Sodium in PDB 8r31: Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-412
Enzymatic activity of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-412
All present enzymatic activity of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-412:
3.5.2.6;
Protein crystallography data
The structure of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-412, PDB code: 8r31
was solved by
C.L.Tooke,
P.Hinchliffe,
J.Spencer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
35.48 /
1.65
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.49,
45.58,
117.65,
90,
90,
90
|
|
R / Rfree (%)
|
17.5 /
21.2
|
Other elements in 8r31:
The structure of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-412 also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-412
(pdb code 8r31). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the
Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-412, PDB code: 8r31:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 8r31
Go back to
Sodium Binding Sites List in 8r31
Sodium binding site 1 out
of 3 in the Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-412
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-412 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na306
b:22.7
occ:1.00
|
HG1
|
A:THR181
|
1.8
|
17.8
|
1.0
|
|
HB2
|
A:PHE160
|
2.6
|
15.8
|
1.0
|
|
OG1
|
A:THR181
|
2.7
|
14.8
|
1.0
|
|
OD2
|
A:ASP157
|
2.7
|
15.3
|
1.0
|
|
HA
|
A:MET186
|
2.7
|
19.7
|
0.3
|
|
HA
|
A:MET186
|
2.7
|
19.8
|
0.7
|
|
HG21
|
A:THR181
|
3.1
|
15.9
|
1.0
|
|
HB2
|
A:MET186
|
3.2
|
17.2
|
0.3
|
|
HD2
|
A:PHE160
|
3.2
|
20.6
|
1.0
|
|
HB2
|
A:MET186
|
3.2
|
17.1
|
0.7
|
|
CA
|
A:MET186
|
3.4
|
16.5
|
0.3
|
|
CA
|
A:MET186
|
3.4
|
16.5
|
0.7
|
|
N
|
A:MET186
|
3.4
|
14.9
|
0.3
|
|
N
|
A:MET186
|
3.4
|
14.9
|
0.7
|
|
HB3
|
A:ALA185
|
3.4
|
19.8
|
1.0
|
|
SD
|
A:MET186
|
3.4
|
16.4
|
0.7
|
|
HB1
|
A:ALA185
|
3.4
|
19.8
|
1.0
|
|
CB
|
A:THR181
|
3.5
|
15.3
|
1.0
|
|
CB
|
A:PHE160
|
3.5
|
13.2
|
1.0
|
|
C
|
A:ALA185
|
3.6
|
14.4
|
1.0
|
|
CG
|
A:ASP157
|
3.6
|
15.2
|
1.0
|
|
HB
|
A:THR181
|
3.6
|
18.4
|
1.0
|
|
CG2
|
A:THR181
|
3.6
|
13.3
|
1.0
|
|
SD
|
A:MET186
|
3.6
|
16.7
|
0.3
|
|
H
|
A:MET186
|
3.7
|
17.9
|
0.3
|
|
H
|
A:MET186
|
3.7
|
17.9
|
0.7
|
|
CB
|
A:MET186
|
3.7
|
14.3
|
0.3
|
|
CB
|
A:MET186
|
3.7
|
14.3
|
0.7
|
|
HG23
|
A:THR181
|
3.7
|
15.9
|
1.0
|
|
O
|
A:ALA185
|
3.7
|
17.0
|
1.0
|
|
H
|
A:PHE160
|
3.8
|
18.5
|
1.0
|
|
CB
|
A:ALA185
|
3.8
|
16.5
|
1.0
|
|
OD1
|
A:ASP157
|
3.8
|
14.5
|
1.0
|
|
HG1
|
A:THR189
|
3.8
|
21.9
|
1.0
|
|
HE2
|
A:MET186
|
3.9
|
15.1
|
0.3
|
|
HA
|
A:PHE160
|
3.9
|
18.5
|
1.0
|
|
HB
|
A:THR189
|
3.9
|
18.6
|
1.0
|
|
CD2
|
A:PHE160
|
4.0
|
17.1
|
1.0
|
|
HE1
|
A:MET75
|
4.0
|
18.0
|
0.6
|
|
HB3
|
A:PHE160
|
4.0
|
15.8
|
1.0
|
|
CA
|
A:PHE160
|
4.1
|
15.5
|
1.0
|
|
HE1
|
A:MET186
|
4.1
|
15.1
|
0.3
|
|
CE
|
A:MET186
|
4.1
|
12.6
|
0.3
|
|
N
|
A:PHE160
|
4.2
|
15.4
|
1.0
|
|
HE2
|
A:MET75
|
4.2
|
18.0
|
0.6
|
|
CG
|
A:MET186
|
4.2
|
12.8
|
0.7
|
|
CG
|
A:PHE160
|
4.2
|
16.8
|
1.0
|
|
CG
|
A:MET186
|
4.3
|
12.9
|
0.3
|
|
HE3
|
A:MET75
|
4.3
|
18.0
|
0.6
|
|
CA
|
A:ALA185
|
4.3
|
17.9
|
1.0
|
|
HB
|
A:THR159
|
4.4
|
25.3
|
1.0
|
|
CE
|
A:MET75
|
4.4
|
15.0
|
0.6
|
|
OG1
|
A:THR189
|
4.4
|
18.2
|
1.0
|
|
HE3
|
A:MET186
|
4.5
|
20.7
|
0.7
|
|
CE
|
A:MET186
|
4.5
|
17.3
|
0.7
|
|
HG22
|
A:THR181
|
4.5
|
15.9
|
1.0
|
|
HB3
|
A:MET186
|
4.6
|
17.2
|
0.3
|
|
CB
|
A:THR189
|
4.6
|
15.6
|
1.0
|
|
HB3
|
A:MET186
|
4.6
|
17.1
|
0.7
|
|
H
|
A:SER182
|
4.6
|
18.5
|
1.0
|
|
HB2
|
A:ALA185
|
4.7
|
19.8
|
1.0
|
|
HE1
|
A:MET186
|
4.7
|
20.7
|
0.7
|
|
O
|
A:SER182
|
4.7
|
18.0
|
1.0
|
|
C
|
A:MET186
|
4.7
|
16.1
|
0.7
|
|
C
|
A:MET186
|
4.7
|
16.1
|
0.3
|
|
HG2
|
A:MET186
|
4.7
|
15.3
|
0.7
|
|
HG2
|
A:MET186
|
4.8
|
15.5
|
0.3
|
|
HG3
|
A:MET186
|
4.9
|
15.3
|
0.7
|
|
HG21
|
A:THR189
|
4.9
|
27.0
|
1.0
|
|
CA
|
A:THR181
|
4.9
|
14.1
|
1.0
|
|
CB
|
A:ASP157
|
5.0
|
14.4
|
1.0
|
|
HA
|
A:ALA185
|
5.0
|
21.4
|
1.0
|
|
Sodium binding site 2 out
of 3 in 8r31
Go back to
Sodium Binding Sites List in 8r31
Sodium binding site 2 out
of 3 in the Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-412
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-412 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na307
b:22.1
occ:1.00
|
H
|
A:GLN222
|
2.1
|
19.7
|
1.0
|
|
HG3
|
A:GLN222
|
2.2
|
26.1
|
1.0
|
|
OD2
|
A:ASP245
|
2.8
|
13.6
|
1.0
|
|
O
|
A:GLY217
|
2.8
|
17.1
|
1.0
|
|
HB
|
A:ILE221
|
2.9
|
19.9
|
1.0
|
|
N
|
A:GLN222
|
2.9
|
16.5
|
1.0
|
|
HE21
|
A:GLN222
|
2.9
|
29.0
|
1.0
|
|
H
|
A:ILE221
|
3.1
|
16.8
|
1.0
|
|
CG
|
A:GLN222
|
3.1
|
21.8
|
1.0
|
|
OD2
|
A:ASP233
|
3.3
|
16.9
|
1.0
|
|
HB2
|
A:GLN222
|
3.3
|
22.8
|
1.0
|
|
CG
|
A:ASP233
|
3.3
|
16.3
|
1.0
|
|
HB2
|
A:SER220
|
3.3
|
20.7
|
1.0
|
|
N
|
A:ILE221
|
3.3
|
14.0
|
1.0
|
|
HA3
|
A:GLY217
|
3.3
|
24.1
|
1.0
|
|
NE2
|
A:GLN222
|
3.5
|
24.1
|
1.0
|
|
CB
|
A:GLN222
|
3.5
|
19.0
|
1.0
|
|
HB3
|
A:ASP233
|
3.6
|
17.2
|
1.0
|
|
OD1
|
A:ASP233
|
3.6
|
18.1
|
1.0
|
|
C
|
A:GLY217
|
3.6
|
15.8
|
1.0
|
|
CD
|
A:GLN222
|
3.7
|
30.3
|
1.0
|
|
HG11
|
A:VAL231
|
3.7
|
27.3
|
1.0
|
|
CB
|
A:ILE221
|
3.7
|
16.6
|
1.0
|
|
CA
|
A:GLN222
|
3.8
|
15.6
|
1.0
|
|
CA
|
A:ILE221
|
3.8
|
14.9
|
1.0
|
|
HG2
|
A:GLN222
|
3.8
|
26.1
|
1.0
|
|
C
|
A:ILE221
|
3.8
|
20.5
|
1.0
|
|
CB
|
A:ASP233
|
3.8
|
14.3
|
1.0
|
|
CG
|
A:ASP245
|
3.8
|
16.0
|
1.0
|
|
HB2
|
A:ASP233
|
3.9
|
17.2
|
1.0
|
|
CA
|
A:GLY217
|
3.9
|
20.1
|
1.0
|
|
H
|
A:SER220
|
3.9
|
19.6
|
1.0
|
|
C
|
A:SER220
|
4.0
|
16.1
|
1.0
|
|
HA2
|
A:GLY217
|
4.1
|
24.1
|
1.0
|
|
CB
|
A:SER220
|
4.1
|
17.3
|
1.0
|
|
HG22
|
A:ILE221
|
4.1
|
16.9
|
1.0
|
|
HA
|
A:GLN222
|
4.1
|
18.7
|
1.0
|
|
HE22
|
A:GLN222
|
4.2
|
29.0
|
1.0
|
|
OD1
|
A:ASP245
|
4.2
|
14.5
|
1.0
|
|
HG12
|
A:VAL231
|
4.2
|
27.3
|
1.0
|
|
HB3
|
A:SER220
|
4.3
|
20.7
|
1.0
|
|
CG1
|
A:VAL231
|
4.4
|
22.8
|
1.0
|
|
CA
|
A:SER220
|
4.4
|
15.8
|
1.0
|
|
HB3
|
A:GLN222
|
4.4
|
22.8
|
1.0
|
|
CG2
|
A:ILE221
|
4.5
|
14.1
|
1.0
|
|
N
|
A:SER220
|
4.5
|
16.4
|
1.0
|
|
HD12
|
A:ILE221
|
4.7
|
18.3
|
1.0
|
|
HA
|
A:ALA218
|
4.7
|
22.8
|
1.0
|
|
HB2
|
A:ALA247
|
4.7
|
18.0
|
1.0
|
|
OE1
|
A:GLN222
|
4.7
|
28.0
|
1.0
|
|
HA
|
A:ILE221
|
4.7
|
17.8
|
1.0
|
|
H
|
A:ALA223
|
4.7
|
22.7
|
1.0
|
|
O
|
A:SER220
|
4.8
|
18.4
|
1.0
|
|
HG22
|
A:THR235
|
4.8
|
20.5
|
1.0
|
|
HG13
|
A:ILE221
|
4.8
|
20.7
|
1.0
|
|
N
|
A:ALA218
|
4.8
|
16.4
|
1.0
|
|
CG1
|
A:ILE221
|
4.8
|
17.3
|
1.0
|
|
O
|
A:ILE221
|
5.0
|
16.3
|
1.0
|
|
HG23
|
A:THR235
|
5.0
|
20.5
|
1.0
|
|
HG21
|
A:ILE221
|
5.0
|
16.9
|
1.0
|
|
Sodium binding site 3 out
of 3 in 8r31
Go back to
Sodium Binding Sites List in 8r31
Sodium binding site 3 out
of 3 in the Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-412
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-412 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na308
b:22.0
occ:1.00
|
HG1
|
A:THR235
|
2.3
|
24.2
|
1.0
|
|
H6
|
A:XQN301
|
2.4
|
33.8
|
1.0
|
|
OG1
|
A:THR235
|
3.0
|
20.2
|
1.0
|
|
O
|
A:HOH515
|
3.0
|
32.7
|
1.0
|
|
HB
|
A:THR235
|
3.1
|
21.4
|
1.0
|
|
HA2
|
A:GLY236
|
3.1
|
17.4
|
1.0
|
|
H9
|
A:XQN301
|
3.1
|
31.4
|
1.0
|
|
N6
|
A:XQN301
|
3.2
|
28.2
|
1.0
|
|
OG
|
A:SER237
|
3.5
|
31.3
|
1.0
|
|
CB
|
A:THR235
|
3.5
|
17.9
|
1.0
|
|
N
|
A:GLY236
|
3.5
|
15.0
|
1.0
|
|
CA
|
A:GLY236
|
3.5
|
14.5
|
1.0
|
|
C
|
A:GLY236
|
3.6
|
19.8
|
1.0
|
|
H
|
A:SER237
|
3.6
|
19.8
|
1.0
|
|
N
|
A:SER237
|
3.7
|
16.5
|
1.0
|
|
C9
|
A:XQN301
|
3.7
|
26.2
|
1.0
|
|
C
|
A:THR235
|
3.7
|
16.6
|
1.0
|
|
O3
|
A:XQN301
|
3.7
|
20.9
|
1.0
|
|
O1
|
A:XQN301
|
3.7
|
22.6
|
1.0
|
|
H5A
|
A:XQN301
|
3.7
|
29.0
|
1.0
|
|
HG
|
A:SER237
|
3.8
|
37.6
|
1.0
|
|
H
|
A:GLY236
|
3.9
|
18.0
|
1.0
|
|
HB2
|
A:SER70
|
3.9
|
17.0
|
1.0
|
|
O16
|
A:XQN301
|
3.9
|
30.7
|
1.0
|
|
O
|
A:THR235
|
3.9
|
16.3
|
1.0
|
|
C5
|
A:XQN301
|
4.0
|
24.2
|
1.0
|
|
S7
|
A:XQN301
|
4.0
|
28.8
|
1.0
|
|
HB3
|
A:SER237
|
4.0
|
29.3
|
1.0
|
|
C8
|
A:XQN301
|
4.1
|
29.7
|
1.0
|
|
O
|
A:GLY236
|
4.1
|
16.4
|
1.0
|
|
HH21
|
A:ARG274
|
4.2
|
43.5
|
1.0
|
|
CB
|
A:SER237
|
4.2
|
24.4
|
1.0
|
|
CA
|
A:THR235
|
4.2
|
15.5
|
1.0
|
|
B2
|
A:XQN301
|
4.3
|
19.8
|
1.0
|
|
HZ3
|
A:LYS234
|
4.4
|
23.2
|
1.0
|
|
C4
|
A:XQN301
|
4.4
|
21.2
|
1.0
|
|
H1
|
A:XQN301
|
4.4
|
27.1
|
1.0
|
|
HZ2
|
A:LYS234
|
4.4
|
23.2
|
1.0
|
|
HA3
|
A:GLY236
|
4.5
|
17.4
|
1.0
|
|
C10
|
A:XQN301
|
4.5
|
20.5
|
1.0
|
|
CA
|
A:SER237
|
4.6
|
25.8
|
1.0
|
|
HB
|
A:THR216
|
4.6
|
23.9
|
1.0
|
|
HG1
|
A:THR216
|
4.6
|
26.8
|
1.0
|
|
OG
|
A:SER130
|
4.7
|
21.0
|
1.0
|
|
H10
|
A:XQN301
|
4.7
|
24.5
|
1.0
|
|
CB
|
A:SER70
|
4.8
|
14.2
|
1.0
|
|
NZ
|
A:LYS234
|
4.8
|
19.4
|
1.0
|
|
CG2
|
A:THR235
|
4.8
|
17.1
|
1.0
|
|
HG21
|
A:THR235
|
4.8
|
20.5
|
1.0
|
|
H5B
|
A:XQN301
|
4.8
|
29.0
|
1.0
|
|
HE
|
A:ARG274
|
4.9
|
38.9
|
1.0
|
|
O
|
A:HOH477
|
4.9
|
17.4
|
1.0
|
|
HZ1
|
A:LYS234
|
4.9
|
23.2
|
1.0
|
|
HA
|
A:THR235
|
4.9
|
18.5
|
1.0
|
|
OG
|
A:SER70
|
5.0
|
13.8
|
1.0
|
|
HG
|
A:SER130
|
5.0
|
25.2
|
1.0
|
|
HB2
|
A:SER130
|
5.0
|
24.2
|
1.0
|
|
Reference:
C.L.Tooke,
P.Hinchliffe,
J.Spencer.
Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-412 To Be Published.
Page generated: Wed Nov 27 20:39:59 2024
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