Iron in PDB 4uam: 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site
Protein crystallography data
The structure of 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site, PDB code: 4uam
was solved by
T.J.Carruthers,
P.D.Carr,
C.J.Jackson,
G.Otting,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.93 /
1.80
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.990,
75.910,
82.360,
83.45,
75.30,
74.01
|
R / Rfree (%)
|
16.2 /
18.2
|
Other elements in 4uam:
The structure of 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site
(pdb code 4uam). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site, PDB code: 4uam:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 4uam
Go back to
Iron Binding Sites List in 4uam
Iron binding site 1 out
of 4 in the 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:18.5
occ:0.84
|
OB2
|
A:FLC303
|
2.0
|
17.8
|
0.9
|
ND1
|
A:HIS79
|
2.1
|
15.0
|
1.0
|
NE2
|
A:HIS139
|
2.1
|
17.1
|
1.0
|
NE2
|
A:HIS77
|
2.1
|
16.1
|
1.0
|
OD1
|
A:CSD158
|
2.5
|
20.6
|
0.3
|
CD2
|
A:HIS77
|
2.9
|
17.6
|
1.0
|
CBC
|
A:FLC303
|
2.9
|
23.8
|
0.9
|
HD2
|
A:HIS77
|
2.9
|
21.1
|
1.0
|
HB2
|
A:HIS79
|
2.9
|
16.2
|
1.0
|
CD2
|
A:HIS139
|
3.0
|
15.9
|
1.0
|
OB1
|
A:FLC303
|
3.0
|
25.0
|
0.9
|
CE1
|
A:HIS79
|
3.0
|
16.2
|
1.0
|
CG
|
A:HIS79
|
3.0
|
14.5
|
1.0
|
HD2
|
A:HIS139
|
3.1
|
19.1
|
1.0
|
CE1
|
A:HIS139
|
3.2
|
16.0
|
1.0
|
HE1
|
A:HIS79
|
3.2
|
19.4
|
1.0
|
CE1
|
A:HIS77
|
3.3
|
18.7
|
1.0
|
CB
|
A:HIS79
|
3.4
|
13.5
|
1.0
|
HE1
|
A:HIS139
|
3.4
|
19.2
|
1.0
|
HB3
|
A:HIS79
|
3.5
|
16.2
|
1.0
|
HB3
|
A:CSD158
|
3.6
|
26.6
|
0.3
|
HB3
|
A:CSD158
|
3.6
|
26.2
|
0.3
|
HE1
|
A:HIS77
|
3.6
|
22.4
|
1.0
|
HB2
|
A:CSD158
|
3.6
|
26.6
|
0.4
|
SG
|
A:CSD158
|
3.6
|
21.7
|
0.4
|
SG
|
A:CSD158
|
3.7
|
22.0
|
0.3
|
HB2
|
A:CSD158
|
3.7
|
26.6
|
0.3
|
HB3
|
A:CSD158
|
3.7
|
26.6
|
0.4
|
ZN
|
A:ZN302
|
3.8
|
21.8
|
0.4
|
SG
|
A:CSD158
|
3.8
|
21.9
|
0.3
|
HB2
|
A:CSD158
|
3.8
|
26.2
|
0.3
|
OD1
|
A:ASP81
|
3.8
|
18.0
|
1.0
|
CB
|
A:CSD158
|
3.9
|
22.2
|
0.4
|
CB
|
A:CSD158
|
3.9
|
22.2
|
0.3
|
CB
|
A:CSD158
|
3.9
|
21.8
|
0.3
|
HG23
|
A:THR140
|
4.1
|
15.4
|
1.0
|
CG
|
A:HIS77
|
4.1
|
15.2
|
1.0
|
HG21
|
A:THR140
|
4.1
|
15.4
|
1.0
|
NE2
|
A:HIS79
|
4.1
|
16.5
|
1.0
|
OG2
|
A:FLC303
|
4.2
|
28.1
|
0.9
|
CD2
|
A:HIS79
|
4.2
|
15.4
|
1.0
|
CG
|
A:HIS139
|
4.2
|
13.8
|
1.0
|
ND1
|
A:HIS139
|
4.2
|
16.6
|
1.0
|
OD2
|
A:ASP81
|
4.3
|
19.1
|
1.0
|
ND1
|
A:HIS77
|
4.3
|
14.8
|
1.0
|
CB
|
A:FLC303
|
4.3
|
30.6
|
0.9
|
CG
|
A:ASP81
|
4.5
|
19.0
|
1.0
|
OHB
|
A:FLC303
|
4.5
|
30.2
|
0.9
|
O
|
A:HOH572
|
4.6
|
47.8
|
1.0
|
CG2
|
A:THR140
|
4.6
|
12.8
|
1.0
|
OD2
|
A:CSD158
|
4.6
|
22.7
|
0.3
|
H
|
A:HIS79
|
4.6
|
17.3
|
1.0
|
CGC
|
A:FLC303
|
4.6
|
29.9
|
0.9
|
OD1
|
A:CSD158
|
4.6
|
21.7
|
0.3
|
HD21
|
A:ASN167
|
4.7
|
43.0
|
1.0
|
OD2
|
A:CSD158
|
4.7
|
21.1
|
0.3
|
CA
|
A:HIS79
|
4.8
|
14.2
|
1.0
|
OA2
|
A:FLC303
|
4.8
|
53.0
|
0.9
|
HE2
|
A:HIS79
|
4.9
|
19.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 4uam
Go back to
Iron Binding Sites List in 4uam
Iron binding site 2 out
of 4 in the 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe301
b:20.3
occ:0.84
|
ND1
|
B:HIS79
|
2.0
|
20.2
|
1.0
|
OB1
|
B:FLC303
|
2.0
|
18.1
|
0.9
|
NE2
|
B:HIS139
|
2.1
|
17.6
|
1.0
|
NE2
|
B:HIS77
|
2.1
|
20.3
|
1.0
|
OD1
|
B:CSD158
|
2.6
|
24.5
|
0.3
|
CBC
|
B:FLC303
|
2.9
|
27.8
|
0.9
|
CD2
|
B:HIS77
|
2.9
|
20.5
|
1.0
|
HD2
|
B:HIS77
|
3.0
|
24.6
|
1.0
|
CE1
|
B:HIS79
|
3.0
|
21.5
|
1.0
|
HB2
|
B:HIS79
|
3.0
|
20.1
|
1.0
|
CG
|
B:HIS79
|
3.0
|
18.6
|
1.0
|
OB2
|
B:FLC303
|
3.1
|
25.2
|
0.9
|
CD2
|
B:HIS139
|
3.1
|
19.7
|
1.0
|
CE1
|
B:HIS139
|
3.1
|
18.9
|
1.0
|
HE1
|
B:HIS79
|
3.1
|
25.8
|
1.0
|
HD2
|
B:HIS139
|
3.2
|
23.6
|
1.0
|
CE1
|
B:HIS77
|
3.3
|
21.0
|
1.0
|
HE1
|
B:HIS139
|
3.3
|
22.7
|
1.0
|
CB
|
B:HIS79
|
3.4
|
16.8
|
1.0
|
HB3
|
B:CSD158
|
3.6
|
29.3
|
0.3
|
HB3
|
B:HIS79
|
3.6
|
20.1
|
1.0
|
HB3
|
B:CSD158
|
3.6
|
29.0
|
0.3
|
HE1
|
B:HIS77
|
3.6
|
25.1
|
1.0
|
SG
|
B:CSD158
|
3.6
|
24.4
|
0.4
|
HB2
|
B:CSD158
|
3.6
|
29.3
|
0.4
|
HB2
|
B:CSD158
|
3.7
|
29.3
|
0.3
|
HB3
|
B:CSD158
|
3.7
|
29.3
|
0.4
|
SG
|
B:CSD158
|
3.8
|
24.6
|
0.3
|
HB2
|
B:CSD158
|
3.8
|
29.0
|
0.3
|
ZN
|
B:ZN302
|
3.8
|
19.7
|
0.4
|
SG
|
B:CSD158
|
3.9
|
24.7
|
0.3
|
OD1
|
B:ASP81
|
3.9
|
20.9
|
1.0
|
CB
|
B:CSD158
|
3.9
|
24.4
|
0.4
|
CB
|
B:CSD158
|
3.9
|
24.4
|
0.3
|
CB
|
B:CSD158
|
3.9
|
24.2
|
0.3
|
HG23
|
B:THR140
|
4.0
|
20.5
|
1.0
|
HG21
|
B:THR140
|
4.1
|
20.5
|
1.0
|
NE2
|
B:HIS79
|
4.1
|
22.5
|
1.0
|
CD2
|
B:HIS79
|
4.1
|
20.2
|
1.0
|
CG
|
B:HIS77
|
4.2
|
16.9
|
1.0
|
OG1
|
B:FLC303
|
4.2
|
30.5
|
0.9
|
ND1
|
B:HIS139
|
4.2
|
18.9
|
1.0
|
CG
|
B:HIS139
|
4.2
|
17.5
|
1.0
|
ND1
|
B:HIS77
|
4.3
|
17.0
|
1.0
|
OD2
|
B:ASP81
|
4.3
|
25.9
|
1.0
|
CB
|
B:FLC303
|
4.3
|
36.3
|
0.9
|
O
|
B:HOH607
|
4.5
|
51.0
|
1.0
|
CG2
|
B:THR140
|
4.5
|
17.1
|
1.0
|
CG
|
B:ASP81
|
4.5
|
23.1
|
1.0
|
OD2
|
B:CSD158
|
4.6
|
26.8
|
0.3
|
OHB
|
B:FLC303
|
4.6
|
35.2
|
0.9
|
H
|
B:HIS79
|
4.6
|
17.5
|
1.0
|
CGC
|
B:FLC303
|
4.6
|
31.2
|
0.9
|
OD2
|
B:CSD158
|
4.7
|
24.2
|
0.3
|
OD1
|
B:CSD158
|
4.7
|
24.4
|
0.3
|
CA
|
B:HIS79
|
4.9
|
14.9
|
1.0
|
HE2
|
B:HIS79
|
4.9
|
27.0
|
1.0
|
HG22
|
B:THR140
|
4.9
|
20.5
|
1.0
|
HD21
|
B:ASN167
|
4.9
|
46.8
|
1.0
|
HD1
|
B:HIS139
|
5.0
|
22.7
|
1.0
|
HD2
|
B:HIS79
|
5.0
|
24.2
|
1.0
|
|
Iron binding site 3 out
of 4 in 4uam
Go back to
Iron Binding Sites List in 4uam
Iron binding site 3 out
of 4 in the 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe301
b:19.7
occ:0.84
|
OB2
|
C:FLC303
|
2.0
|
20.6
|
0.9
|
ND1
|
C:HIS79
|
2.0
|
18.4
|
1.0
|
NE2
|
C:HIS139
|
2.0
|
18.8
|
1.0
|
NE2
|
C:HIS77
|
2.1
|
16.1
|
1.0
|
OD1
|
C:CSD158
|
2.7
|
21.7
|
0.3
|
CBC
|
C:FLC303
|
2.9
|
24.2
|
0.9
|
CD2
|
C:HIS77
|
2.9
|
17.3
|
1.0
|
OB1
|
C:FLC303
|
3.0
|
20.1
|
0.9
|
CE1
|
C:HIS79
|
3.0
|
17.9
|
1.0
|
HB2
|
C:HIS79
|
3.0
|
19.6
|
1.0
|
HD2
|
C:HIS77
|
3.0
|
20.7
|
1.0
|
CD2
|
C:HIS139
|
3.0
|
21.2
|
1.0
|
CE1
|
C:HIS139
|
3.0
|
17.7
|
1.0
|
CG
|
C:HIS79
|
3.1
|
19.2
|
1.0
|
HE1
|
C:HIS79
|
3.1
|
21.5
|
1.0
|
CE1
|
C:HIS77
|
3.2
|
15.9
|
1.0
|
HD2
|
C:HIS139
|
3.2
|
25.4
|
1.0
|
HE1
|
C:HIS139
|
3.2
|
21.2
|
1.0
|
CB
|
C:HIS79
|
3.4
|
16.3
|
1.0
|
HE1
|
C:HIS77
|
3.5
|
19.0
|
1.0
|
HB3
|
C:CSD158
|
3.5
|
22.0
|
0.3
|
HB3
|
C:CSD158
|
3.5
|
21.6
|
0.3
|
SG
|
C:CSD158
|
3.6
|
19.9
|
0.4
|
HB3
|
C:HIS79
|
3.6
|
19.6
|
1.0
|
HB2
|
C:CSD158
|
3.6
|
22.2
|
0.4
|
HB2
|
C:CSD158
|
3.7
|
22.0
|
0.3
|
HB3
|
C:CSD158
|
3.8
|
22.2
|
0.4
|
HB2
|
C:CSD158
|
3.8
|
21.6
|
0.3
|
SG
|
C:CSD158
|
3.8
|
21.7
|
0.3
|
ZN
|
C:ZN302
|
3.8
|
18.7
|
0.4
|
SG
|
C:CSD158
|
3.9
|
22.2
|
0.3
|
OD1
|
C:ASP81
|
3.9
|
17.6
|
1.0
|
CB
|
C:CSD158
|
3.9
|
18.5
|
0.4
|
CB
|
C:CSD158
|
3.9
|
18.4
|
0.3
|
CB
|
C:CSD158
|
3.9
|
18.0
|
0.3
|
HG23
|
C:THR140
|
4.0
|
19.8
|
1.0
|
HG21
|
C:THR140
|
4.1
|
19.8
|
1.0
|
NE2
|
C:HIS79
|
4.1
|
19.1
|
1.0
|
CG
|
C:HIS77
|
4.1
|
15.7
|
1.0
|
ND1
|
C:HIS139
|
4.1
|
17.2
|
1.0
|
CG
|
C:HIS139
|
4.2
|
17.3
|
1.0
|
CD2
|
C:HIS79
|
4.2
|
17.4
|
1.0
|
OG2
|
C:FLC303
|
4.2
|
26.9
|
0.9
|
ND1
|
C:HIS77
|
4.2
|
14.8
|
1.0
|
CB
|
C:FLC303
|
4.3
|
33.7
|
0.9
|
OD2
|
C:ASP81
|
4.3
|
19.7
|
1.0
|
CG
|
C:ASP81
|
4.5
|
20.4
|
1.0
|
CG2
|
C:THR140
|
4.5
|
16.5
|
1.0
|
OHB
|
C:FLC303
|
4.6
|
35.8
|
0.9
|
H
|
C:HIS79
|
4.6
|
16.2
|
1.0
|
CGC
|
C:FLC303
|
4.6
|
30.4
|
0.9
|
OD1
|
C:CSD158
|
4.7
|
20.4
|
0.3
|
OD2
|
C:CSD158
|
4.7
|
20.8
|
0.3
|
OD2
|
C:CSD158
|
4.7
|
25.1
|
0.3
|
HD22
|
C:ASN167
|
4.8
|
44.7
|
1.0
|
CA
|
C:HIS79
|
4.9
|
15.4
|
1.0
|
HE2
|
C:HIS79
|
4.9
|
22.9
|
1.0
|
HG22
|
C:THR140
|
4.9
|
19.8
|
1.0
|
HD1
|
C:HIS139
|
4.9
|
20.7
|
1.0
|
|
Iron binding site 4 out
of 4 in 4uam
Go back to
Iron Binding Sites List in 4uam
Iron binding site 4 out
of 4 in the 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe301
b:19.9
occ:0.84
|
OB1
|
D:FLC303
|
2.0
|
19.6
|
0.9
|
ND1
|
D:HIS79
|
2.0
|
18.8
|
1.0
|
NE2
|
D:HIS139
|
2.1
|
17.9
|
1.0
|
NE2
|
D:HIS77
|
2.1
|
16.3
|
1.0
|
OD1
|
D:CSD158
|
2.5
|
23.5
|
0.3
|
CBC
|
D:FLC303
|
2.9
|
25.0
|
0.9
|
CD2
|
D:HIS77
|
2.9
|
17.1
|
1.0
|
HB2
|
D:HIS79
|
2.9
|
23.0
|
1.0
|
HD2
|
D:HIS77
|
3.0
|
20.5
|
1.0
|
OB2
|
D:FLC303
|
3.0
|
19.0
|
0.9
|
CE1
|
D:HIS79
|
3.0
|
22.6
|
1.0
|
CD2
|
D:HIS139
|
3.0
|
18.4
|
1.0
|
CG
|
D:HIS79
|
3.0
|
18.3
|
1.0
|
CE1
|
D:HIS139
|
3.1
|
17.4
|
1.0
|
HD2
|
D:HIS139
|
3.2
|
22.0
|
1.0
|
HE1
|
D:HIS79
|
3.2
|
27.2
|
1.0
|
CE1
|
D:HIS77
|
3.2
|
18.5
|
1.0
|
HE1
|
D:HIS139
|
3.3
|
20.9
|
1.0
|
CB
|
D:HIS79
|
3.4
|
19.2
|
1.0
|
HE1
|
D:HIS77
|
3.5
|
22.2
|
1.0
|
HB3
|
D:CSD158
|
3.6
|
24.4
|
0.3
|
HB3
|
D:HIS79
|
3.6
|
23.0
|
1.0
|
HB3
|
D:CSD158
|
3.6
|
23.7
|
0.3
|
SG
|
D:CSD158
|
3.6
|
21.9
|
0.4
|
HB2
|
D:CSD158
|
3.6
|
25.1
|
0.4
|
SG
|
D:CSD158
|
3.7
|
23.4
|
0.3
|
HB2
|
D:CSD158
|
3.7
|
24.4
|
0.3
|
HB3
|
D:CSD158
|
3.8
|
25.1
|
0.4
|
ZN
|
D:ZN302
|
3.8
|
21.6
|
0.4
|
SG
|
D:CSD158
|
3.8
|
22.6
|
0.3
|
HB2
|
D:CSD158
|
3.8
|
23.7
|
0.3
|
OD1
|
D:ASP81
|
3.9
|
18.5
|
1.0
|
CB
|
D:CSD158
|
3.9
|
20.9
|
0.4
|
CB
|
D:CSD158
|
3.9
|
20.3
|
0.3
|
CB
|
D:CSD158
|
4.0
|
19.7
|
0.3
|
HG21
|
D:THR140
|
4.1
|
21.3
|
1.0
|
HG23
|
D:THR140
|
4.1
|
21.3
|
1.0
|
NE2
|
D:HIS79
|
4.1
|
19.6
|
1.0
|
CG
|
D:HIS77
|
4.1
|
15.0
|
1.0
|
OG1
|
D:FLC303
|
4.1
|
30.1
|
0.9
|
CD2
|
D:HIS79
|
4.2
|
17.5
|
1.0
|
CG
|
D:HIS139
|
4.2
|
14.6
|
1.0
|
ND1
|
D:HIS139
|
4.2
|
16.0
|
1.0
|
ND1
|
D:HIS77
|
4.2
|
15.9
|
1.0
|
CB
|
D:FLC303
|
4.3
|
32.8
|
0.9
|
OD2
|
D:ASP81
|
4.3
|
18.1
|
1.0
|
CG
|
D:ASP81
|
4.5
|
17.0
|
1.0
|
CG2
|
D:THR140
|
4.5
|
17.8
|
1.0
|
OD2
|
D:CSD158
|
4.5
|
25.4
|
0.3
|
OHB
|
D:FLC303
|
4.6
|
30.8
|
0.9
|
CGC
|
D:FLC303
|
4.6
|
32.1
|
0.9
|
H
|
D:HIS79
|
4.6
|
15.6
|
1.0
|
OD2
|
D:CSD158
|
4.7
|
20.8
|
0.3
|
OD1
|
D:CSD158
|
4.7
|
21.4
|
0.3
|
HD22
|
D:ASN167
|
4.8
|
50.8
|
1.0
|
CA
|
D:HIS79
|
4.8
|
16.9
|
1.0
|
HE2
|
D:HIS79
|
4.9
|
23.5
|
1.0
|
HG22
|
D:THR140
|
5.0
|
21.3
|
1.0
|
HD1
|
D:HIS139
|
5.0
|
19.2
|
1.0
|
OA2
|
D:FLC303
|
5.0
|
69.5
|
0.9
|
|
Reference:
T.J.Carruthers,
P.D.Carr,
C.T.Loh,
C.J.Jackson,
G.Otting.
Iron(III) Located in the Dinuclear Metallo-Beta-Lactamase Imp-1 By Pseudocontact Shifts. Angew.Chem.Int.Ed.Engl. 2014.
ISSN: ESSN 1521-3773
PubMed: 25320022
DOI: 10.1002/ANIE.201408693
Page generated: Mon Aug 5 12:00:12 2024
|