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Bromine in PDB 5mnu: Oxa-10 Avibactam Complex with Bound Bromide

Enzymatic activity of Oxa-10 Avibactam Complex with Bound Bromide

All present enzymatic activity of Oxa-10 Avibactam Complex with Bound Bromide:
3.5.2.6;

Protein crystallography data

The structure of Oxa-10 Avibactam Complex with Bound Bromide, PDB code: 5mnu was solved by J.Brem, M.Mcdonough, I.Clifton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.66 / 1.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.771, 101.421, 127.221, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 20.8

Other elements in 5mnu:

The structure of Oxa-10 Avibactam Complex with Bound Bromide also contains other interesting chemical elements:

Sodium (Na) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Oxa-10 Avibactam Complex with Bound Bromide (pdb code 5mnu). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Oxa-10 Avibactam Complex with Bound Bromide, PDB code: 5mnu:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in 5mnu

Go back to Bromine Binding Sites List in 5mnu
Bromine binding site 1 out of 6 in the Oxa-10 Avibactam Complex with Bound Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Oxa-10 Avibactam Complex with Bound Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br307

b:14.9
occ:0.75
 NE1 A:TRP154 3.2 11.5 1.0
NZ A:LYS70 3.2 14.2 1.0
O A:HOH633 3.3 13.2 1.0
O A:HOH609 3.6 31.6 1.0
CE A:LYS70 3.7 13.7 1.0
CG A:LYS70 3.8 12.7 1.0
CG2 A:VAL117 3.9 12.3 1.0
CE2 A:TRP154 4.1 9.9 1.0
CA A:VAL117 4.2 12.8 1.0
CD1 A:TRP154 4.2 11.6 1.0
CZ2 A:TRP154 4.3 11.6 1.0
CA A:SER67 4.3 12.2 1.0
CD2 A:LEU155 4.3 15.1 1.0
OG A:SER67 4.3 13.7 1.0
CB A:PHE120 4.3 11.8 1.0
CD A:LYS70 4.4 12.3 1.0
CB A:VAL117 4.4 13.7 1.0
CG1 A:VAL117 4.4 13.1 1.0
O A:ALA66 4.7 11.5 1.0
O A:VAL117 4.8 12.5 1.0
CB A:SER67 4.9 12.6 1.0
N A:SER67 4.9 13.5 1.0
N A:VAL117 4.9 12.8 1.0
CG A:PHE120 5.0 12.6 1.0

Bromine binding site 2 out of 6 in 5mnu

Go back to Bromine Binding Sites List in 5mnu
Bromine binding site 2 out of 6 in the Oxa-10 Avibactam Complex with Bound Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Oxa-10 Avibactam Complex with Bound Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br308

b:16.8
occ:1.00
 N A:ALA98 3.3 15.0 1.0
CG A:PRO118 3.7 12.8 1.0
CA A:ARG97 3.8 14.9 1.0
CD A:PRO118 3.8 11.1 1.0
CZ3 A:TRP102 3.9 12.2 1.0
CB A:ALA98 3.9 15.8 1.0
CB A:ARG97 4.0 15.2 1.0
CB A:PRO118 4.0 13.5 1.0
CE3 A:TRP102 4.0 11.8 1.0
C A:ARG97 4.1 15.6 1.0
CG A:ARG97 4.2 13.9 1.0
CA A:ALA98 4.2 15.7 1.0
N A:PRO118 4.8 12.0 1.0
CA A:PRO118 5.0 12.7 1.0
CD A:ARG97 5.0 14.4 1.0

Bromine binding site 3 out of 6 in 5mnu

Go back to Bromine Binding Sites List in 5mnu
Bromine binding site 3 out of 6 in the Oxa-10 Avibactam Complex with Bound Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Oxa-10 Avibactam Complex with Bound Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br309

b:27.2
occ:0.80
 O A:HOH715 3.1 31.2 1.0
O A:HOH702 3.2 40.7 1.0
NE A:ARG250 3.3 18.1 1.0
NH1 A:ARG250 3.4 20.7 1.0
CZ A:ARG250 3.8 18.7 1.0
CA A:PRO248 3.9 20.0 1.0
CD A:LYS251 4.1 27.7 1.0
CE A:LYS251 4.2 32.9 1.0
CG A:LYS251 4.2 25.8 1.0
CG A:ARG250 4.3 17.3 1.0
O A:LEU247 4.3 17.3 1.0
CD A:ARG250 4.4 17.8 1.0
N A:PRO248 4.5 19.2 1.0
CB A:PRO248 4.6 22.4 1.0
C A:LEU247 4.6 17.3 1.0
CB A:LYS251 4.6 21.2 1.0
O A:PRO248 4.7 19.9 1.0
C A:PRO248 4.7 18.8 1.0
NZ A:LYS251 4.8 38.4 1.0
O A:HOH499 4.8 23.8 1.0
CG A:PRO248 4.9 23.3 1.0

Bromine binding site 4 out of 6 in 5mnu

Go back to Bromine Binding Sites List in 5mnu
Bromine binding site 4 out of 6 in the Oxa-10 Avibactam Complex with Bound Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Oxa-10 Avibactam Complex with Bound Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br304

b:54.9
occ:1.00
 NE B:ARG250 3.2 42.4 1.0
NH1 B:ARG250 3.6 45.5 1.0
CA B:PRO248 3.8 45.5 1.0
CZ B:ARG250 3.9 44.1 1.0
CG B:LYS251 4.1 44.6 1.0
CE B:LYS251 4.1 49.6 1.0
CG B:ARG250 4.1 39.1 1.0
CD B:ARG250 4.3 40.8 1.0
CD B:LYS251 4.3 45.9 1.0
O B:LEU247 4.3 46.5 1.0
N B:PRO248 4.4 46.9 1.0
CB B:PRO248 4.6 48.3 1.0
C B:LEU247 4.6 47.1 1.0
O B:PRO248 4.6 45.1 1.0
C B:PRO248 4.7 46.4 1.0
CB B:LYS251 4.7 43.3 1.0
NZ B:LYS251 4.9 51.0 1.0
CG B:PRO248 5.0 50.1 1.0

Bromine binding site 5 out of 6 in 5mnu

Go back to Bromine Binding Sites List in 5mnu
Bromine binding site 5 out of 6 in the Oxa-10 Avibactam Complex with Bound Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Oxa-10 Avibactam Complex with Bound Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br305

b:49.2
occ:1.00
 O B:HOH535 3.1 43.1 1.0
O B:HOH501 3.2 33.9 1.0
NE1 B:TRP154 3.4 40.5 1.0
CAN B:NXL301 3.4 40.7 1.0
N B:SER67 3.5 39.1 1.0
C B:ALA66 3.6 36.5 1.0
OG B:SER67 3.6 40.1 1.0
N B:NXL301 3.6 42.4 1.0
O B:NXL301 3.7 47.9 1.0
CD1 B:TRP154 3.7 39.8 1.0
OAC B:NXL301 3.8 40.3 1.0
CA B:SER67 3.8 38.5 1.0
CA B:ALA66 3.9 37.6 1.0
O B:ALA66 4.0 36.1 1.0
CD1 B:LEU155 4.1 43.5 1.0
CD2 B:LEU155 4.2 45.6 1.0
CB B:LEU155 4.2 43.9 1.0
CAJ B:NXL301 4.4 42.7 1.0
CB B:SER67 4.4 37.9 1.0
CG B:LEU155 4.4 44.8 1.0
CB B:ALA66 4.4 37.8 1.0
C B:NXL301 4.5 46.7 1.0
O B:HOH487 4.6 38.2 1.0
CA B:NXL301 4.6 43.5 1.0
CE2 B:TRP154 4.7 41.1 1.0
CG2 B:VAL117 4.8 43.1 1.0
NZ B:LYS70 4.8 37.5 1.0

Bromine binding site 6 out of 6 in 5mnu

Go back to Bromine Binding Sites List in 5mnu
Bromine binding site 6 out of 6 in the Oxa-10 Avibactam Complex with Bound Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Oxa-10 Avibactam Complex with Bound Bromide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br306

b:65.4
occ:1.00
 N B:ALA98 3.3 54.7 1.0
CG B:PRO118 3.7 46.9 1.0
CA B:ARG97 3.7 52.7 1.0
CD B:PRO118 3.7 45.8 1.0
CB B:ARG97 3.7 50.8 1.0
CG B:ARG97 4.0 50.8 1.0
C B:ARG97 4.0 52.5 1.0
CZ3 B:TRP102 4.1 47.6 1.0
CB B:ALA98 4.1 53.9 1.0
CE3 B:TRP102 4.1 47.5 1.0
CB B:PRO118 4.1 47.6 1.0
CA B:ALA98 4.3 55.5 1.0
O B:HOH522 4.4 58.0 1.0
N B:PRO118 4.7 45.1 1.0
CD B:ARG97 4.8 49.0 1.0
O B:PRO96 4.9 56.9 1.0

Reference:

C.T.Lohans, D.Y.Wang, C.Jorgensen, S.T.Cahill, I.J.Clifton, M.A.Mcdonough, H.P.Oswin, J.Spencer, C.Domene, T.D.W.Claridge, J.Brem, C.J.Schofield. (13)C-Carbamylation As A Mechanistic Probe For the Inhibition of Class D Beta-Lactamases By Avibactam and Halide Ions. Org. Biomol. Chem. V. 15 6024 2017.
ISSN: ESSN 1477-0539
PubMed: 28678295
DOI: 10.1039/C7OB01514C
Page generated: Thu Jul 11 00:19:50 2024

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