 A:G301 4.5 23.9 0.5
C3 A:G301 4.6 26.1 0.5
C1 A:G301 4.8 24.1 0.5
O A:GLY238 4.8 14.9 1.0
N A:SER237 4.9 19.0 1.0
O A:HOH395 4.9 33.4 1.0
O15 A:G301 4.9 25.9 0.5
C A:GLY238 4.9 15.2 1.0

Fluorine binding site 3 out of 6 in 3g30

Go back to Fluorine Binding Sites List in 3g30
Fluorine binding site 3 out of 6 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2

b:30.3
occ:1.00
 F11 A:G302 0.0 30.3 1.0
C11 A:G302 1.3 30.4 1.0
C10 A:G302 2.3 31.6 1.0
C12 A:G302 2.4 30.4 1.0
N A:ALA150 3.0 18.5 1.0
CA A:ALA150 3.1 18.6 1.0
C A:THR149 3.2 16.9 1.0
O A:THR149 3.4 16.7 1.0
CG2 A:THR149 3.5 18.6 1.0
C9 A:G302 3.5 33.1 1.0
C13 A:G302 3.6 29.2 1.0
O A:GLY146 3.6 18.4 1.0
CB A:THR149 3.6 18.2 1.0
CG A:ARG153 3.7 23.0 1.0
CB A:ALA150 3.9 19.2 1.0
CA A:THR149 4.0 17.7 1.0
C14 A:G302 4.0 32.0 1.0
F14 A:G303 4.2 36.3 1.0
C A:ALA150 4.4 18.4 1.0
CB A:ARG153 4.4 22.1 1.0
O15 A:G302 4.6 38.8 1.0
N5 A:G302 4.7 34.6 1.0
C A:GLY146 4.7 17.1 1.0
NE A:ARG153 4.8 26.2 1.0
C14 A:G303 4.8 35.7 1.0
O A:ALA150 4.8 18.7 1.0
O8 A:G303 4.8 49.8 1.0
CD A:ARG153 4.9 22.2 1.0
N A:THR149 4.9 16.7 1.0
OG1 A:THR149 5.0 18.5 1.0

Fluorine binding site 4 out of 6 in 3g30

Go back to Fluorine Binding Sites List in 3g30
Fluorine binding site 4 out of 6 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2

b:31.5
occ:1.00
 F14 A:G302 0.0 31.5 1.0
C14 A:G302 1.3 32.0 1.0
C9 A:G302 2.4 33.1 1.0
C13 A:G302 2.4 29.2 1.0
N5 A:G302 2.7 34.6 1.0
C12 A:G302 3.6 30.4 1.0
C10 A:G302 3.6 31.6 1.0
O A:HOH356 3.8 48.5 1.0
C12 A:G303 3.8 37.4 1.0
C4 A:G302 4.0 40.6 1.0
C11 A:G302 4.1 30.4 1.0
C13 A:G303 4.2 35.0 1.0
C11 A:G303 4.3 36.2 1.0
O A:HOH368 4.4 46.2 1.0
O A:HOH11 4.6 49.5 1.0
F11 A:G303 4.6 40.0 1.0
C3 A:G302 4.7 44.9 1.0
O15 A:G302 4.9 38.8 1.0
C14 A:G303 4.9 35.7 1.0

Fluorine binding site 5 out of 6 in 3g30

Go back to Fluorine Binding Sites List in 3g30
Fluorine binding site 5 out of 6 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3

b:40.0
occ:1.00
 F11 A:G303 0.0 40.0 1.0
C11 A:G303 1.3 36.2 1.0
C12 A:G303 2.3 37.4 1.0
C10 A:G303 2.4 35.7 1.0
C13 A:G303 3.6 35.0 1.0
C9 A:G303 3.6 37.6 1.0
C14 A:G303 4.1 35.7 1.0
O A:HOH356 4.3 48.5 1.0
N5 A:G302 4.3 34.6 1.0
F14 A:G302 4.6 31.5 1.0
C4 A:G302 4.7 40.6 1.0
C3 A:G302 4.8 44.9 1.0
N5 A:G303 4.8 40.8 1.0

Fluorine binding site 6 out of 6 in 3g30

Go back to Fluorine Binding Sites List in 3g30
Fluorine binding site 6 out of 6 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 3 (G30) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3

b:36.3
occ:1.00
 F14 A:G303 0.0 36.3 1.0
C14 A:G303 1.3 35.7 1.0
C13 A:G303 2.4 35.0 1.0
C9 A:G303 2.4 37.6 1.0
N5 A:G303 2.7 40.8 1.0
O8 A:G303 3.0 49.8 1.0
C12 A:G303 3.6 37.4 1.0
C10 A:G303 3.7 35.7 1.0
C10 A:G302 3.7 31.6 1.0
C4 A:G303 4.0 45.0 1.0
C11 A:G302 4.0 30.4 1.0
C6 A:G303 4.0 50.6 1.0
C11 A:G303 4.1 36.2 1.0
O15 A:G302 4.1 38.8 1.0
F11 A:G302 4.2 30.3 1.0
C9 A:G302 4.2 33.1 1.0
N5 A:G302 4.6 34.6 1.0
C4 A:G302 4.7 40.6 1.0
O15 A:G303 4.7 47.0 1.0
C12 A:G302 4.7 30.4 1.0
O7 A:G303 4.8 51.8 1.0
C2 A:G303 4.8 48.7 1.0
C14 A:G302 4.9 32.0 1.0
C3 A:G303 4.9 48.0 1.0
C1 A:G303 5.0 50.1 1.0

Reference:

Y.Chen, B.K.Shoichet. Molecular Docking and Ligand Specificity in Fragment-Based Inhibitor Discovery Nat.Chem.Biol. V. 5 358 2009.
ISSN: ISSN 1552-4450
PubMed: 19305397
DOI: 10.1038/NCHEMBIO.155
Page generated: Wed Jul 31 18:43:11 2024

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