Iron in PDB 2yoo: Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis
Protein crystallography data
The structure of Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis, PDB code: 2yoo
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)
|
126.53 /
1.69
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.683,
106.213,
126.536,
90.00,
90.67,
90.00
|
R / Rfree (%)
|
16.5 /
21.9
|
Other elements in 2yoo:
The structure of Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis
(pdb code 2yoo). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis, PDB code: 2yoo:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 2yoo
Go back to
Iron Binding Sites List in 2yoo
Iron binding site 1 out
of 4 in the Cholest-4-En-3-One Bound 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 Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1402
b:9.0
occ:1.00
|
FE
|
A:HEM1402
|
0.0
|
9.0
|
1.0
|
NB
|
A:HEM1402
|
2.1
|
8.4
|
1.0
|
NC
|
A:HEM1402
|
2.1
|
6.1
|
1.0
|
NA
|
A:HEM1402
|
2.1
|
8.7
|
1.0
|
ND
|
A:HEM1402
|
2.1
|
9.6
|
1.0
|
SG
|
A:CYS343
|
2.4
|
8.1
|
1.0
|
C4B
|
A:HEM1402
|
3.1
|
8.6
|
1.0
|
C4A
|
A:HEM1402
|
3.1
|
7.8
|
1.0
|
C4C
|
A:HEM1402
|
3.1
|
4.2
|
1.0
|
C1B
|
A:HEM1402
|
3.1
|
8.2
|
1.0
|
C1C
|
A:HEM1402
|
3.1
|
8.5
|
1.0
|
C1A
|
A:HEM1402
|
3.1
|
9.4
|
1.0
|
C4D
|
A:HEM1402
|
3.1
|
9.3
|
1.0
|
C1D
|
A:HEM1402
|
3.2
|
8.1
|
1.0
|
CHC
|
A:HEM1402
|
3.4
|
7.4
|
1.0
|
CB
|
A:CYS343
|
3.4
|
8.5
|
1.0
|
CHB
|
A:HEM1402
|
3.5
|
4.4
|
1.0
|
CHA
|
A:HEM1402
|
3.5
|
7.6
|
1.0
|
CHD
|
A:HEM1402
|
3.5
|
7.9
|
1.0
|
CA
|
A:CYS343
|
4.0
|
7.7
|
1.0
|
C26
|
A:K2B1404
|
4.1
|
12.6
|
1.0
|
C3B
|
A:HEM1402
|
4.3
|
12.7
|
1.0
|
C3C
|
A:HEM1402
|
4.3
|
7.4
|
1.0
|
C2C
|
A:HEM1402
|
4.3
|
7.5
|
1.0
|
C2B
|
A:HEM1402
|
4.3
|
8.2
|
1.0
|
C2A
|
A:HEM1402
|
4.3
|
6.4
|
1.0
|
C3A
|
A:HEM1402
|
4.3
|
5.9
|
1.0
|
C2D
|
A:HEM1402
|
4.4
|
11.1
|
1.0
|
C3D
|
A:HEM1402
|
4.4
|
6.2
|
1.0
|
N
|
A:GLY345
|
4.6
|
9.8
|
1.0
|
N
|
A:LEU344
|
4.6
|
7.5
|
1.0
|
C
|
A:CYS343
|
4.7
|
7.8
|
1.0
|
CA
|
A:GLY233
|
4.9
|
9.3
|
1.0
|
|
Iron binding site 2 out
of 4 in 2yoo
Go back to
Iron Binding Sites List in 2yoo
Iron binding site 2 out
of 4 in the Cholest-4-En-3-One Bound 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 Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1402
b:8.2
occ:1.00
|
FE
|
B:HEM1402
|
0.0
|
8.2
|
1.0
|
NB
|
B:HEM1402
|
2.0
|
6.3
|
1.0
|
NA
|
B:HEM1402
|
2.1
|
6.9
|
1.0
|
ND
|
B:HEM1402
|
2.1
|
6.6
|
1.0
|
NC
|
B:HEM1402
|
2.1
|
5.0
|
1.0
|
SG
|
B:CYS343
|
2.4
|
8.4
|
1.0
|
C4B
|
B:HEM1402
|
3.1
|
7.2
|
1.0
|
C4A
|
B:HEM1402
|
3.1
|
6.1
|
1.0
|
C4D
|
B:HEM1402
|
3.1
|
4.0
|
1.0
|
C1B
|
B:HEM1402
|
3.1
|
8.8
|
1.0
|
C1A
|
B:HEM1402
|
3.1
|
5.6
|
1.0
|
C1C
|
B:HEM1402
|
3.1
|
9.1
|
1.0
|
C4C
|
B:HEM1402
|
3.1
|
6.4
|
1.0
|
C1D
|
B:HEM1402
|
3.2
|
10.4
|
1.0
|
CB
|
B:CYS343
|
3.4
|
6.5
|
1.0
|
CHC
|
B:HEM1402
|
3.4
|
7.4
|
1.0
|
CHA
|
B:HEM1402
|
3.4
|
4.8
|
1.0
|
CHB
|
B:HEM1402
|
3.4
|
5.7
|
1.0
|
CHD
|
B:HEM1402
|
3.5
|
5.3
|
1.0
|
C26
|
B:K2B1404
|
3.9
|
11.1
|
1.0
|
CA
|
B:CYS343
|
4.0
|
7.6
|
1.0
|
C3B
|
B:HEM1402
|
4.3
|
5.1
|
1.0
|
C2B
|
B:HEM1402
|
4.3
|
7.4
|
1.0
|
C3A
|
B:HEM1402
|
4.3
|
9.0
|
1.0
|
C2A
|
B:HEM1402
|
4.3
|
8.6
|
1.0
|
C3D
|
B:HEM1402
|
4.3
|
7.6
|
1.0
|
C3C
|
B:HEM1402
|
4.4
|
5.3
|
1.0
|
C2C
|
B:HEM1402
|
4.4
|
8.3
|
1.0
|
C2D
|
B:HEM1402
|
4.4
|
9.7
|
1.0
|
N
|
B:GLY345
|
4.5
|
7.2
|
1.0
|
C
|
B:CYS343
|
4.6
|
7.8
|
1.0
|
N
|
B:LEU344
|
4.7
|
6.6
|
1.0
|
CD1
|
B:PHE336
|
5.0
|
4.0
|
1.0
|
|
Iron binding site 3 out
of 4 in 2yoo
Go back to
Iron Binding Sites List in 2yoo
Iron binding site 3 out
of 4 in the Cholest-4-En-3-One Bound 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 Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1402
b:8.4
occ:1.00
|
FE
|
C:HEM1402
|
0.0
|
8.4
|
1.0
|
NB
|
C:HEM1402
|
2.0
|
8.0
|
1.0
|
NA
|
C:HEM1402
|
2.1
|
8.3
|
1.0
|
ND
|
C:HEM1402
|
2.1
|
9.5
|
1.0
|
NC
|
C:HEM1402
|
2.2
|
7.5
|
1.0
|
SG
|
C:CYS343
|
2.4
|
7.8
|
1.0
|
C1A
|
C:HEM1402
|
3.0
|
7.1
|
1.0
|
C4D
|
C:HEM1402
|
3.1
|
6.7
|
1.0
|
C4B
|
C:HEM1402
|
3.1
|
9.6
|
1.0
|
C4A
|
C:HEM1402
|
3.1
|
5.3
|
1.0
|
C1C
|
C:HEM1402
|
3.1
|
9.1
|
1.0
|
C1B
|
C:HEM1402
|
3.1
|
8.0
|
1.0
|
C1D
|
C:HEM1402
|
3.1
|
8.6
|
1.0
|
C4C
|
C:HEM1402
|
3.2
|
5.6
|
1.0
|
CHA
|
C:HEM1402
|
3.4
|
7.7
|
1.0
|
CHC
|
C:HEM1402
|
3.4
|
11.6
|
1.0
|
CB
|
C:CYS343
|
3.4
|
5.4
|
1.0
|
CHD
|
C:HEM1402
|
3.5
|
7.7
|
1.0
|
CHB
|
C:HEM1402
|
3.5
|
8.9
|
1.0
|
C26
|
C:K2B1404
|
4.0
|
11.8
|
1.0
|
CA
|
C:CYS343
|
4.0
|
5.4
|
1.0
|
C2A
|
C:HEM1402
|
4.3
|
7.9
|
1.0
|
C3A
|
C:HEM1402
|
4.3
|
7.2
|
1.0
|
C3B
|
C:HEM1402
|
4.3
|
8.5
|
1.0
|
C2B
|
C:HEM1402
|
4.3
|
9.2
|
1.0
|
C3D
|
C:HEM1402
|
4.3
|
10.7
|
1.0
|
C2D
|
C:HEM1402
|
4.3
|
10.1
|
1.0
|
C2C
|
C:HEM1402
|
4.3
|
8.9
|
1.0
|
C3C
|
C:HEM1402
|
4.4
|
10.3
|
1.0
|
N
|
C:GLY345
|
4.6
|
7.7
|
1.0
|
C
|
C:CYS343
|
4.6
|
5.9
|
1.0
|
N
|
C:LEU344
|
4.6
|
7.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 2yoo
Go back to
Iron Binding Sites List in 2yoo
Iron binding site 4 out
of 4 in the Cholest-4-En-3-One Bound 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 Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1402
b:8.1
occ:1.00
|
FE
|
D:HEM1402
|
0.0
|
8.1
|
1.0
|
NC
|
D:HEM1402
|
2.1
|
6.3
|
1.0
|
ND
|
D:HEM1402
|
2.1
|
9.8
|
1.0
|
NB
|
D:HEM1402
|
2.1
|
9.1
|
1.0
|
NA
|
D:HEM1402
|
2.1
|
5.5
|
1.0
|
SG
|
D:CYS343
|
2.4
|
9.0
|
1.0
|
C4C
|
D:HEM1402
|
3.0
|
7.5
|
1.0
|
C1C
|
D:HEM1402
|
3.1
|
8.7
|
1.0
|
C4A
|
D:HEM1402
|
3.1
|
2.7
|
1.0
|
C1D
|
D:HEM1402
|
3.1
|
7.4
|
1.0
|
C4D
|
D:HEM1402
|
3.1
|
9.6
|
1.0
|
C1A
|
D:HEM1402
|
3.1
|
4.6
|
1.0
|
C4B
|
D:HEM1402
|
3.1
|
7.4
|
1.0
|
C1B
|
D:HEM1402
|
3.1
|
6.3
|
1.0
|
CHD
|
D:HEM1402
|
3.4
|
8.7
|
1.0
|
CB
|
D:CYS343
|
3.4
|
7.3
|
1.0
|
CHB
|
D:HEM1402
|
3.5
|
3.1
|
1.0
|
CHA
|
D:HEM1402
|
3.5
|
6.7
|
1.0
|
CHC
|
D:HEM1402
|
3.5
|
8.6
|
1.0
|
CA
|
D:CYS343
|
4.0
|
8.1
|
1.0
|
C26
|
D:K2B1404
|
4.0
|
11.4
|
1.0
|
C3C
|
D:HEM1402
|
4.3
|
9.2
|
1.0
|
C2C
|
D:HEM1402
|
4.3
|
6.9
|
1.0
|
C3A
|
D:HEM1402
|
4.3
|
6.1
|
1.0
|
C3D
|
D:HEM1402
|
4.3
|
8.1
|
1.0
|
C2D
|
D:HEM1402
|
4.3
|
8.0
|
1.0
|
C2A
|
D:HEM1402
|
4.3
|
5.3
|
1.0
|
C2B
|
D:HEM1402
|
4.3
|
8.5
|
1.0
|
C3B
|
D:HEM1402
|
4.4
|
8.0
|
1.0
|
N
|
D:GLY345
|
4.5
|
7.8
|
1.0
|
N
|
D:LEU344
|
4.6
|
7.7
|
1.0
|
C
|
D:CYS343
|
4.6
|
7.4
|
1.0
|
O
|
D:GLY233
|
5.0
|
9.6
|
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 Aug 4 05:40:59 2024
|