Gold in PDB 1e3u: Mad Structure of OXA10 Class D Beta-Lactamase
Enzymatic activity of Mad Structure of OXA10 Class D Beta-Lactamase
All present enzymatic activity of Mad Structure of OXA10 Class D Beta-Lactamase:
3.5.2.6;
Protein crystallography data
The structure of Mad Structure of OXA10 Class D Beta-Lactamase, PDB code: 1e3u
was solved by
L.Maveyraud,
D.Golemi,
L.P.Kotra,
S.Tranier,
S.Vakulenko,
S.Mobashery,
J.P.Samama,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.00 /
1.66
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.530,
82.940,
101.420,
90.00,
95.03,
90.00
|
R / Rfree (%)
|
18.1 /
21
|
Gold Binding Sites:
The binding sites of Gold atom in the Mad Structure of OXA10 Class D Beta-Lactamase
(pdb code 1e3u). This binding sites where shown within
5.0 Angstroms radius around Gold atom.
In total 8 binding sites of Gold where determined in the
Mad Structure of OXA10 Class D Beta-Lactamase, PDB code: 1e3u:
Jump to Gold binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Gold binding site 1 out
of 8 in 1e3u
Go back to
Gold Binding Sites List in 1e3u
Gold binding site 1 out
of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Gold with other atoms in the Au binding
site number 1 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Au301
b:18.6
occ:1.00
|
AU
|
A:AUC301
|
0.0
|
18.6
|
1.0
|
C1
|
A:AUC301
|
1.7
|
19.0
|
1.0
|
C2
|
A:AUC301
|
1.7
|
19.1
|
1.0
|
O
|
A:HOH401
|
2.3
|
47.8
|
1.0
|
N2
|
A:AUC301
|
2.9
|
18.4
|
1.0
|
N1
|
A:AUC301
|
2.9
|
18.5
|
1.0
|
NE1
|
A:TRP154
|
3.1
|
16.8
|
1.0
|
CD1
|
A:TRP154
|
3.3
|
16.5
|
1.0
|
CE2
|
A:TRP154
|
3.6
|
15.8
|
1.0
|
NZ
|
A:LYS70
|
3.7
|
11.9
|
1.0
|
O
|
A:ALA66
|
3.8
|
12.2
|
1.0
|
CG
|
A:TRP154
|
3.8
|
15.6
|
1.0
|
CA
|
A:SER67
|
3.9
|
12.2
|
1.0
|
CD2
|
A:TRP154
|
4.0
|
15.1
|
1.0
|
CG
|
A:LYS70
|
4.0
|
11.2
|
1.0
|
C
|
A:ALA66
|
4.1
|
12.3
|
1.0
|
N
|
A:SER67
|
4.2
|
12.3
|
1.0
|
CZ2
|
A:TRP154
|
4.3
|
16.4
|
1.0
|
CE
|
A:LYS70
|
4.3
|
11.4
|
1.0
|
CB
|
A:SER67
|
4.6
|
14.3
|
1.0
|
N
|
A:LYS70
|
4.6
|
11.4
|
1.0
|
C
|
A:SER67
|
4.7
|
11.9
|
1.0
|
CB
|
A:TRP154
|
4.8
|
16.1
|
1.0
|
OG
|
A:SER67
|
4.8
|
15.8
|
1.0
|
CB
|
A:PHE69
|
4.8
|
12.5
|
1.0
|
O
|
A:SER67
|
4.8
|
12.0
|
1.0
|
CD
|
A:LYS70
|
4.8
|
11.6
|
1.0
|
CB
|
A:PHE120
|
5.0
|
13.0
|
1.0
|
CG2
|
A:VAL117
|
5.0
|
14.5
|
1.0
|
CE3
|
A:TRP154
|
5.0
|
15.2
|
1.0
|
|
Gold binding site 2 out
of 8 in 1e3u
Go back to
Gold Binding Sites List in 1e3u
Gold binding site 2 out
of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Gold with other atoms in the Au binding
site number 2 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Au301
b:18.8
occ:1.00
|
AU
|
B:AUC301
|
0.0
|
18.8
|
1.0
|
C1
|
B:AUC301
|
1.7
|
18.8
|
1.0
|
C2
|
B:AUC301
|
1.7
|
19.2
|
1.0
|
N2
|
B:AUC301
|
2.9
|
18.9
|
1.0
|
N1
|
B:AUC301
|
2.9
|
18.3
|
1.0
|
NE1
|
B:TRP154
|
3.1
|
18.5
|
1.0
|
CD1
|
B:TRP154
|
3.2
|
18.7
|
1.0
|
O
|
B:ALA66
|
3.6
|
10.7
|
1.0
|
CE2
|
B:TRP154
|
3.6
|
16.8
|
1.0
|
NZ
|
B:LYS70
|
3.7
|
13.9
|
1.0
|
CG
|
B:TRP154
|
3.8
|
16.6
|
1.0
|
CA
|
B:SER67
|
3.9
|
11.2
|
1.0
|
CG
|
B:LYS70
|
4.0
|
10.9
|
1.0
|
CD2
|
B:TRP154
|
4.0
|
15.1
|
1.0
|
C
|
B:ALA66
|
4.0
|
11.3
|
1.0
|
CE
|
B:LYS70
|
4.2
|
12.7
|
1.0
|
N
|
B:SER67
|
4.2
|
11.1
|
1.0
|
CZ2
|
B:TRP154
|
4.3
|
17.4
|
1.0
|
CB
|
B:PHE69
|
4.6
|
12.5
|
1.0
|
N
|
B:LYS70
|
4.7
|
11.7
|
1.0
|
C
|
B:SER67
|
4.7
|
11.2
|
1.0
|
CB
|
B:SER67
|
4.7
|
11.7
|
1.0
|
CB
|
B:TRP154
|
4.7
|
17.1
|
1.0
|
CD
|
B:LYS70
|
4.8
|
11.9
|
1.0
|
O
|
B:SER67
|
4.8
|
11.5
|
1.0
|
OG
|
B:SER67
|
4.8
|
13.9
|
1.0
|
CB
|
B:PHE120
|
4.9
|
13.6
|
1.0
|
|
Gold binding site 3 out
of 8 in 1e3u
Go back to
Gold Binding Sites List in 1e3u
Gold binding site 3 out
of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Gold with other atoms in the Au binding
site number 3 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Au301
b:17.1
occ:1.00
|
AU
|
C:AUC301
|
0.0
|
17.1
|
1.0
|
C1
|
C:AUC301
|
1.7
|
17.4
|
1.0
|
C2
|
C:AUC301
|
1.7
|
16.7
|
1.0
|
N2
|
C:AUC301
|
2.9
|
16.3
|
1.0
|
N1
|
C:AUC301
|
2.9
|
17.2
|
1.0
|
AU
|
C:AUC302
|
3.2
|
15.0
|
1.0
|
C1
|
C:AUC302
|
3.2
|
15.4
|
1.0
|
CA
|
C:VAL117
|
3.6
|
15.0
|
1.0
|
CG2
|
C:VAL117
|
3.7
|
15.9
|
1.0
|
N1
|
C:AUC302
|
4.0
|
15.3
|
1.0
|
CB
|
C:PHE120
|
4.0
|
15.1
|
1.0
|
C2
|
C:AUC302
|
4.0
|
14.6
|
1.0
|
CB
|
C:VAL117
|
4.1
|
15.2
|
1.0
|
O
|
C:VAL117
|
4.3
|
15.0
|
1.0
|
N
|
C:VAL117
|
4.3
|
15.0
|
1.0
|
CG1
|
C:VAL117
|
4.4
|
15.0
|
1.0
|
C
|
C:VAL117
|
4.5
|
15.2
|
1.0
|
O
|
C:ALA116
|
4.6
|
15.1
|
1.0
|
C
|
C:ALA116
|
4.6
|
15.3
|
1.0
|
NE1
|
C:TRP154
|
4.6
|
13.4
|
1.0
|
N2
|
C:AUC302
|
4.7
|
15.0
|
1.0
|
CG
|
C:PHE120
|
4.7
|
15.9
|
1.0
|
CD1
|
C:PHE120
|
4.7
|
16.1
|
1.0
|
|
Gold binding site 4 out
of 8 in 1e3u
Go back to
Gold Binding Sites List in 1e3u
Gold binding site 4 out
of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Gold with other atoms in the Au binding
site number 4 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Au302
b:15.0
occ:1.00
|
AU
|
C:AUC302
|
0.0
|
15.0
|
1.0
|
C2
|
C:AUC302
|
1.7
|
14.6
|
1.0
|
C1
|
C:AUC302
|
1.7
|
15.4
|
1.0
|
N1
|
C:AUC302
|
2.9
|
15.3
|
1.0
|
N2
|
C:AUC302
|
2.9
|
15.0
|
1.0
|
NE1
|
C:TRP154
|
3.0
|
13.4
|
1.0
|
AU
|
C:AUC301
|
3.2
|
17.1
|
1.0
|
CD1
|
C:TRP154
|
3.4
|
12.9
|
1.0
|
C2
|
C:AUC301
|
3.6
|
16.7
|
1.0
|
O
|
C:ALA66
|
3.7
|
11.2
|
1.0
|
CA
|
C:SER67
|
3.8
|
11.2
|
1.0
|
C1
|
C:AUC301
|
3.9
|
17.4
|
1.0
|
CG
|
C:LYS70
|
3.9
|
14.4
|
1.0
|
CE2
|
C:TRP154
|
3.9
|
12.5
|
1.0
|
N2
|
C:AUC301
|
3.9
|
16.3
|
1.0
|
C
|
C:ALA66
|
4.1
|
11.2
|
1.0
|
N
|
C:SER67
|
4.2
|
11.6
|
1.0
|
CG
|
C:TRP154
|
4.4
|
12.3
|
1.0
|
CB
|
C:SER67
|
4.4
|
13.1
|
1.0
|
CD
|
C:LYS70
|
4.5
|
17.5
|
1.0
|
CZ2
|
C:TRP154
|
4.6
|
12.7
|
1.0
|
N
|
C:LYS70
|
4.6
|
9.9
|
1.0
|
C
|
C:SER67
|
4.6
|
11.2
|
1.0
|
CD2
|
C:TRP154
|
4.7
|
11.9
|
1.0
|
CB
|
C:PHE69
|
4.7
|
10.5
|
1.0
|
O
|
C:SER67
|
4.7
|
11.3
|
1.0
|
N1
|
C:AUC301
|
4.8
|
17.2
|
1.0
|
CB
|
C:PHE120
|
4.9
|
15.1
|
1.0
|
|
Gold binding site 5 out
of 8 in 1e3u
Go back to
Gold Binding Sites List in 1e3u
Gold binding site 5 out
of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Gold with other atoms in the Au binding
site number 5 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Au303
b:28.9
occ:1.00
|
AU
|
C:AUC303
|
0.0
|
28.9
|
1.0
|
C1
|
C:AUC303
|
1.7
|
28.5
|
1.0
|
C2
|
C:AUC303
|
1.7
|
28.8
|
1.0
|
N2
|
C:AUC303
|
2.9
|
28.9
|
1.0
|
N1
|
C:AUC303
|
2.9
|
28.4
|
1.0
|
O
|
C:GLU129
|
3.7
|
16.1
|
1.0
|
CB
|
C:GLN133
|
3.7
|
14.3
|
1.0
|
OE1
|
C:GLN133
|
4.0
|
17.7
|
1.0
|
CG
|
C:GLN133
|
4.0
|
14.4
|
1.0
|
C
|
C:GLU129
|
4.2
|
16.2
|
1.0
|
CB
|
C:GLU129
|
4.3
|
17.7
|
1.0
|
CD1
|
C:ILE146
|
4.3
|
14.6
|
1.0
|
CD
|
C:GLN133
|
4.5
|
16.6
|
1.0
|
N
|
C:VAL130
|
4.6
|
16.0
|
1.0
|
CA
|
C:VAL130
|
4.6
|
15.6
|
1.0
|
CG1
|
C:ILE146
|
4.9
|
13.0
|
1.0
|
CA
|
C:GLU129
|
4.9
|
16.5
|
1.0
|
|
Gold binding site 6 out
of 8 in 1e3u
Go back to
Gold Binding Sites List in 1e3u
Gold binding site 6 out
of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Gold with other atoms in the Au binding
site number 6 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Au301
b:14.6
occ:1.00
|
AU
|
D:AUC301
|
0.0
|
14.6
|
1.0
|
C1
|
D:AUC301
|
1.7
|
14.1
|
1.0
|
C2
|
D:AUC301
|
1.7
|
14.5
|
1.0
|
N2
|
D:AUC301
|
2.9
|
15.1
|
1.0
|
N1
|
D:AUC301
|
2.9
|
14.4
|
1.0
|
NE1
|
D:TRP154
|
3.1
|
12.1
|
1.0
|
AU
|
D:AUC302
|
3.2
|
16.2
|
1.0
|
CD1
|
D:TRP154
|
3.5
|
11.2
|
1.0
|
C1
|
D:AUC302
|
3.6
|
15.4
|
1.0
|
O
|
D:ALA66
|
3.7
|
10.5
|
1.0
|
CA
|
D:SER67
|
3.7
|
10.8
|
1.0
|
CG
|
D:LYS70
|
3.8
|
16.0
|
1.0
|
C2
|
D:AUC302
|
3.9
|
16.1
|
1.0
|
N1
|
D:AUC302
|
3.9
|
15.3
|
1.0
|
CE2
|
D:TRP154
|
4.0
|
11.2
|
1.0
|
C
|
D:ALA66
|
4.1
|
10.0
|
1.0
|
N
|
D:SER67
|
4.2
|
10.4
|
1.0
|
CD
|
D:LYS70
|
4.4
|
17.9
|
1.0
|
CB
|
D:SER67
|
4.4
|
13.2
|
1.0
|
CG
|
D:TRP154
|
4.4
|
10.5
|
1.0
|
N
|
D:LYS70
|
4.6
|
10.7
|
1.0
|
C
|
D:SER67
|
4.6
|
10.9
|
1.0
|
CZ2
|
D:TRP154
|
4.6
|
12.2
|
1.0
|
CD2
|
D:TRP154
|
4.7
|
11.0
|
1.0
|
O
|
D:SER67
|
4.7
|
11.6
|
1.0
|
CB
|
D:PHE69
|
4.7
|
11.7
|
1.0
|
CB
|
D:PHE120
|
4.8
|
15.1
|
1.0
|
N2
|
D:AUC302
|
4.8
|
16.1
|
1.0
|
|
Gold binding site 7 out
of 8 in 1e3u
Go back to
Gold Binding Sites List in 1e3u
Gold binding site 7 out
of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Gold with other atoms in the Au binding
site number 7 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Au302
b:16.2
occ:1.00
|
AU
|
D:AUC302
|
0.0
|
16.2
|
1.0
|
C2
|
D:AUC302
|
1.7
|
16.1
|
1.0
|
C1
|
D:AUC302
|
1.7
|
15.4
|
1.0
|
N1
|
D:AUC302
|
2.9
|
15.3
|
1.0
|
N2
|
D:AUC302
|
2.9
|
16.1
|
1.0
|
C2
|
D:AUC301
|
3.2
|
14.5
|
1.0
|
AU
|
D:AUC301
|
3.2
|
14.6
|
1.0
|
CA
|
D:VAL117
|
3.6
|
17.1
|
1.0
|
CG2
|
D:VAL117
|
3.7
|
16.1
|
1.0
|
O
|
D:HOH542
|
3.9
|
26.6
|
1.0
|
N2
|
D:AUC301
|
3.9
|
15.1
|
1.0
|
C1
|
D:AUC301
|
4.0
|
14.1
|
1.0
|
CB
|
D:PHE120
|
4.0
|
15.1
|
1.0
|
CB
|
D:VAL117
|
4.1
|
16.2
|
1.0
|
N
|
D:VAL117
|
4.3
|
16.3
|
1.0
|
O
|
D:VAL117
|
4.3
|
17.5
|
1.0
|
CG1
|
D:VAL117
|
4.5
|
16.1
|
1.0
|
O
|
D:HOH613
|
4.5
|
32.0
|
1.0
|
C
|
D:VAL117
|
4.5
|
17.9
|
1.0
|
O
|
D:ALA116
|
4.6
|
15.3
|
1.0
|
C
|
D:ALA116
|
4.6
|
15.9
|
1.0
|
CG
|
D:PHE120
|
4.7
|
15.2
|
1.0
|
CD1
|
D:PHE120
|
4.7
|
15.3
|
1.0
|
NE1
|
D:TRP154
|
4.7
|
12.1
|
1.0
|
N1
|
D:AUC301
|
4.7
|
14.4
|
1.0
|
|
Gold binding site 8 out
of 8 in 1e3u
Go back to
Gold Binding Sites List in 1e3u
Gold binding site 8 out
of 8 in the Mad Structure of OXA10 Class D Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Gold with other atoms in the Au binding
site number 8 of Mad Structure of OXA10 Class D Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Au303
b:34.6
occ:1.00
|
AU
|
D:AUC303
|
0.0
|
34.6
|
1.0
|
C1
|
D:AUC303
|
1.7
|
34.0
|
1.0
|
C2
|
D:AUC303
|
1.7
|
34.8
|
1.0
|
N1
|
D:AUC303
|
2.9
|
34.2
|
1.0
|
N2
|
D:AUC303
|
2.9
|
34.8
|
1.0
|
O
|
D:HOH531
|
3.5
|
45.3
|
1.0
|
O
|
D:GLU129
|
3.8
|
17.1
|
1.0
|
CB
|
D:GLN133
|
3.8
|
15.9
|
1.0
|
NE2
|
D:GLN133
|
4.0
|
16.6
|
1.0
|
C
|
D:GLU129
|
4.1
|
17.5
|
1.0
|
CG
|
D:GLN133
|
4.1
|
17.2
|
1.0
|
CB
|
D:GLU129
|
4.1
|
24.2
|
1.0
|
CD1
|
D:ILE146
|
4.4
|
13.9
|
1.0
|
N
|
D:VAL130
|
4.5
|
16.8
|
1.0
|
CA
|
D:VAL130
|
4.6
|
16.7
|
1.0
|
CD
|
D:GLN133
|
4.6
|
18.7
|
1.0
|
CA
|
D:GLU129
|
4.7
|
18.9
|
1.0
|
CG1
|
D:ILE146
|
4.9
|
13.5
|
1.0
|
CG
|
D:GLU129
|
5.0
|
31.8
|
1.0
|
|
Reference:
L.Maveyraud,
D.Golemi,
L.P.Kotra,
S.Tranier,
S.Vakulenko,
S.Mobashery,
J.P.Samama.
Insights Into Class D Beta-Lactamases Are Revealed By the Crystal Structure of the OXA10 Enzyme From Pseudomonas Aeruginosa Structure V. 8 1289 2000.
ISSN: ISSN 0969-2126
PubMed: 11188693
DOI: 10.1016/S0969-2126(00)00534-7
Page generated: Wed Jul 10 14:08:51 2024
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