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Bromine in PDB 4de3: Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4

Enzymatic activity of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4

All present enzymatic activity of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4:
3.5.2.6;

Protein crystallography data

The structure of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4, PDB code: 4de3 was solved by D.A.Nichols, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.44
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.174, 107.188, 47.487, 90.00, 100.38, 90.00
R / Rfree (%) 16.3 / 20.6

Bromine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Bromine atom in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4 (pdb code 4de3). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 11 binding sites of Bromine where determined in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4, PDB code: 4de3:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 11 in 4de3

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Bromine binding site 1 out of 11 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br301

b:14.4
occ:1.00
 BR1 A:DN8301 0.0 14.4 1.0
C6 A:DN8301 1.9 11.3 1.0
C5 A:DN8301 2.8 10.2 1.0
C1 A:DN8301 2.8 11.4 1.0
O A:HOH526 3.4 28.7 1.0
O A:PRO167 3.6 8.0 1.0
CG2 A:THR171 3.9 8.8 1.0
C4 A:DN8301 4.1 9.4 1.0
N A:THR171 4.1 8.1 1.0
C2 A:DN8301 4.2 11.2 1.0
O A:HOH608 4.2 29.1 1.0
CA A:THR168 4.2 8.4 1.0
C A:PRO167 4.3 7.8 1.0
C A:ASN170 4.3 7.9 1.0
CA A:THR171 4.3 8.1 1.0
O A:ASN170 4.5 8.6 1.0
OD2 A:ASP240 4.6 15.1 1.0
C3 A:DN8301 4.7 10.1 1.0
CB A:ASN170 4.7 7.9 1.0
N A:THR168 4.7 8.1 1.0
O A:THR168 4.8 8.5 1.0
C A:THR168 4.8 8.1 1.0
CB A:THR171 4.8 8.2 1.0
CB A:PRO167 4.8 8.2 1.0
CA A:ASN170 4.9 7.8 1.0
N A:ASN170 4.9 7.9 1.0

Bromine binding site 2 out of 11 in 4de3

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Bromine binding site 2 out of 11 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br302

b:17.2
occ:1.00
 BR1 A:DN8302 0.0 17.2 1.0
C6 A:DN8302 1.9 16.4 1.0
C5 A:DN8302 2.8 16.4 1.0
C1 A:DN8302 2.9 15.5 1.0
OH A:TYR105 3.6 12.3 1.0
O A:HOH407 3.7 12.6 1.0
CE1 A:TYR105 3.8 9.9 1.0
CG2 A:THR216 3.8 8.1 1.0
N16 A:DN8301 3.9 8.9 1.0
CZ A:TYR105 3.9 10.4 1.0
CB A:SER130 4.0 7.7 1.0
O A:TYR129 4.1 8.0 1.0
C4 A:DN8302 4.2 17.8 1.0
C2 A:DN8302 4.2 16.8 1.0
N17 A:DN8301 4.2 9.3 1.0
CB A:THR216 4.4 8.0 1.0
C15 A:DN8301 4.4 8.4 1.0
C12 A:DN8301 4.6 8.3 1.0
C3 A:DN8302 4.7 16.4 1.0
CD1 A:TYR105 4.7 8.0 1.0
C11 A:DN8301 4.8 7.4 1.0
OG A:SER130 4.8 8.5 1.0
CE2 A:TYR105 4.9 10.9 1.0
N18 A:DN8301 4.9 8.8 1.0
C A:TYR129 4.9 7.7 1.0
N19 A:DN8301 4.9 8.6 1.0

Bromine binding site 3 out of 11 in 4de3

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Bromine binding site 3 out of 11 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br303

b:18.6
occ:1.00
 BR1 A:DN8303 0.0 18.6 1.0
C6 A:DN8303 1.9 18.7 1.0
C5 A:DN8303 2.8 20.2 1.0
C1 A:DN8303 2.9 18.8 1.0
O A:ALA79 3.2 8.7 1.0
CD1 A:PHE151 3.7 10.0 1.0
CG A:GLN83 3.9 12.1 1.0
C A:ALA79 3.9 8.6 1.0
CB A:ALA79 4.0 8.6 1.0
CA A:ALA79 4.0 8.1 1.0
CB A:LYS82 4.1 8.9 1.0
CG A:LYS82 4.1 10.1 1.0
C4 A:DN8303 4.1 22.6 1.0
CB A:PHE151 4.1 9.7 1.0
C2 A:DN8303 4.1 19.5 1.0
CG A:PHE151 4.2 9.5 1.0
CD2 A:LEU142 4.4 14.2 1.0
CE1 A:PHE151 4.5 11.3 1.0
N A:GLN83 4.5 10.0 1.0
C3 A:DN8303 4.6 21.5 1.0
CD A:GLN83 4.7 15.6 1.0
NE2 A:GLN83 4.8 17.2 1.0
CA A:PHE151 5.0 9.5 1.0

Bromine binding site 4 out of 11 in 4de3

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Bromine binding site 4 out of 11 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br304

b:21.8
occ:1.00
 BR1 A:DN8304 0.0 21.8 1.0
C6 A:DN8304 1.9 22.1 1.0
C5 A:DN8304 2.8 24.1 1.0
C1 A:DN8304 2.9 23.0 1.0
OD2 A:ASP176 3.3 10.7 1.0
CG A:ASP176 3.5 10.1 1.0
NH2 A:ARG178 3.7 9.5 1.0
CD1 A:ILE173 3.7 12.9 1.0
CB A:ASP176 3.8 9.3 1.0
CG2 A:ILE173 4.0 10.1 1.0
OD1 A:ASP176 4.1 9.2 1.0
C4 A:DN8304 4.2 24.9 1.0
C2 A:DN8304 4.2 23.9 1.0
CB A:ILE173 4.3 9.1 1.0
O A:HOH425 4.4 17.6 1.0
O A:HOH554 4.4 28.9 1.0
CA A:ASP176 4.6 9.2 1.0
CG1 A:ILE173 4.6 11.0 1.0
C3 A:DN8304 4.7 24.8 1.0
CZ A:ARG178 4.7 9.8 1.0
NE A:ARG178 5.0 10.2 1.0

Bromine binding site 5 out of 11 in 4de3

Go back to Bromine Binding Sites List in 4de3
Bromine binding site 5 out of 11 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br305

b:39.7
occ:1.00
 BR1 A:DN8305 0.0 39.7 1.0
C6 A:DN8305 1.9 32.8 1.0
C5 A:DN8305 2.8 31.1 1.0
C1 A:DN8305 2.9 30.5 1.0
CG A:GLN188 3.3 15.9 1.0
CG A:GLN192 3.5 12.6 1.0
O A:HOH505 3.5 31.7 1.0
OE1 A:GLN192 3.8 21.1 1.0
O A:GLN188 3.9 9.8 1.0
CD A:GLN192 4.0 17.0 1.0
CD A:GLN188 4.1 21.6 1.0
C4 A:DN8305 4.2 30.1 1.0
C2 A:DN8305 4.2 28.1 1.0
CD A:ARG191 4.3 12.8 1.0
NE2 A:GLN188 4.3 24.3 1.0
CB A:GLN188 4.4 11.0 1.0
CA A:GLN188 4.5 10.3 1.0
C A:GLN188 4.5 9.8 1.0
C3 A:DN8305 4.7 29.2 1.0
CB A:ARG191 4.8 9.7 1.0
CB A:GLN192 4.9 10.2 1.0
N A:GLN192 4.9 9.4 1.0
CG A:ARG191 4.9 11.4 1.0
OE1 A:GLN188 4.9 26.5 1.0
NH1 A:ARG191 4.9 15.8 1.0
NE A:ARG191 5.0 14.5 1.0

Bromine binding site 6 out of 11 in 4de3

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Bromine binding site 6 out of 11 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br306

b:43.7
occ:1.00
 BR1 A:DN8306 0.0 43.7 1.0
C6 A:DN8306 1.9 37.4 1.0
C5 A:DN8306 2.8 35.2 1.0
C1 A:DN8306 2.9 36.5 1.0
C4 A:DN8306 4.1 32.8 1.0
C2 A:DN8306 4.2 34.6 1.0
C3 A:DN8306 4.6 33.6 1.0

Bromine binding site 7 out of 11 in 4de3

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Bromine binding site 7 out of 11 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br301

b:20.0
occ:1.00
 BR1 B:DN8301 0.0 20.0 1.0
C6 B:DN8301 1.9 13.7 1.0
C5 B:DN8301 2.8 13.1 1.0
C1 B:DN8301 2.8 14.2 1.0
O B:HOH598 3.4 36.2 1.0
O B:PRO167 3.5 9.3 1.0
O B:HOH523 3.8 33.1 1.0
CG2 B:THR171 4.0 10.6 1.0
C4 B:DN8301 4.1 11.3 1.0
C2 B:DN8301 4.1 13.6 1.0
C B:PRO167 4.2 9.0 1.0
CA B:THR168 4.2 9.3 1.0
N B:THR171 4.2 8.6 1.0
C B:ASN170 4.4 9.0 1.0
CA B:THR171 4.4 9.7 1.0
O B:ASN170 4.6 8.4 1.0
CB B:PRO167 4.6 9.3 1.0
N B:THR168 4.6 8.9 1.0
CB B:ASN170 4.7 8.8 1.0
C3 B:DN8301 4.7 12.9 1.0
OD2 B:ASP240 4.7 16.4 1.0
C B:THR168 4.8 8.8 1.0
CB B:THR171 4.9 9.3 1.0
CA B:ASN170 4.9 8.6 1.0
O B:THR168 4.9 9.1 1.0
N B:ASN170 5.0 9.1 1.0

Bromine binding site 8 out of 11 in 4de3

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Bromine binding site 8 out of 11 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br302

b:26.9
occ:1.00
 BR1 B:DN8302 0.0 26.9 1.0
C6 B:DN8302 1.9 27.2 1.0
C1 B:DN8302 2.8 27.3 1.0
C5 B:DN8302 2.9 27.1 1.0
OH B:TYR105 3.6 17.4 1.0
O B:HOH448 3.7 19.8 1.0
CE1 B:TYR105 3.7 15.1 1.0
CG2 B:THR216 3.8 9.4 1.0
N16 B:DN8301 3.8 9.7 1.0
CZ B:TYR105 3.8 16.7 1.0
CB B:SER130 3.9 8.4 1.0
O B:TYR129 4.0 9.2 1.0
C2 B:DN8302 4.1 27.3 1.0
C4 B:DN8302 4.1 28.3 1.0
N17 B:DN8301 4.2 9.4 1.0
C15 B:DN8301 4.3 9.3 1.0
CB B:THR216 4.5 8.4 1.0
C12 B:DN8301 4.6 9.9 1.0
CD1 B:TYR105 4.6 13.7 1.0
O B:HOH585 4.6 33.6 1.0
C3 B:DN8302 4.6 28.1 1.0
OG B:SER130 4.7 8.5 1.0
C11 B:DN8301 4.8 9.3 1.0
CE2 B:TYR105 4.9 17.2 1.0
N18 B:DN8301 4.9 9.8 1.0
C B:TYR129 4.9 8.5 1.0
N19 B:DN8301 5.0 9.9 1.0

Bromine binding site 9 out of 11 in 4de3

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Bromine binding site 9 out of 11 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br303

b:18.2
occ:1.00
 BR1 B:DN8303 0.0 18.2 1.0
C6 B:DN8303 1.9 18.2 1.0
C5 B:DN8303 2.8 19.3 1.0
C1 B:DN8303 2.9 18.9 1.0
O B:ALA79 3.3 9.0 1.0
CD1 B:PHE151 3.7 10.5 1.0
CG B:LYS82 3.8 11.6 1.0
CB B:LYS82 3.8 9.2 1.0
CG B:GLN83 3.9 11.5 1.0
C B:ALA79 4.1 8.5 1.0
CD1 B:LEU142 4.1 13.3 1.0
C4 B:DN8303 4.1 19.4 1.0
C2 B:DN8303 4.1 17.1 1.0
CB B:PHE151 4.2 10.2 1.0
CA B:ALA79 4.2 8.4 1.0
N B:GLN83 4.2 9.3 1.0
CB B:ALA79 4.2 8.7 1.0
CG B:PHE151 4.2 10.2 1.0
CE1 B:PHE151 4.5 11.1 1.0
C3 B:DN8303 4.6 18.9 1.0
C B:LYS82 4.7 9.2 1.0
O B:HOH493 4.7 25.1 1.0
CA B:GLN83 4.8 10.5 1.0
CD B:GLN83 4.8 12.6 1.0
CA B:LYS82 4.8 9.3 1.0
CA B:PHE151 4.9 9.8 1.0
CB B:GLN83 4.9 10.2 1.0
NE2 B:GLN83 5.0 15.5 1.0

Bromine binding site 10 out of 11 in 4de3

Go back to Bromine Binding Sites List in 4de3
Bromine binding site 10 out of 11 in the Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Ctx-M-9 Class A Beta-Lactamase Complexed with Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br304

b:54.0
occ:1.00
 BR1 B:DN8304 0.0 54.0 1.0
C6 B:DN8304 1.9 49.6 1.0
OE2 B:GLU158 2.4 15.4 0.0
C1 B:DN8304 2.9 48.6 1.0
C5 B:DN8304 2.9 47.3 1.0
O B:HOH518 3.2 29.1 1.0
CD B:GLU158 3.6 12.3 0.0
CB B:ARG153 3.9 11.0 1.0
CD B:ARG153 4.0 11.5 1.0
OE1 B:GLU158 4.1 14.0 0.0
C2 B:DN8304 4.2 47.4 1.0
C4 B:DN8304 4.2 45.2 1.0
CG B:ARG153 4.2 11.3 1.0
O B:HOH584 4.4 46.3 1.0
O B:ARG153 4.5 12.6 1.0
CA B:ARG153 4.7 11.0 1.0
C3 B:DN8304 4.7 46.2 1.0
CG B:GLU158 4.8 9.8 0.0
C B:ARG153 4.8 11.4 1.0
CG B:GLU158 4.9 9.8 0.5

Reference:

D.A.Nichols, P.Jaishankar, W.Larson, E.Smith, G.Liu, R.Beyrouthy, R.Bonnet, A.R.Renslo, Y.Chen. Structure-Based Design of Potent and Ligand-Efficient Inhibitors of Ctx-M Class A Beta-Lactamase J.Med.Chem. V. 55 2163 2012.
ISSN: ISSN 0022-2623
PubMed: 22296601
DOI: 10.1021/JM2014138
Page generated: Wed Jul 10 21:06:23 2024

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