Iron in PDB 7zzl: Crystal Structure of CYP106A1
Protein crystallography data
The structure of Crystal Structure of CYP106A1, PDB code: 7zzl
was solved by
Y.Carius,
F.Kiss,
M.Hutter,
R.Bernhardt,
C.R.D.Lancaster,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.82 /
1.70
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.69,
82.87,
84.86,
95.36,
90,
90
|
R / Rfree (%)
|
16.9 /
20.6
|
Other elements in 7zzl:
The structure of Crystal Structure of CYP106A1 also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of CYP106A1
(pdb code 7zzl). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of CYP106A1, PDB code: 7zzl:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 7zzl
Go back to
Iron Binding Sites List in 7zzl
Iron binding site 1 out
of 4 in the Crystal Structure of CYP106A1
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of CYP106A1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:11.8
occ:1.00
|
FE
|
A:HEM501
|
0.0
|
11.8
|
1.0
|
ND
|
A:HEM501
|
2.0
|
12.3
|
1.0
|
NA
|
A:HEM501
|
2.0
|
11.7
|
1.0
|
NB
|
A:HEM501
|
2.1
|
10.9
|
1.0
|
NC
|
A:HEM501
|
2.1
|
12.0
|
1.0
|
SG
|
A:CYS356
|
2.3
|
12.4
|
1.0
|
O
|
A:HOH663
|
2.4
|
25.8
|
1.0
|
C1D
|
A:HEM501
|
3.0
|
13.8
|
1.0
|
C4D
|
A:HEM501
|
3.0
|
12.5
|
1.0
|
C1A
|
A:HEM501
|
3.0
|
13.4
|
1.0
|
C4B
|
A:HEM501
|
3.0
|
10.7
|
1.0
|
C1B
|
A:HEM501
|
3.1
|
11.8
|
1.0
|
C4C
|
A:HEM501
|
3.1
|
12.5
|
1.0
|
C4A
|
A:HEM501
|
3.1
|
11.9
|
1.0
|
C1C
|
A:HEM501
|
3.1
|
11.0
|
1.0
|
CB
|
A:CYS356
|
3.4
|
11.3
|
1.0
|
CHA
|
A:HEM501
|
3.4
|
11.6
|
1.0
|
CHD
|
A:HEM501
|
3.4
|
12.8
|
1.0
|
CHC
|
A:HEM501
|
3.4
|
11.3
|
1.0
|
CHB
|
A:HEM501
|
3.5
|
11.5
|
1.0
|
CA
|
A:CYS356
|
4.0
|
10.9
|
1.0
|
O
|
A:ALA244
|
4.2
|
17.8
|
1.0
|
C2D
|
A:HEM501
|
4.3
|
13.0
|
1.0
|
C2A
|
A:HEM501
|
4.3
|
13.7
|
1.0
|
C2B
|
A:HEM501
|
4.3
|
10.4
|
1.0
|
C2C
|
A:HEM501
|
4.3
|
11.8
|
1.0
|
C3A
|
A:HEM501
|
4.3
|
12.7
|
1.0
|
C3D
|
A:HEM501
|
4.3
|
12.5
|
1.0
|
C3C
|
A:HEM501
|
4.3
|
12.5
|
1.0
|
C3B
|
A:HEM501
|
4.3
|
11.0
|
1.0
|
CB
|
A:ALA244
|
4.6
|
16.7
|
1.0
|
N
|
A:GLY358
|
4.6
|
11.4
|
1.0
|
C
|
A:CYS356
|
4.7
|
10.7
|
1.0
|
N
|
A:LEU357
|
4.8
|
10.6
|
1.0
|
C
|
A:ALA244
|
4.9
|
15.9
|
1.0
|
CA
|
A:GLY358
|
4.9
|
12.9
|
1.0
|
|
Iron binding site 2 out
of 4 in 7zzl
Go back to
Iron Binding Sites List in 7zzl
Iron binding site 2 out
of 4 in the Crystal Structure of CYP106A1
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of CYP106A1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:10.8
occ:1.00
|
FE
|
B:HEM501
|
0.0
|
10.8
|
1.0
|
ND
|
B:HEM501
|
2.0
|
10.0
|
1.0
|
NA
|
B:HEM501
|
2.0
|
9.7
|
1.0
|
NC
|
B:HEM501
|
2.0
|
9.8
|
1.0
|
NB
|
B:HEM501
|
2.0
|
9.3
|
1.0
|
O
|
B:HOH708
|
2.2
|
22.7
|
1.0
|
SG
|
B:CYS356
|
2.3
|
10.9
|
1.0
|
C1D
|
B:HEM501
|
3.0
|
10.9
|
1.0
|
C4D
|
B:HEM501
|
3.0
|
10.9
|
1.0
|
C4B
|
B:HEM501
|
3.0
|
9.4
|
1.0
|
C1B
|
B:HEM501
|
3.0
|
10.1
|
1.0
|
C1A
|
B:HEM501
|
3.0
|
11.0
|
1.0
|
C4C
|
B:HEM501
|
3.0
|
11.3
|
1.0
|
C1C
|
B:HEM501
|
3.1
|
9.6
|
1.0
|
C4A
|
B:HEM501
|
3.1
|
10.8
|
1.0
|
CHA
|
B:HEM501
|
3.4
|
10.9
|
1.0
|
CB
|
B:CYS356
|
3.4
|
10.0
|
1.0
|
CHD
|
B:HEM501
|
3.4
|
11.0
|
1.0
|
CHC
|
B:HEM501
|
3.4
|
10.1
|
1.0
|
CHB
|
B:HEM501
|
3.4
|
10.6
|
1.0
|
CA
|
B:CYS356
|
4.0
|
9.8
|
1.0
|
O
|
B:ALA244
|
4.1
|
17.2
|
1.0
|
C2D
|
B:HEM501
|
4.2
|
10.9
|
1.0
|
C2B
|
B:HEM501
|
4.2
|
10.4
|
1.0
|
C3D
|
B:HEM501
|
4.2
|
10.9
|
1.0
|
C3C
|
B:HEM501
|
4.3
|
10.5
|
1.0
|
C3A
|
B:HEM501
|
4.3
|
11.4
|
1.0
|
C3B
|
B:HEM501
|
4.3
|
10.7
|
1.0
|
C2C
|
B:HEM501
|
4.3
|
10.6
|
1.0
|
C2A
|
B:HEM501
|
4.3
|
11.7
|
1.0
|
O2
|
B:PEG506
|
4.5
|
56.7
|
1.0
|
O4
|
B:PEG506
|
4.5
|
50.6
|
1.0
|
CB
|
B:ALA244
|
4.6
|
14.0
|
1.0
|
N
|
B:GLY358
|
4.7
|
12.0
|
1.0
|
C
|
B:CYS356
|
4.7
|
10.4
|
1.0
|
N
|
B:LEU357
|
4.8
|
11.9
|
1.0
|
C
|
B:ALA244
|
4.9
|
14.9
|
1.0
|
CA
|
B:GLY358
|
5.0
|
12.7
|
1.0
|
|
Iron binding site 3 out
of 4 in 7zzl
Go back to
Iron Binding Sites List in 7zzl
Iron binding site 3 out
of 4 in the Crystal Structure of CYP106A1
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of CYP106A1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:14.2
occ:1.00
|
FE
|
C:HEM501
|
0.0
|
14.2
|
1.0
|
ND
|
C:HEM501
|
2.0
|
15.1
|
1.0
|
NA
|
C:HEM501
|
2.0
|
14.3
|
1.0
|
NB
|
C:HEM501
|
2.1
|
14.7
|
1.0
|
NC
|
C:HEM501
|
2.1
|
13.6
|
1.0
|
O
|
C:HOH720
|
2.2
|
24.0
|
1.0
|
SG
|
C:CYS356
|
2.3
|
13.1
|
1.0
|
C4D
|
C:HEM501
|
3.0
|
16.8
|
1.0
|
C1A
|
C:HEM501
|
3.0
|
15.9
|
1.0
|
C1D
|
C:HEM501
|
3.0
|
15.1
|
1.0
|
C1B
|
C:HEM501
|
3.0
|
14.5
|
1.0
|
C4A
|
C:HEM501
|
3.1
|
15.0
|
1.0
|
C4B
|
C:HEM501
|
3.1
|
15.0
|
1.0
|
C4C
|
C:HEM501
|
3.1
|
14.3
|
1.0
|
C1C
|
C:HEM501
|
3.1
|
14.3
|
1.0
|
CHA
|
C:HEM501
|
3.4
|
15.5
|
1.0
|
CB
|
C:CYS356
|
3.4
|
12.7
|
1.0
|
CHD
|
C:HEM501
|
3.4
|
14.8
|
1.0
|
CHB
|
C:HEM501
|
3.4
|
14.1
|
1.0
|
CHC
|
C:HEM501
|
3.5
|
13.3
|
1.0
|
CA
|
C:CYS356
|
4.0
|
13.4
|
1.0
|
O
|
C:ALA244
|
4.2
|
22.6
|
1.0
|
C2A
|
C:HEM501
|
4.2
|
15.9
|
1.0
|
C3D
|
C:HEM501
|
4.3
|
16.1
|
1.0
|
C2B
|
C:HEM501
|
4.3
|
13.9
|
1.0
|
C3A
|
C:HEM501
|
4.3
|
15.2
|
1.0
|
C2D
|
C:HEM501
|
4.3
|
16.6
|
1.0
|
C3C
|
C:HEM501
|
4.3
|
14.9
|
1.0
|
C2C
|
C:HEM501
|
4.3
|
14.5
|
1.0
|
C3B
|
C:HEM501
|
4.3
|
14.0
|
1.0
|
N
|
C:GLY358
|
4.6
|
12.6
|
1.0
|
N
|
C:LEU357
|
4.7
|
15.1
|
1.0
|
C
|
C:CYS356
|
4.7
|
13.9
|
1.0
|
CB
|
C:ALA244
|
4.8
|
18.9
|
1.0
|
O1
|
C:PEG505
|
5.0
|
49.9
|
1.0
|
C2
|
C:PEG505
|
5.0
|
52.5
|
1.0
|
CA
|
C:GLY358
|
5.0
|
12.2
|
1.0
|
C
|
C:ALA244
|
5.0
|
18.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 7zzl
Go back to
Iron Binding Sites List in 7zzl
Iron binding site 4 out
of 4 in the Crystal Structure of CYP106A1
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of CYP106A1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:13.0
occ:1.00
|
FE
|
D:HEM501
|
0.0
|
13.0
|
1.0
|
ND
|
D:HEM501
|
1.9
|
13.2
|
1.0
|
NA
|
D:HEM501
|
2.0
|
12.4
|
1.0
|
NB
|
D:HEM501
|
2.1
|
12.9
|
1.0
|
NC
|
D:HEM501
|
2.1
|
12.6
|
1.0
|
O
|
D:HOH708
|
2.1
|
23.4
|
1.0
|
SG
|
D:CYS356
|
2.2
|
12.7
|
1.0
|
C4D
|
D:HEM501
|
2.9
|
14.5
|
1.0
|
C1D
|
D:HEM501
|
3.0
|
13.6
|
1.0
|
C1A
|
D:HEM501
|
3.0
|
15.0
|
1.0
|
C1B
|
D:HEM501
|
3.0
|
13.6
|
1.0
|
C4A
|
D:HEM501
|
3.0
|
13.2
|
1.0
|
C4C
|
D:HEM501
|
3.0
|
13.5
|
1.0
|
C4B
|
D:HEM501
|
3.1
|
13.6
|
1.0
|
C1C
|
D:HEM501
|
3.1
|
13.5
|
1.0
|
CHA
|
D:HEM501
|
3.4
|
13.5
|
1.0
|
CB
|
D:CYS356
|
3.4
|
12.6
|
1.0
|
CHB
|
D:HEM501
|
3.4
|
12.9
|
1.0
|
CHD
|
D:HEM501
|
3.4
|
13.3
|
1.0
|
CHC
|
D:HEM501
|
3.5
|
13.0
|
1.0
|
CA
|
D:CYS356
|
4.1
|
12.6
|
1.0
|
C3D
|
D:HEM501
|
4.2
|
14.9
|
1.0
|
C2D
|
D:HEM501
|
4.2
|
15.0
|
1.0
|
C3A
|
D:HEM501
|
4.2
|
13.6
|
1.0
|
C3C
|
D:HEM501
|
4.2
|
15.1
|
1.0
|
C2A
|
D:HEM501
|
4.2
|
15.5
|
1.0
|
O
|
D:ALA244
|
4.3
|
18.8
|
1.0
|
C2B
|
D:HEM501
|
4.3
|
13.2
|
1.0
|
C2C
|
D:HEM501
|
4.3
|
13.6
|
1.0
|
C3B
|
D:HEM501
|
4.3
|
13.5
|
1.0
|
N
|
D:GLY358
|
4.6
|
13.6
|
1.0
|
C
|
D:CYS356
|
4.7
|
12.6
|
1.0
|
N
|
D:LEU357
|
4.8
|
14.4
|
1.0
|
CB
|
D:ALA244
|
4.8
|
18.8
|
1.0
|
|
Reference:
Y.Carius,
M.Hutter,
F.Kiss,
R.Bernhardt,
C.R.D.Lancaster.
Structural Comparison of the Cytochrome P450 Enzymes CYP106A1 and CYP106A2 Provides Insight Into Their Differences in Steroid Conversion. Febs Lett. V. 596 3133 2022.
ISSN: ISSN 0014-5793
PubMed: 36151590
DOI: 10.1002/1873-3468.14502
Page generated: Fri Aug 9 16:01:29 2024
|