Iron in PDB 6oyu: Structure of An Ancestral-Reconstructed Cytochrome P450 1B1 with Alpha-Naphthoflavone
Protein crystallography data
The structure of Structure of An Ancestral-Reconstructed Cytochrome P450 1B1 with Alpha-Naphthoflavone, PDB code: 6oyu
was solved by
A.G.Bart,
K.L.Harris,
E.E.Scott,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.15 /
2.95
|
Space group
|
I 4
|
Cell size a, b, c (Å), α, β, γ (°)
|
164.641,
164.641,
96.301,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.9 /
25.8
|
Iron Binding Sites:
The binding sites of Iron atom in the Structure of An Ancestral-Reconstructed Cytochrome P450 1B1 with Alpha-Naphthoflavone
(pdb code 6oyu). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the
Structure of An Ancestral-Reconstructed Cytochrome P450 1B1 with Alpha-Naphthoflavone, PDB code: 6oyu:
Jump to Iron binding site number:
1;
2;
Iron binding site 1 out
of 2 in 6oyu
Go back to
Iron Binding Sites List in 6oyu
Iron binding site 1 out
of 2 in the Structure of An Ancestral-Reconstructed Cytochrome P450 1B1 with Alpha-Naphthoflavone
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of An Ancestral-Reconstructed Cytochrome P450 1B1 with Alpha-Naphthoflavone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe605
b:35.1
occ:1.00
|
FE
|
A:HEM605
|
0.0
|
35.1
|
1.0
|
NB
|
A:HEM605
|
2.0
|
29.0
|
1.0
|
NA
|
A:HEM605
|
2.0
|
32.2
|
1.0
|
ND
|
A:HEM605
|
2.1
|
29.8
|
1.0
|
NC
|
A:HEM605
|
2.1
|
26.1
|
1.0
|
SG
|
A:CYS470
|
2.7
|
67.3
|
1.0
|
HB2
|
A:CYS470
|
2.9
|
36.6
|
1.0
|
C1B
|
A:HEM605
|
3.0
|
30.2
|
1.0
|
C4A
|
A:HEM605
|
3.0
|
28.6
|
1.0
|
C4B
|
A:HEM605
|
3.0
|
31.9
|
1.0
|
C1A
|
A:HEM605
|
3.1
|
30.3
|
1.0
|
C1C
|
A:HEM605
|
3.1
|
26.9
|
1.0
|
C4D
|
A:HEM605
|
3.1
|
24.8
|
1.0
|
C4C
|
A:HEM605
|
3.1
|
32.9
|
1.0
|
C1D
|
A:HEM605
|
3.1
|
31.8
|
1.0
|
CB
|
A:CYS470
|
3.3
|
30.3
|
1.0
|
CHB
|
A:HEM605
|
3.4
|
37.3
|
1.0
|
CHC
|
A:HEM605
|
3.4
|
31.7
|
1.0
|
CHA
|
A:HEM605
|
3.4
|
24.9
|
1.0
|
CHD
|
A:HEM605
|
3.5
|
34.7
|
1.0
|
HB1
|
A:ALA330
|
3.5
|
47.1
|
1.0
|
O
|
A:HOH710
|
3.6
|
25.1
|
1.0
|
HA
|
A:CYS470
|
3.9
|
41.4
|
1.0
|
HD1
|
A:PHE463
|
3.9
|
55.6
|
1.0
|
HB3
|
A:CYS470
|
4.1
|
36.6
|
1.0
|
C2B
|
A:HEM605
|
4.2
|
26.5
|
1.0
|
CA
|
A:CYS470
|
4.2
|
34.3
|
1.0
|
C3B
|
A:HEM605
|
4.2
|
32.7
|
1.0
|
C3A
|
A:HEM605
|
4.2
|
31.2
|
1.0
|
H
|
A:GLY472
|
4.3
|
36.3
|
1.0
|
C2A
|
A:HEM605
|
4.3
|
36.9
|
1.0
|
C2C
|
A:HEM605
|
4.3
|
32.7
|
1.0
|
C3C
|
A:HEM605
|
4.3
|
39.5
|
1.0
|
C3D
|
A:HEM605
|
4.3
|
30.8
|
1.0
|
HE1
|
A:PHE463
|
4.3
|
60.7
|
1.0
|
C2D
|
A:HEM605
|
4.3
|
31.7
|
1.0
|
HHB
|
A:HEM605
|
4.3
|
45.1
|
1.0
|
HB3
|
A:ALA330
|
4.3
|
47.1
|
1.0
|
CB
|
A:ALA330
|
4.4
|
39.0
|
1.0
|
HHC
|
A:HEM605
|
4.4
|
38.3
|
1.0
|
HHA
|
A:HEM605
|
4.4
|
30.2
|
1.0
|
HHD
|
A:HEM605
|
4.4
|
42.0
|
1.0
|
HG21
|
A:THR334
|
4.6
|
31.8
|
1.0
|
CD1
|
A:PHE463
|
4.7
|
46.1
|
1.0
|
H
|
A:ILE471
|
4.7
|
45.5
|
1.0
|
O
|
A:ALA330
|
4.7
|
33.0
|
1.0
|
HB2
|
A:ALA330
|
4.8
|
47.1
|
1.0
|
CE1
|
A:PHE463
|
4.9
|
50.3
|
1.0
|
|
Iron binding site 2 out
of 2 in 6oyu
Go back to
Iron Binding Sites List in 6oyu
Iron binding site 2 out
of 2 in the Structure of An Ancestral-Reconstructed Cytochrome P450 1B1 with Alpha-Naphthoflavone
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of An Ancestral-Reconstructed Cytochrome P450 1B1 with Alpha-Naphthoflavone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe605
b:31.4
occ:1.00
|
FE
|
B:HEM605
|
0.0
|
31.4
|
1.0
|
NB
|
B:HEM605
|
2.0
|
31.9
|
1.0
|
NA
|
B:HEM605
|
2.0
|
25.7
|
1.0
|
NC
|
B:HEM605
|
2.1
|
37.9
|
1.0
|
ND
|
B:HEM605
|
2.1
|
36.6
|
1.0
|
SG
|
B:CYS470
|
2.7
|
51.1
|
1.0
|
HB2
|
B:CYS470
|
2.9
|
34.3
|
1.0
|
C1B
|
B:HEM605
|
3.0
|
34.7
|
1.0
|
C4A
|
B:HEM605
|
3.0
|
26.2
|
1.0
|
C4B
|
B:HEM605
|
3.0
|
30.8
|
1.0
|
C1A
|
B:HEM605
|
3.0
|
28.4
|
1.0
|
C1C
|
B:HEM605
|
3.1
|
34.4
|
1.0
|
C4C
|
B:HEM605
|
3.1
|
35.9
|
1.0
|
C4D
|
B:HEM605
|
3.1
|
32.4
|
1.0
|
C1D
|
B:HEM605
|
3.1
|
32.6
|
1.0
|
CB
|
B:CYS470
|
3.3
|
28.4
|
1.0
|
CHB
|
B:HEM605
|
3.4
|
31.3
|
1.0
|
CHC
|
B:HEM605
|
3.4
|
33.1
|
1.0
|
CHA
|
B:HEM605
|
3.4
|
30.5
|
1.0
|
CHD
|
B:HEM605
|
3.5
|
33.8
|
1.0
|
HA
|
B:CYS470
|
3.5
|
36.4
|
1.0
|
O
|
B:HOH706
|
3.8
|
24.2
|
1.0
|
HB1
|
B:ALA330
|
3.9
|
38.0
|
1.0
|
CA
|
B:CYS470
|
4.0
|
30.1
|
1.0
|
HB3
|
B:CYS470
|
4.1
|
34.3
|
1.0
|
C3A
|
B:HEM605
|
4.2
|
25.6
|
1.0
|
C2A
|
B:HEM605
|
4.2
|
27.7
|
1.0
|
C2B
|
B:HEM605
|
4.2
|
26.8
|
1.0
|
C3B
|
B:HEM605
|
4.2
|
31.2
|
1.0
|
C2C
|
B:HEM605
|
4.3
|
34.2
|
1.0
|
C3C
|
B:HEM605
|
4.3
|
37.0
|
1.0
|
C3D
|
B:HEM605
|
4.3
|
31.7
|
1.0
|
C2D
|
B:HEM605
|
4.3
|
34.1
|
1.0
|
HD1
|
B:PHE463
|
4.3
|
45.0
|
1.0
|
O
|
B:HOH720
|
4.4
|
27.9
|
1.0
|
HHB
|
B:HEM605
|
4.4
|
37.8
|
1.0
|
HHC
|
B:HEM605
|
4.4
|
39.9
|
1.0
|
H
|
B:GLY472
|
4.4
|
36.4
|
1.0
|
HHA
|
B:HEM605
|
4.4
|
36.9
|
1.0
|
HHD
|
B:HEM605
|
4.5
|
40.9
|
1.0
|
HG21
|
B:THR334
|
4.5
|
36.3
|
1.0
|
O
|
B:ALA330
|
4.6
|
32.3
|
1.0
|
CB
|
B:ALA330
|
4.7
|
31.4
|
1.0
|
HB3
|
B:ALA330
|
4.7
|
38.0
|
1.0
|
H
|
B:ILE471
|
4.7
|
42.9
|
1.0
|
C
|
B:CYS470
|
4.9
|
31.7
|
1.0
|
HG1
|
B:THR334
|
4.9
|
41.5
|
1.0
|
|
Reference:
A.G.Bart,
K.L.Harris,
E.M.J.Gillam,
E.E.Scott.
Structure of An Ancestral Mammalian Family 1B1 Cytochrome P450 with Increased Thermostability J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
Page generated: Wed Aug 7 05:30:54 2024
|