Iron in PDB 3ofu: Crystal Structure of Cytochrome P450 CYP101C1
Protein crystallography data
The structure of Crystal Structure of Cytochrome P450 CYP101C1, PDB code: 3ofu
was solved by
W.Zhou,
M.Ma,
S.G.Bell,
W.Yang,
Y.Hao,
N.H.Rees,
M.Bartlam,
L.-L.Wong,
Z.Rao,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.360,
113.418,
150.234,
90.00,
89.90,
90.00
|
R / Rfree (%)
|
19.3 /
30.3
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Cytochrome P450 CYP101C1
(pdb code 3ofu). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of Cytochrome P450 CYP101C1, PDB code: 3ofu:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3ofu
Go back to
Iron Binding Sites List in 3ofu
Iron binding site 1 out
of 6 in the Crystal Structure of Cytochrome P450 CYP101C1
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 Cytochrome P450 CYP101C1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe417
b:13.9
occ:1.00
|
FE
|
A:HEM417
|
0.0
|
13.9
|
1.0
|
NA
|
A:HEM417
|
1.9
|
6.1
|
1.0
|
NB
|
A:HEM417
|
2.0
|
7.4
|
1.0
|
SG
|
A:CYS345
|
2.0
|
9.2
|
1.0
|
ND
|
A:HEM417
|
2.0
|
11.0
|
1.0
|
NC
|
A:HEM417
|
2.1
|
6.9
|
1.0
|
C1A
|
A:HEM417
|
2.8
|
8.2
|
1.0
|
C4B
|
A:HEM417
|
3.0
|
7.7
|
1.0
|
C4A
|
A:HEM417
|
3.0
|
5.8
|
1.0
|
C4D
|
A:HEM417
|
3.0
|
10.1
|
1.0
|
C1C
|
A:HEM417
|
3.0
|
8.0
|
1.0
|
C1B
|
A:HEM417
|
3.0
|
7.3
|
1.0
|
C1D
|
A:HEM417
|
3.1
|
12.8
|
1.0
|
C4C
|
A:HEM417
|
3.1
|
6.8
|
1.0
|
CHA
|
A:HEM417
|
3.2
|
7.7
|
1.0
|
CHC
|
A:HEM417
|
3.3
|
9.7
|
1.0
|
CB
|
A:CYS345
|
3.4
|
7.9
|
1.0
|
CHB
|
A:HEM417
|
3.4
|
7.4
|
1.0
|
CHD
|
A:HEM417
|
3.6
|
6.1
|
1.0
|
O
|
A:GLY234
|
4.1
|
21.6
|
1.0
|
C2A
|
A:HEM417
|
4.1
|
10.3
|
1.0
|
C3A
|
A:HEM417
|
4.2
|
9.3
|
1.0
|
CA
|
A:CYS345
|
4.2
|
6.5
|
1.0
|
C3B
|
A:HEM417
|
4.2
|
8.6
|
1.0
|
C2B
|
A:HEM417
|
4.3
|
5.9
|
1.0
|
C3D
|
A:HEM417
|
4.3
|
9.8
|
1.0
|
C3C
|
A:HEM417
|
4.3
|
9.4
|
1.0
|
C2C
|
A:HEM417
|
4.3
|
7.5
|
1.0
|
CE
|
A:MET338
|
4.3
|
14.6
|
1.0
|
C2D
|
A:HEM417
|
4.4
|
14.2
|
1.0
|
C
|
A:GLY234
|
4.9
|
19.8
|
1.0
|
|
Iron binding site 2 out
of 6 in 3ofu
Go back to
Iron Binding Sites List in 3ofu
Iron binding site 2 out
of 6 in the Crystal Structure of Cytochrome P450 CYP101C1
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 Cytochrome P450 CYP101C1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe417
b:11.1
occ:1.00
|
FE
|
B:HEM417
|
0.0
|
11.1
|
1.0
|
NB
|
B:HEM417
|
1.9
|
10.4
|
1.0
|
NC
|
B:HEM417
|
2.0
|
10.4
|
1.0
|
ND
|
B:HEM417
|
2.0
|
10.4
|
1.0
|
NA
|
B:HEM417
|
2.0
|
12.4
|
1.0
|
SG
|
B:CYS345
|
2.2
|
9.6
|
1.0
|
C4B
|
B:HEM417
|
3.0
|
10.0
|
1.0
|
C1C
|
B:HEM417
|
3.0
|
9.3
|
1.0
|
C1B
|
B:HEM417
|
3.0
|
11.0
|
1.0
|
C4C
|
B:HEM417
|
3.0
|
9.0
|
1.0
|
C1D
|
B:HEM417
|
3.0
|
9.6
|
1.0
|
C4D
|
B:HEM417
|
3.0
|
8.2
|
1.0
|
C4A
|
B:HEM417
|
3.0
|
11.1
|
1.0
|
C1A
|
B:HEM417
|
3.1
|
8.8
|
1.0
|
CHC
|
B:HEM417
|
3.3
|
8.5
|
1.0
|
CHD
|
B:HEM417
|
3.4
|
6.1
|
1.0
|
CHB
|
B:HEM417
|
3.4
|
10.0
|
1.0
|
CHA
|
B:HEM417
|
3.4
|
8.0
|
1.0
|
CB
|
B:CYS345
|
3.4
|
9.3
|
1.0
|
CA
|
B:CYS345
|
4.1
|
9.1
|
1.0
|
O
|
B:GLY234
|
4.1
|
21.9
|
1.0
|
C3B
|
B:HEM417
|
4.2
|
8.3
|
1.0
|
C2C
|
B:HEM417
|
4.2
|
14.2
|
1.0
|
C3C
|
B:HEM417
|
4.2
|
13.4
|
1.0
|
C2D
|
B:HEM417
|
4.2
|
11.4
|
1.0
|
C2B
|
B:HEM417
|
4.2
|
11.2
|
1.0
|
C3D
|
B:HEM417
|
4.2
|
7.2
|
1.0
|
C3A
|
B:HEM417
|
4.3
|
9.7
|
1.0
|
C2A
|
B:HEM417
|
4.3
|
7.1
|
1.0
|
C
|
B:GLY234
|
4.8
|
20.9
|
1.0
|
CE
|
B:MET338
|
4.8
|
17.0
|
1.0
|
N
|
B:GLY347
|
4.9
|
10.8
|
1.0
|
C
|
B:CYS345
|
5.0
|
9.3
|
1.0
|
|
Iron binding site 3 out
of 6 in 3ofu
Go back to
Iron Binding Sites List in 3ofu
Iron binding site 3 out
of 6 in the Crystal Structure of Cytochrome P450 CYP101C1
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 Cytochrome P450 CYP101C1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe417
b:12.8
occ:1.00
|
FE
|
C:HEM417
|
0.0
|
12.8
|
1.0
|
NA
|
C:HEM417
|
2.0
|
8.1
|
1.0
|
ND
|
C:HEM417
|
2.0
|
11.0
|
1.0
|
NB
|
C:HEM417
|
2.0
|
10.0
|
1.0
|
NC
|
C:HEM417
|
2.0
|
11.8
|
1.0
|
SG
|
C:CYS345
|
2.2
|
10.1
|
1.0
|
C4D
|
C:HEM417
|
2.9
|
11.0
|
1.0
|
C1A
|
C:HEM417
|
3.0
|
6.4
|
1.0
|
C4B
|
C:HEM417
|
3.0
|
11.2
|
1.0
|
C4A
|
C:HEM417
|
3.0
|
9.0
|
1.0
|
C1D
|
C:HEM417
|
3.0
|
12.5
|
1.0
|
C1C
|
C:HEM417
|
3.0
|
10.1
|
1.0
|
C1B
|
C:HEM417
|
3.1
|
9.6
|
1.0
|
C4C
|
C:HEM417
|
3.1
|
11.3
|
1.0
|
CHA
|
C:HEM417
|
3.2
|
8.4
|
1.0
|
CB
|
C:CYS345
|
3.3
|
9.9
|
1.0
|
CHC
|
C:HEM417
|
3.3
|
13.7
|
1.0
|
CHB
|
C:HEM417
|
3.4
|
8.1
|
1.0
|
CHD
|
C:HEM417
|
3.5
|
9.3
|
1.0
|
O
|
C:GLY234
|
3.8
|
20.0
|
1.0
|
CA
|
C:CYS345
|
4.2
|
8.4
|
1.0
|
C3B
|
C:HEM417
|
4.2
|
8.9
|
1.0
|
C3A
|
C:HEM417
|
4.2
|
9.9
|
1.0
|
C2A
|
C:HEM417
|
4.2
|
10.6
|
1.0
|
C3D
|
C:HEM417
|
4.2
|
9.5
|
1.0
|
C2D
|
C:HEM417
|
4.3
|
11.1
|
1.0
|
C2B
|
C:HEM417
|
4.3
|
8.0
|
1.0
|
C3C
|
C:HEM417
|
4.3
|
10.3
|
1.0
|
C2C
|
C:HEM417
|
4.3
|
7.9
|
1.0
|
CE
|
C:MET338
|
4.6
|
14.7
|
1.0
|
C
|
C:GLY234
|
4.7
|
18.9
|
1.0
|
CA
|
C:GLY234
|
4.9
|
19.3
|
1.0
|
C
|
C:CYS345
|
5.0
|
9.9
|
1.0
|
OG1
|
C:THR238
|
5.0
|
14.2
|
1.0
|
N
|
C:GLY347
|
5.0
|
6.1
|
1.0
|
|
Iron binding site 4 out
of 6 in 3ofu
Go back to
Iron Binding Sites List in 3ofu
Iron binding site 4 out
of 6 in the Crystal Structure of Cytochrome P450 CYP101C1
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 Cytochrome P450 CYP101C1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe417
b:13.1
occ:1.00
|
FE
|
D:HEM417
|
0.0
|
13.1
|
1.0
|
ND
|
D:HEM417
|
2.0
|
11.0
|
1.0
|
NB
|
D:HEM417
|
2.0
|
12.5
|
1.0
|
NC
|
D:HEM417
|
2.0
|
12.8
|
1.0
|
NA
|
D:HEM417
|
2.0
|
13.0
|
1.0
|
SG
|
D:CYS345
|
2.3
|
10.6
|
1.0
|
C1D
|
D:HEM417
|
2.9
|
12.1
|
1.0
|
C4C
|
D:HEM417
|
2.9
|
11.0
|
1.0
|
C4B
|
D:HEM417
|
3.0
|
14.2
|
1.0
|
C4D
|
D:HEM417
|
3.0
|
8.9
|
1.0
|
C1B
|
D:HEM417
|
3.0
|
14.6
|
1.0
|
C4A
|
D:HEM417
|
3.0
|
12.8
|
1.0
|
C1C
|
D:HEM417
|
3.1
|
10.4
|
1.0
|
C1A
|
D:HEM417
|
3.1
|
11.2
|
1.0
|
CB
|
D:CYS345
|
3.2
|
6.7
|
1.0
|
CHD
|
D:HEM417
|
3.3
|
7.2
|
1.0
|
CHA
|
D:HEM417
|
3.4
|
11.6
|
1.0
|
CHB
|
D:HEM417
|
3.4
|
14.2
|
1.0
|
CHC
|
D:HEM417
|
3.4
|
9.8
|
1.0
|
CA
|
D:CYS345
|
4.0
|
8.2
|
1.0
|
O
|
D:GLY234
|
4.0
|
17.0
|
1.0
|
C2D
|
D:HEM417
|
4.2
|
13.1
|
1.0
|
C3C
|
D:HEM417
|
4.2
|
14.1
|
1.0
|
C3B
|
D:HEM417
|
4.2
|
14.6
|
1.0
|
C3D
|
D:HEM417
|
4.2
|
10.2
|
1.0
|
C2B
|
D:HEM417
|
4.3
|
15.9
|
1.0
|
C2A
|
D:HEM417
|
4.3
|
9.1
|
1.0
|
C3A
|
D:HEM417
|
4.3
|
12.5
|
1.0
|
C2C
|
D:HEM417
|
4.3
|
13.1
|
1.0
|
C
|
D:GLY234
|
4.7
|
17.2
|
1.0
|
CE
|
D:MET338
|
4.8
|
22.1
|
1.0
|
C
|
D:CYS345
|
4.8
|
9.1
|
1.0
|
N
|
D:GLY347
|
4.8
|
9.9
|
1.0
|
|
Iron binding site 5 out
of 6 in 3ofu
Go back to
Iron Binding Sites List in 3ofu
Iron binding site 5 out
of 6 in the Crystal Structure of Cytochrome P450 CYP101C1
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Cytochrome P450 CYP101C1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe417
b:25.4
occ:1.00
|
FE
|
E:HEM417
|
0.0
|
25.4
|
1.0
|
NA
|
E:HEM417
|
2.0
|
20.5
|
1.0
|
NC
|
E:HEM417
|
2.0
|
25.7
|
1.0
|
ND
|
E:HEM417
|
2.1
|
23.6
|
1.0
|
NB
|
E:HEM417
|
2.2
|
25.1
|
1.0
|
SG
|
E:CYS345
|
2.3
|
23.1
|
1.0
|
C1A
|
E:HEM417
|
3.0
|
18.9
|
1.0
|
C4A
|
E:HEM417
|
3.0
|
21.9
|
1.0
|
C4C
|
E:HEM417
|
3.0
|
30.3
|
1.0
|
C4D
|
E:HEM417
|
3.1
|
24.2
|
1.0
|
C1C
|
E:HEM417
|
3.1
|
24.5
|
1.0
|
C1D
|
E:HEM417
|
3.1
|
23.5
|
1.0
|
C4B
|
E:HEM417
|
3.2
|
24.0
|
1.0
|
C1B
|
E:HEM417
|
3.2
|
23.7
|
1.0
|
CHA
|
E:HEM417
|
3.4
|
23.3
|
1.0
|
CHD
|
E:HEM417
|
3.4
|
28.1
|
1.0
|
CHB
|
E:HEM417
|
3.4
|
18.0
|
1.0
|
CHC
|
E:HEM417
|
3.5
|
27.8
|
1.0
|
CB
|
E:CYS345
|
3.6
|
22.7
|
1.0
|
O
|
E:GLY234
|
4.2
|
32.9
|
1.0
|
C2A
|
E:HEM417
|
4.2
|
20.4
|
1.0
|
C3A
|
E:HEM417
|
4.2
|
24.6
|
1.0
|
C3C
|
E:HEM417
|
4.2
|
29.6
|
1.0
|
CA
|
E:CYS345
|
4.2
|
22.9
|
1.0
|
C2C
|
E:HEM417
|
4.3
|
24.8
|
1.0
|
C3D
|
E:HEM417
|
4.3
|
25.3
|
1.0
|
C3B
|
E:HEM417
|
4.4
|
21.9
|
1.0
|
C2B
|
E:HEM417
|
4.4
|
23.5
|
1.0
|
C2D
|
E:HEM417
|
4.4
|
26.3
|
1.0
|
CE
|
E:MET338
|
4.8
|
35.0
|
1.0
|
C
|
E:GLY234
|
5.0
|
31.9
|
1.0
|
|
Iron binding site 6 out
of 6 in 3ofu
Go back to
Iron Binding Sites List in 3ofu
Iron binding site 6 out
of 6 in the Crystal Structure of Cytochrome P450 CYP101C1
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of Cytochrome P450 CYP101C1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe417
b:22.4
occ:1.00
|
FE
|
F:HEM417
|
0.0
|
22.4
|
1.0
|
NA
|
F:HEM417
|
2.0
|
20.6
|
1.0
|
ND
|
F:HEM417
|
2.0
|
25.4
|
1.0
|
NC
|
F:HEM417
|
2.1
|
23.5
|
1.0
|
NB
|
F:HEM417
|
2.2
|
19.7
|
1.0
|
SG
|
F:CYS345
|
2.3
|
24.9
|
1.0
|
C4C
|
F:HEM417
|
3.0
|
24.4
|
1.0
|
C4A
|
F:HEM417
|
3.0
|
19.8
|
1.0
|
C1D
|
F:HEM417
|
3.0
|
27.1
|
1.0
|
C1A
|
F:HEM417
|
3.0
|
20.9
|
1.0
|
C4D
|
F:HEM417
|
3.1
|
25.5
|
1.0
|
C1C
|
F:HEM417
|
3.2
|
21.1
|
1.0
|
C1B
|
F:HEM417
|
3.2
|
17.7
|
1.0
|
C4B
|
F:HEM417
|
3.2
|
18.9
|
1.0
|
CHD
|
F:HEM417
|
3.3
|
25.4
|
1.0
|
CHB
|
F:HEM417
|
3.4
|
15.6
|
1.0
|
CHA
|
F:HEM417
|
3.4
|
23.8
|
1.0
|
CHC
|
F:HEM417
|
3.6
|
22.1
|
1.0
|
CB
|
F:CYS345
|
3.6
|
25.5
|
1.0
|
O
|
F:GLY234
|
3.8
|
36.5
|
1.0
|
C3C
|
F:HEM417
|
4.2
|
25.2
|
1.0
|
C2A
|
F:HEM417
|
4.2
|
22.3
|
1.0
|
C3A
|
F:HEM417
|
4.2
|
22.0
|
1.0
|
CA
|
F:CYS345
|
4.3
|
25.4
|
1.0
|
C2C
|
F:HEM417
|
4.3
|
19.1
|
1.0
|
C2D
|
F:HEM417
|
4.3
|
26.9
|
1.0
|
C3D
|
F:HEM417
|
4.3
|
26.1
|
1.0
|
C3B
|
F:HEM417
|
4.4
|
19.9
|
1.0
|
C2B
|
F:HEM417
|
4.4
|
19.1
|
1.0
|
CE
|
F:MET338
|
4.7
|
31.0
|
1.0
|
C
|
F:GLY234
|
4.9
|
33.8
|
1.0
|
|
Reference:
M.Ma,
S.G.Bell,
W.Yang,
Y.Hao,
N.H.Rees,
M.Bartlam,
W.Zhou,
L.L.Wong,
Z.Rao.
Structural Analysis of CYP101C1 From Novosphingobium Aromaticivorans DSM12444. Chembiochem V. 12 88 2011.
ISSN: ISSN 1439-4227
PubMed: 21154803
DOI: 10.1002/CBIC.201000537
Page generated: Sun Aug 4 17:05:18 2024
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