Iron in PDB 3zby: Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis
Protein crystallography data
The structure of Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis, PDB code: 3zby
was solved by
E.Garcia-Fernandez,
D.J.Frank,
B.Galan,
P.M.Kells,
L.M.Podust,
J.L.Garcia,
P.R.Ortiz De Montellano,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
266.44 /
1.93
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.051,
162.847,
266.443,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
19 /
23
|
Iron Binding Sites:
The binding sites of Iron atom in the Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis
(pdb code 3zby). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis, PDB code: 3zby:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3zby
Go back to
Iron Binding Sites List in 3zby
Iron binding site 1 out
of 6 in the Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1402
b:14.6
occ:1.00
|
FE
|
A:HEM1402
|
0.0
|
14.6
|
1.0
|
|
O1
|
A:EDO1406
|
1.8
|
23.3
|
1.0
|
|
NC
|
A:HEM1402
|
2.1
|
15.1
|
1.0
|
|
NB
|
A:HEM1402
|
2.1
|
13.7
|
1.0
|
|
NA
|
A:HEM1402
|
2.1
|
13.6
|
1.0
|
|
ND
|
A:HEM1402
|
2.1
|
15.1
|
1.0
|
|
SG
|
A:CYS343
|
2.2
|
15.8
|
1.0
|
|
C4C
|
A:HEM1402
|
3.0
|
13.8
|
1.0
|
|
C4B
|
A:HEM1402
|
3.1
|
15.0
|
1.0
|
|
C4A
|
A:HEM1402
|
3.1
|
12.1
|
1.0
|
|
C1B
|
A:HEM1402
|
3.1
|
15.0
|
1.0
|
|
C1A
|
A:HEM1402
|
3.1
|
15.0
|
1.0
|
|
C1C
|
A:HEM1402
|
3.1
|
15.0
|
1.0
|
|
C1D
|
A:HEM1402
|
3.1
|
17.1
|
1.0
|
|
C4D
|
A:HEM1402
|
3.2
|
16.6
|
1.0
|
|
C1
|
A:EDO1406
|
3.2
|
19.7
|
1.0
|
|
CB
|
A:CYS343
|
3.3
|
14.2
|
1.0
|
|
CHD
|
A:HEM1402
|
3.4
|
14.4
|
1.0
|
|
CHB
|
A:HEM1402
|
3.4
|
15.3
|
1.0
|
|
CHC
|
A:HEM1402
|
3.5
|
11.9
|
1.0
|
|
CHA
|
A:HEM1402
|
3.5
|
13.1
|
1.0
|
|
C2
|
A:EDO1406
|
4.0
|
22.4
|
1.0
|
|
CA
|
A:CYS343
|
4.0
|
14.6
|
1.0
|
|
O
|
A:GLY233
|
4.1
|
16.7
|
1.0
|
|
C3C
|
A:HEM1402
|
4.3
|
14.7
|
1.0
|
|
C3B
|
A:HEM1402
|
4.3
|
15.1
|
1.0
|
|
C3A
|
A:HEM1402
|
4.3
|
14.0
|
1.0
|
|
C2B
|
A:HEM1402
|
4.3
|
12.4
|
1.0
|
|
C2A
|
A:HEM1402
|
4.3
|
14.6
|
1.0
|
|
C2C
|
A:HEM1402
|
4.3
|
16.3
|
1.0
|
|
C3D
|
A:HEM1402
|
4.4
|
17.7
|
1.0
|
|
C2D
|
A:HEM1402
|
4.4
|
15.1
|
1.0
|
|
N
|
A:GLY345
|
4.6
|
14.6
|
1.0
|
|
C
|
A:CYS343
|
4.7
|
15.1
|
1.0
|
|
N
|
A:LEU344
|
4.8
|
16.3
|
1.0
|
|
C
|
A:GLY233
|
4.8
|
17.1
|
1.0
|
|
Iron binding site 2 out
of 6 in 3zby
Go back to
Iron Binding Sites List in 3zby
Iron binding site 2 out
of 6 in the Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1402
b:13.6
occ:1.00
|
FE
|
B:HEM1402
|
0.0
|
13.6
|
1.0
|
|
O2
|
B:EDO1409
|
1.9
|
20.4
|
1.0
|
|
NB
|
B:HEM1402
|
2.0
|
13.7
|
1.0
|
|
NC
|
B:HEM1402
|
2.1
|
13.6
|
1.0
|
|
NA
|
B:HEM1402
|
2.1
|
12.5
|
1.0
|
|
ND
|
B:HEM1402
|
2.1
|
14.7
|
1.0
|
|
SG
|
B:CYS343
|
2.2
|
14.6
|
1.0
|
|
C4C
|
B:HEM1402
|
3.0
|
14.1
|
1.0
|
|
C4B
|
B:HEM1402
|
3.0
|
12.1
|
1.0
|
|
C1D
|
B:HEM1402
|
3.1
|
14.9
|
1.0
|
|
C4A
|
B:HEM1402
|
3.1
|
11.7
|
1.0
|
|
C1C
|
B:HEM1402
|
3.1
|
13.4
|
1.0
|
|
C1B
|
B:HEM1402
|
3.1
|
15.8
|
1.0
|
|
C1A
|
B:HEM1402
|
3.1
|
12.3
|
1.0
|
|
C4D
|
B:HEM1402
|
3.1
|
14.9
|
1.0
|
|
C2
|
B:EDO1409
|
3.2
|
19.9
|
1.0
|
|
CB
|
B:CYS343
|
3.3
|
13.3
|
1.0
|
|
CHD
|
B:HEM1402
|
3.4
|
14.8
|
1.0
|
|
CHC
|
B:HEM1402
|
3.4
|
12.8
|
1.0
|
|
CHB
|
B:HEM1402
|
3.5
|
13.1
|
1.0
|
|
CHA
|
B:HEM1402
|
3.5
|
13.0
|
1.0
|
|
C1
|
B:EDO1409
|
3.9
|
22.4
|
1.0
|
|
CA
|
B:CYS343
|
4.1
|
13.1
|
1.0
|
|
O
|
B:GLY233
|
4.2
|
16.7
|
1.0
|
|
C3B
|
B:HEM1402
|
4.3
|
12.4
|
1.0
|
|
C3C
|
B:HEM1402
|
4.3
|
15.8
|
1.0
|
|
C3A
|
B:HEM1402
|
4.3
|
10.4
|
1.0
|
|
C2A
|
B:HEM1402
|
4.3
|
13.6
|
1.0
|
|
C2B
|
B:HEM1402
|
4.3
|
11.1
|
1.0
|
|
C2C
|
B:HEM1402
|
4.3
|
15.2
|
1.0
|
|
C2D
|
B:HEM1402
|
4.3
|
13.5
|
1.0
|
|
C3D
|
B:HEM1402
|
4.3
|
14.1
|
1.0
|
|
N
|
B:GLY345
|
4.7
|
13.7
|
1.0
|
|
C
|
B:CYS343
|
4.7
|
14.2
|
1.0
|
|
N
|
B:LEU344
|
4.8
|
13.8
|
1.0
|
|
C
|
B:GLY233
|
4.9
|
17.4
|
1.0
|
|
Iron binding site 3 out
of 6 in 3zby
Go back to
Iron Binding Sites List in 3zby
Iron binding site 3 out
of 6 in the Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1402
b:14.2
occ:1.00
|
FE
|
C:HEM1402
|
0.0
|
14.2
|
1.0
|
|
O2
|
C:EDO1407
|
1.8
|
26.4
|
1.0
|
|
NC
|
C:HEM1402
|
2.1
|
15.2
|
1.0
|
|
NA
|
C:HEM1402
|
2.1
|
14.3
|
1.0
|
|
NB
|
C:HEM1402
|
2.1
|
12.5
|
1.0
|
|
ND
|
C:HEM1402
|
2.2
|
17.1
|
1.0
|
|
SG
|
C:CYS343
|
2.2
|
15.6
|
1.0
|
|
C4C
|
C:HEM1402
|
3.0
|
15.0
|
1.0
|
|
C4A
|
C:HEM1402
|
3.1
|
12.8
|
1.0
|
|
C4B
|
C:HEM1402
|
3.1
|
15.0
|
1.0
|
|
C1A
|
C:HEM1402
|
3.1
|
16.3
|
1.0
|
|
C1C
|
C:HEM1402
|
3.1
|
15.5
|
1.0
|
|
C1B
|
C:HEM1402
|
3.1
|
14.8
|
1.0
|
|
C1D
|
C:HEM1402
|
3.1
|
16.5
|
1.0
|
|
C4D
|
C:HEM1402
|
3.2
|
15.5
|
1.0
|
|
C2
|
C:EDO1407
|
3.2
|
21.6
|
1.0
|
|
CB
|
C:CYS343
|
3.3
|
14.9
|
1.0
|
|
CHD
|
C:HEM1402
|
3.4
|
15.5
|
1.0
|
|
CHB
|
C:HEM1402
|
3.5
|
11.6
|
1.0
|
|
CHC
|
C:HEM1402
|
3.5
|
11.3
|
1.0
|
|
CHA
|
C:HEM1402
|
3.5
|
12.1
|
1.0
|
|
C1
|
C:EDO1407
|
4.0
|
23.4
|
1.0
|
|
CA
|
C:CYS343
|
4.1
|
13.9
|
1.0
|
|
O
|
C:GLY233
|
4.1
|
17.9
|
1.0
|
|
C3C
|
C:HEM1402
|
4.2
|
15.4
|
1.0
|
|
C3B
|
C:HEM1402
|
4.3
|
15.1
|
1.0
|
|
C2C
|
C:HEM1402
|
4.3
|
16.6
|
1.0
|
|
C3A
|
C:HEM1402
|
4.3
|
11.4
|
1.0
|
|
C2A
|
C:HEM1402
|
4.3
|
13.9
|
1.0
|
|
C2B
|
C:HEM1402
|
4.3
|
12.7
|
1.0
|
|
C3D
|
C:HEM1402
|
4.4
|
17.7
|
1.0
|
|
C2D
|
C:HEM1402
|
4.4
|
16.3
|
1.0
|
|
C
|
C:CYS343
|
4.7
|
14.9
|
1.0
|
|
N
|
C:GLY345
|
4.7
|
14.5
|
1.0
|
|
N
|
C:LEU344
|
4.8
|
15.2
|
1.0
|
|
O1
|
C:EDO1407
|
4.8
|
30.8
|
1.0
|
|
C
|
C:GLY233
|
4.8
|
17.6
|
1.0
|
|
Iron binding site 4 out
of 6 in 3zby
Go back to
Iron Binding Sites List in 3zby
Iron binding site 4 out
of 6 in the Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1402
b:14.6
occ:1.00
|
FE
|
D:HEM1402
|
0.0
|
14.6
|
1.0
|
|
O2
|
D:EDO1407
|
2.0
|
20.8
|
1.0
|
|
NB
|
D:HEM1402
|
2.0
|
14.2
|
1.0
|
|
ND
|
D:HEM1402
|
2.0
|
16.7
|
1.0
|
|
NC
|
D:HEM1402
|
2.0
|
13.6
|
1.0
|
|
NA
|
D:HEM1402
|
2.1
|
14.6
|
1.0
|
|
SG
|
D:CYS343
|
2.2
|
15.2
|
1.0
|
|
C4C
|
D:HEM1402
|
3.0
|
14.2
|
1.0
|
|
C4B
|
D:HEM1402
|
3.0
|
14.1
|
1.0
|
|
C1D
|
D:HEM1402
|
3.0
|
15.8
|
1.0
|
|
C1B
|
D:HEM1402
|
3.1
|
15.3
|
1.0
|
|
C4A
|
D:HEM1402
|
3.1
|
14.5
|
1.0
|
|
C1A
|
D:HEM1402
|
3.1
|
16.3
|
1.0
|
|
C4D
|
D:HEM1402
|
3.1
|
15.7
|
1.0
|
|
C1C
|
D:HEM1402
|
3.1
|
15.4
|
1.0
|
|
CB
|
D:CYS343
|
3.3
|
14.5
|
1.0
|
|
C2
|
D:EDO1407
|
3.3
|
19.5
|
1.0
|
|
CHD
|
D:HEM1402
|
3.4
|
12.7
|
1.0
|
|
CHB
|
D:HEM1402
|
3.4
|
12.8
|
1.0
|
|
CHA
|
D:HEM1402
|
3.4
|
13.4
|
1.0
|
|
CHC
|
D:HEM1402
|
3.5
|
16.0
|
1.0
|
|
C1
|
D:EDO1407
|
4.0
|
21.6
|
1.0
|
|
CA
|
D:CYS343
|
4.1
|
14.7
|
1.0
|
|
O
|
D:GLY233
|
4.2
|
15.8
|
1.0
|
|
C3B
|
D:HEM1402
|
4.3
|
15.1
|
1.0
|
|
C3C
|
D:HEM1402
|
4.3
|
15.9
|
1.0
|
|
C2B
|
D:HEM1402
|
4.3
|
12.9
|
1.0
|
|
C3A
|
D:HEM1402
|
4.3
|
13.2
|
1.0
|
|
C2A
|
D:HEM1402
|
4.3
|
13.4
|
1.0
|
|
C2C
|
D:HEM1402
|
4.3
|
16.4
|
1.0
|
|
C2D
|
D:HEM1402
|
4.3
|
16.2
|
1.0
|
|
C3D
|
D:HEM1402
|
4.3
|
14.6
|
1.0
|
|
N
|
D:GLY345
|
4.6
|
13.9
|
1.0
|
|
C
|
D:CYS343
|
4.7
|
15.9
|
1.0
|
|
N
|
D:LEU344
|
4.7
|
13.8
|
1.0
|
|
C
|
D:GLY233
|
4.9
|
16.7
|
1.0
|
|
Iron binding site 5 out
of 6 in 3zby
Go back to
Iron Binding Sites List in 3zby
Iron binding site 5 out
of 6 in the Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe1402
b:14.4
occ:1.00
|
FE
|
E:HEM1402
|
0.0
|
14.4
|
1.0
|
|
O1
|
E:EDO1407
|
2.0
|
22.1
|
1.0
|
|
NB
|
E:HEM1402
|
2.0
|
14.7
|
1.0
|
|
NC
|
E:HEM1402
|
2.0
|
14.7
|
1.0
|
|
NA
|
E:HEM1402
|
2.1
|
15.1
|
1.0
|
|
ND
|
E:HEM1402
|
2.1
|
17.1
|
1.0
|
|
SG
|
E:CYS343
|
2.3
|
15.4
|
1.0
|
|
C4B
|
E:HEM1402
|
3.0
|
14.7
|
1.0
|
|
C4A
|
E:HEM1402
|
3.0
|
13.2
|
1.0
|
|
C4C
|
E:HEM1402
|
3.0
|
18.0
|
1.0
|
|
C1B
|
E:HEM1402
|
3.1
|
15.9
|
1.0
|
|
C1C
|
E:HEM1402
|
3.1
|
14.1
|
1.0
|
|
C1A
|
E:HEM1402
|
3.1
|
17.5
|
1.0
|
|
C1D
|
E:HEM1402
|
3.1
|
17.0
|
1.0
|
|
C4D
|
E:HEM1402
|
3.2
|
17.4
|
1.0
|
|
C1
|
E:EDO1407
|
3.3
|
23.1
|
1.0
|
|
CB
|
E:CYS343
|
3.4
|
14.9
|
1.0
|
|
CHC
|
E:HEM1402
|
3.4
|
12.3
|
1.0
|
|
CHB
|
E:HEM1402
|
3.4
|
13.2
|
1.0
|
|
CHD
|
E:HEM1402
|
3.4
|
15.6
|
1.0
|
|
CHA
|
E:HEM1402
|
3.5
|
13.4
|
1.0
|
|
C2
|
E:EDO1407
|
4.0
|
23.7
|
1.0
|
|
CA
|
E:CYS343
|
4.1
|
13.8
|
1.0
|
|
O
|
E:GLY233
|
4.2
|
17.7
|
1.0
|
|
C3B
|
E:HEM1402
|
4.2
|
15.8
|
1.0
|
|
C2B
|
E:HEM1402
|
4.3
|
12.6
|
1.0
|
|
C3A
|
E:HEM1402
|
4.3
|
12.3
|
1.0
|
|
C3C
|
E:HEM1402
|
4.3
|
15.6
|
1.0
|
|
C2C
|
E:HEM1402
|
4.3
|
16.7
|
1.0
|
|
C2A
|
E:HEM1402
|
4.3
|
15.9
|
1.0
|
|
C2D
|
E:HEM1402
|
4.4
|
15.6
|
1.0
|
|
C3D
|
E:HEM1402
|
4.4
|
17.3
|
1.0
|
|
N
|
E:GLY345
|
4.7
|
15.9
|
1.0
|
|
C
|
E:CYS343
|
4.7
|
15.0
|
1.0
|
|
N
|
E:LEU344
|
4.8
|
14.6
|
1.0
|
|
C
|
E:GLY233
|
4.8
|
17.0
|
1.0
|
|
Iron binding site 6 out
of 6 in 3zby
Go back to
Iron Binding Sites List in 3zby
Iron binding site 6 out
of 6 in the Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe1402
b:14.3
occ:1.00
|
FE
|
F:HEM1402
|
0.0
|
14.3
|
1.0
|
|
O2
|
F:EDO1407
|
1.9
|
22.7
|
1.0
|
|
NC
|
F:HEM1402
|
2.0
|
15.9
|
1.0
|
|
NB
|
F:HEM1402
|
2.1
|
13.8
|
1.0
|
|
NA
|
F:HEM1402
|
2.1
|
14.0
|
1.0
|
|
ND
|
F:HEM1402
|
2.1
|
17.0
|
1.0
|
|
SG
|
F:CYS343
|
2.2
|
15.8
|
1.0
|
|
C4B
|
F:HEM1402
|
3.0
|
14.7
|
1.0
|
|
C1C
|
F:HEM1402
|
3.0
|
12.5
|
1.0
|
|
C4C
|
F:HEM1402
|
3.0
|
16.1
|
1.0
|
|
C1D
|
F:HEM1402
|
3.1
|
19.4
|
1.0
|
|
C4A
|
F:HEM1402
|
3.1
|
12.2
|
1.0
|
|
C1A
|
F:HEM1402
|
3.1
|
14.6
|
1.0
|
|
C1B
|
F:HEM1402
|
3.1
|
15.9
|
1.0
|
|
C4D
|
F:HEM1402
|
3.1
|
16.2
|
1.0
|
|
C2
|
F:EDO1407
|
3.3
|
18.4
|
1.0
|
|
CB
|
F:CYS343
|
3.3
|
13.3
|
1.0
|
|
CHC
|
F:HEM1402
|
3.4
|
15.5
|
1.0
|
|
CHD
|
F:HEM1402
|
3.4
|
15.3
|
1.0
|
|
CHB
|
F:HEM1402
|
3.5
|
12.6
|
1.0
|
|
CHA
|
F:HEM1402
|
3.5
|
14.7
|
1.0
|
|
C1
|
F:EDO1407
|
4.0
|
21.5
|
1.0
|
|
CA
|
F:CYS343
|
4.0
|
13.7
|
1.0
|
|
O
|
F:GLY233
|
4.2
|
17.0
|
1.0
|
|
C3C
|
F:HEM1402
|
4.2
|
16.8
|
1.0
|
|
C3B
|
F:HEM1402
|
4.3
|
13.8
|
1.0
|
|
C3A
|
F:HEM1402
|
4.3
|
12.4
|
1.0
|
|
C2C
|
F:HEM1402
|
4.3
|
15.4
|
1.0
|
|
C2A
|
F:HEM1402
|
4.3
|
16.5
|
1.0
|
|
C2B
|
F:HEM1402
|
4.3
|
12.8
|
1.0
|
|
C2D
|
F:HEM1402
|
4.3
|
15.7
|
1.0
|
|
C3D
|
F:HEM1402
|
4.3
|
17.0
|
1.0
|
|
N
|
F:GLY345
|
4.6
|
14.0
|
1.0
|
|
C
|
F:CYS343
|
4.7
|
13.4
|
1.0
|
|
N
|
F:LEU344
|
4.7
|
12.9
|
1.0
|
|
C
|
F:GLY233
|
4.9
|
16.8
|
1.0
|
|
Reference:
E.Garcia-Fernandez,
D.J.Frank,
B.Galan,
P.M.Kells,
L.M.Podust,
J.L.Garcia,
P.R.Ortiz De Montellano.
A Highly Conserved Mycobacterial Cholesterol Catabolic Pathway. Environ.Microbiol. V. 15 2342 2013.
ISSN: ISSN 1462-2912
PubMed: 23489718
DOI: 10.1111/1462-2920.12108
Page generated: Sun Dec 13 15:26:46 2020
|
