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Fluorine in PDB 3g35: Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 12 (F13)

Enzymatic activity of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 12 (F13)

All present enzymatic activity of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 12 (F13):
3.5.2.6;

Protein crystallography data

The structure of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 12 (F13), PDB code: 3g35 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) 35.36 / 1.41
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.265, 107.243, 47.727, 90.00, 99.93, 90.00
R / Rfree (%) 15.5 / 18.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 12 (F13) (pdb code 3g35). 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 12 (F13), PDB code: 3g35:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3g35

Go back to Fluorine Binding Sites List in 3g35
Fluorine binding site 1 out of 6 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 12 (F13)


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 12 (F13) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:17.1
occ:1.00
 F21 A:F131 0.0 17.1 1.0
C16 A:F131 1.4 15.0 1.0
C15 A:F131 2.4 14.4 1.0
C17 A:F131 2.4 14.6 1.0
O A:PRO167 3.4 10.6 1.0
C14 A:F131 3.6 12.9 1.0
C18 A:F131 3.7 14.8 1.0
CG2 A:THR171 4.0 11.8 1.0
N A:THR171 4.1 10.3 1.0
C A:ASN170 4.1 10.6 1.0
C19 A:F131 4.1 14.2 1.0
O A:HOH466 4.2 41.9 1.0
C A:PRO167 4.2 10.6 1.0
O A:ASN170 4.3 10.5 1.0
CA A:THR171 4.3 10.9 1.0
CB A:ASN170 4.4 10.5 1.0
CA A:THR168 4.4 10.4 1.0
OD2 A:ASP240 4.6 16.8 1.0
CB A:PRO167 4.6 10.8 1.0
CA A:ASN170 4.6 10.3 1.0
N A:THR168 4.8 10.4 1.0
N A:ASN170 4.8 10.4 1.0
CB A:THR171 4.8 11.0 1.0
C13 A:F131 4.9 13.2 1.0
C A:THR168 4.9 10.7 1.0
O A:THR168 4.9 11.2 1.0
CG A:ASP240 5.0 14.1 1.0

Fluorine binding site 2 out of 6 in 3g35

Go back to Fluorine Binding Sites List in 3g35
Fluorine binding site 2 out of 6 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 12 (F13)


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 12 (F13) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3

b:23.0
occ:1.00
 F21 A:F133 0.0 23.0 1.0
C16 A:F133 1.3 21.2 1.0
C15 A:F133 2.4 20.9 1.0
C17 A:F133 2.4 21.7 1.0
O A:GLY147 2.9 12.7 1.0
CA A:GLY147 3.3 12.6 1.0
CB A:ALA150 3.5 12.3 1.0
C A:GLY147 3.5 12.1 1.0
C14 A:F133 3.6 21.1 1.0
C18 A:F133 3.6 21.4 1.0
C19 A:F133 4.1 21.3 1.0
O A:LEU142 4.1 13.3 1.0
N A:PHE151 4.3 11.8 1.0
CA A:ALA150 4.5 11.7 1.0
C A:ALA150 4.6 11.8 1.0
N A:GLY147 4.7 12.2 1.0
N A:VAL148 4.9 12.1 1.0
C13 A:F133 4.9 20.6 1.0
O A:GLY146 4.9 12.8 1.0
N A:ALA150 5.0 11.5 1.0

Fluorine binding site 3 out of 6 in 3g35

Go back to Fluorine Binding Sites List in 3g35
Fluorine binding site 3 out of 6 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 12 (F13)


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 12 (F13) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:18.7
occ:1.00
 F21 B:F132 0.0 18.7 1.0
C16 B:F132 1.3 15.5 1.0
C15 B:F132 2.4 14.2 1.0
C17 B:F132 2.4 15.1 1.0
O B:PRO167 3.3 12.3 1.0
O B:HOH522 3.6 40.1 1.0
C14 B:F132 3.6 13.7 1.0
C18 B:F132 3.6 15.4 1.0
C B:PRO167 4.1 12.1 1.0
C19 B:F132 4.1 15.1 1.0
C B:ASN170 4.3 12.1 1.0
CG2 B:THR171 4.3 13.6 1.0
N B:THR171 4.3 12.6 1.0
CB B:ASN170 4.4 12.2 1.0
O B:ASN170 4.4 11.5 1.0
CB B:PRO167 4.4 12.7 1.0
CA B:THR168 4.5 12.3 1.0
CA B:THR171 4.6 13.1 1.0
CA B:ASN170 4.7 11.9 1.0
N B:THR168 4.7 12.3 1.0
N B:ASN170 4.8 11.8 1.0
OD2 B:ASP240 4.8 17.5 1.0
C13 B:F132 4.9 13.4 1.0
O B:HOH552 4.9 36.1 1.0
CA B:PRO167 4.9 12.2 1.0
C B:THR168 5.0 12.3 1.0
O20 B:F132 5.0 12.7 1.0

Fluorine binding site 4 out of 6 in 3g35

Go back to Fluorine Binding Sites List in 3g35
Fluorine binding site 4 out of 6 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 12 (F13)


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 12 (F13) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F4

b:17.3
occ:1.00
 F21 B:F134 0.0 17.3 1.0
C16 B:F134 1.3 30.9 1.0
C15 B:F134 2.4 22.7 1.0
C17 B:F134 2.4 19.5 1.0
N1 B:F135 3.4 41.8 1.0
N5 B:F135 3.5 38.6 1.0
CG B:LYS82 3.6 14.7 1.0
O B:ALA79 3.6 11.3 1.0
C18 B:F134 3.6 22.6 1.0
C14 B:F134 3.6 17.5 1.0
N2 B:F135 3.7 41.3 1.0
C4 B:F135 3.7 50.5 1.0
N3 B:F135 3.8 38.4 1.0
CG B:GLN83 3.8 13.0 1.0
CB B:LYS82 3.9 12.1 1.0
CD1 B:PHE151 4.0 12.1 1.0
C19 B:F134 4.1 30.6 1.0
N B:GLN83 4.2 12.2 1.0
CB B:PHE151 4.5 12.3 1.0
C B:ALA79 4.5 10.8 1.0
C6 B:F135 4.5 33.1 1.0
O B:HOH502 4.6 26.1 1.0
C B:LYS82 4.6 12.0 1.0
CA B:GLN83 4.6 12.4 1.0
CG B:PHE151 4.6 12.0 1.0
CA B:ALA79 4.7 10.3 1.0
O B:HOH374 4.7 51.7 1.0
CB B:GLN83 4.8 12.3 1.0
CE1 B:PHE151 4.8 12.5 1.0
CB B:ALA79 4.8 10.8 1.0
CA B:LYS82 4.9 12.0 1.0
CD B:GLN83 4.9 13.4 1.0
C13 B:F134 4.9 29.6 1.0

Fluorine binding site 5 out of 6 in 3g35

Go back to Fluorine Binding Sites List in 3g35
Fluorine binding site 5 out of 6 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 12 (F13)


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 12 (F13) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F5

b:36.4
occ:1.00
 F21 B:F135 0.0 36.4 1.0
C16 B:F135 1.3 51.3 1.0
C17 B:F135 2.4 37.8 1.0
C15 B:F135 2.4 42.8 1.0
C18 B:F135 3.6 40.3 1.0
C14 B:F135 3.6 37.5 1.0
N3 B:F134 4.0 20.5 1.0
N2 B:F134 4.0 21.0 1.0
C19 B:F135 4.1 49.3 1.0
O B:HOH510 4.5 28.7 1.0
C4 B:F134 4.7 21.1 1.0
N1 B:F134 4.7 20.6 1.0
C13 B:F135 4.9 52.6 1.0

Fluorine binding site 6 out of 6 in 3g35

Go back to Fluorine Binding Sites List in 3g35
Fluorine binding site 6 out of 6 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 12 (F13)


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 12 (F13) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F6

b:45.6
occ:1.00
 F21 B:F136 0.0 45.6 1.0
C16 B:F136 1.3 34.0 1.0
C17 B:F136 2.4 45.4 1.0
C15 B:F136 2.4 41.0 1.0
OH B:TYR105 3.3 17.5 1.0
CE1 B:TYR105 3.3 15.0 1.0
CZ B:TYR105 3.5 16.4 1.0
O B:HOH376 3.6 18.0 1.0
C18 B:F136 3.6 40.1 1.0
C14 B:F136 3.6 43.8 1.0
CB B:SER130 3.8 11.2 1.0
O B:TYR129 3.8 11.6 1.0
CG2 B:THR216 3.9 11.2 1.0
N3 B:F132 4.0 11.1 1.0
C19 B:F136 4.1 33.5 1.0
C7 B:F132 4.2 11.3 1.0
C4 B:F132 4.3 11.3 1.0
CD1 B:TYR105 4.3 14.0 1.0
N2 B:F132 4.4 11.7 1.0
OG B:SER130 4.6 10.7 1.0
CE2 B:TYR105 4.6 17.6 1.0
C6 B:F132 4.6 10.8 1.0
CB B:THR216 4.7 10.4 1.0
C B:TYR129 4.7 10.5 1.0
N5 B:F132 4.9 11.6 1.0
C13 B:F136 4.9 34.3 1.0
CA B:SER130 4.9 10.7 1.0
N1 B:F132 4.9 10.8 1.0
O B:SER130 5.0 11.6 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 18:43:14 2024

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