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:
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
|