Iron in PDB 5kyo: Crystal Structure of CYP101J2
Protein crystallography data
The structure of Crystal Structure of CYP101J2, PDB code: 5kyo
was solved by
B.Unterweger,
N.Drinkwater,
G.J.Dumsday,
S.Mcgowan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
42.60 /
1.80
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
99.426,
100.031,
99.963,
63.46,
63.66,
63.67
|
|
R / Rfree (%)
|
22.3 /
27.6
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of CYP101J2
(pdb code 5kyo). 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 CYP101J2, PDB code: 5kyo:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 5kyo
Go back to
Iron Binding Sites List in 5kyo
Iron binding site 1 out
of 6 in the Crystal Structure of CYP101J2
 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 CYP101J2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:15.8
occ:1.00
|
FE
|
A:HEM501
|
0.0
|
15.8
|
1.0
|
|
NB
|
A:HEM501
|
2.0
|
17.7
|
1.0
|
|
NA
|
A:HEM501
|
2.1
|
14.5
|
1.0
|
|
ND
|
A:HEM501
|
2.1
|
15.1
|
1.0
|
|
NC
|
A:HEM501
|
2.1
|
17.9
|
1.0
|
|
SG
|
A:CYS359
|
2.4
|
17.4
|
1.0
|
|
O
|
A:HOH647
|
2.6
|
31.3
|
1.0
|
|
C4D
|
A:HEM501
|
3.1
|
22.2
|
1.0
|
|
C1B
|
A:HEM501
|
3.1
|
15.1
|
1.0
|
|
C4B
|
A:HEM501
|
3.1
|
16.3
|
1.0
|
|
C1A
|
A:HEM501
|
3.1
|
14.6
|
1.0
|
|
C4C
|
A:HEM501
|
3.1
|
16.1
|
1.0
|
|
C4A
|
A:HEM501
|
3.1
|
16.2
|
1.0
|
|
C1D
|
A:HEM501
|
3.1
|
22.3
|
1.0
|
|
C1C
|
A:HEM501
|
3.1
|
14.4
|
1.0
|
|
CB
|
A:CYS359
|
3.4
|
14.6
|
1.0
|
|
CHA
|
A:HEM501
|
3.4
|
24.6
|
1.0
|
|
CHB
|
A:HEM501
|
3.4
|
17.1
|
1.0
|
|
CHD
|
A:HEM501
|
3.5
|
16.5
|
1.0
|
|
CHC
|
A:HEM501
|
3.5
|
14.4
|
1.0
|
|
O
|
A:GLY250
|
3.9
|
17.1
|
1.0
|
|
CA
|
A:CYS359
|
4.2
|
21.4
|
1.0
|
|
C2B
|
A:HEM501
|
4.3
|
14.4
|
1.0
|
|
C3B
|
A:HEM501
|
4.3
|
14.4
|
1.0
|
|
C3D
|
A:HEM501
|
4.3
|
16.4
|
1.0
|
|
C3C
|
A:HEM501
|
4.3
|
18.9
|
1.0
|
|
C2C
|
A:HEM501
|
4.3
|
20.8
|
1.0
|
|
C3A
|
A:HEM501
|
4.3
|
14.6
|
1.0
|
|
C2A
|
A:HEM501
|
4.3
|
18.8
|
1.0
|
|
C2D
|
A:HEM501
|
4.3
|
14.5
|
1.0
|
|
C
|
A:GLY250
|
4.7
|
21.3
|
1.0
|
|
N
|
A:GLY361
|
4.8
|
16.3
|
1.0
|
|
CG2
|
A:THR254
|
4.9
|
14.3
|
1.0
|
|
CD
|
A:PRO360
|
4.9
|
14.6
|
1.0
|
|
C
|
A:CYS359
|
5.0
|
22.3
|
1.0
|
|
Iron binding site 2 out
of 6 in 5kyo
Go back to
Iron Binding Sites List in 5kyo
Iron binding site 2 out
of 6 in the Crystal Structure of CYP101J2
 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 CYP101J2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:19.1
occ:1.00
|
FE
|
B:HEM501
|
0.0
|
19.1
|
1.0
|
|
ND
|
B:HEM501
|
2.1
|
17.0
|
1.0
|
|
NC
|
B:HEM501
|
2.1
|
21.6
|
1.0
|
|
NB
|
B:HEM501
|
2.1
|
14.4
|
1.0
|
|
NA
|
B:HEM501
|
2.1
|
16.9
|
1.0
|
|
SG
|
B:CYS359
|
2.4
|
18.1
|
1.0
|
|
C4C
|
B:HEM501
|
3.0
|
15.7
|
1.0
|
|
C1D
|
B:HEM501
|
3.1
|
19.2
|
1.0
|
|
C1C
|
B:HEM501
|
3.1
|
23.0
|
1.0
|
|
C4D
|
B:HEM501
|
3.1
|
22.1
|
1.0
|
|
C4B
|
B:HEM501
|
3.1
|
26.0
|
1.0
|
|
C4A
|
B:HEM501
|
3.1
|
14.9
|
1.0
|
|
C1B
|
B:HEM501
|
3.1
|
14.8
|
1.0
|
|
C1A
|
B:HEM501
|
3.1
|
19.6
|
1.0
|
|
CHD
|
B:HEM501
|
3.4
|
16.1
|
1.0
|
|
CHC
|
B:HEM501
|
3.4
|
26.2
|
1.0
|
|
CHA
|
B:HEM501
|
3.5
|
19.7
|
1.0
|
|
CB
|
B:CYS359
|
3.5
|
28.4
|
1.0
|
|
CHB
|
B:HEM501
|
3.5
|
17.9
|
1.0
|
|
O
|
B:GLY250
|
4.0
|
16.0
|
1.0
|
|
CA
|
B:CYS359
|
4.2
|
21.7
|
1.0
|
|
C3C
|
B:HEM501
|
4.3
|
14.4
|
1.0
|
|
C2C
|
B:HEM501
|
4.3
|
14.4
|
1.0
|
|
C3D
|
B:HEM501
|
4.3
|
19.7
|
1.0
|
|
C3A
|
B:HEM501
|
4.3
|
16.4
|
1.0
|
|
C2B
|
B:HEM501
|
4.3
|
14.4
|
1.0
|
|
C3B
|
B:HEM501
|
4.3
|
18.8
|
1.0
|
|
C2D
|
B:HEM501
|
4.3
|
14.6
|
1.0
|
|
C2A
|
B:HEM501
|
4.3
|
18.6
|
1.0
|
|
C
|
B:GLY250
|
4.7
|
24.8
|
1.0
|
|
CD
|
B:PRO360
|
4.9
|
21.2
|
1.0
|
|
N
|
B:GLY361
|
5.0
|
14.6
|
1.0
|
|
Iron binding site 3 out
of 6 in 5kyo
Go back to
Iron Binding Sites List in 5kyo
Iron binding site 3 out
of 6 in the Crystal Structure of CYP101J2
 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 CYP101J2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:17.0
occ:1.00
|
FE
|
C:HEM501
|
0.0
|
17.0
|
1.0
|
|
NC
|
C:HEM501
|
2.0
|
17.2
|
1.0
|
|
NA
|
C:HEM501
|
2.1
|
14.6
|
1.0
|
|
NB
|
C:HEM501
|
2.1
|
14.5
|
1.0
|
|
ND
|
C:HEM501
|
2.1
|
14.6
|
1.0
|
|
SG
|
C:CYS359
|
2.4
|
14.9
|
1.0
|
|
O
|
C:HOH734
|
2.8
|
27.4
|
1.0
|
|
C1C
|
C:HEM501
|
3.0
|
16.4
|
1.0
|
|
C4D
|
C:HEM501
|
3.1
|
22.1
|
1.0
|
|
C1D
|
C:HEM501
|
3.1
|
22.1
|
1.0
|
|
C4C
|
C:HEM501
|
3.1
|
17.0
|
1.0
|
|
C1A
|
C:HEM501
|
3.1
|
14.6
|
1.0
|
|
C4B
|
C:HEM501
|
3.1
|
14.4
|
1.0
|
|
C1B
|
C:HEM501
|
3.1
|
14.5
|
1.0
|
|
C4A
|
C:HEM501
|
3.1
|
18.4
|
1.0
|
|
CB
|
C:CYS359
|
3.4
|
17.1
|
1.0
|
|
CHC
|
C:HEM501
|
3.4
|
16.8
|
1.0
|
|
CHA
|
C:HEM501
|
3.4
|
21.7
|
1.0
|
|
CHD
|
C:HEM501
|
3.5
|
14.5
|
1.0
|
|
CHB
|
C:HEM501
|
3.5
|
17.8
|
1.0
|
|
O
|
C:GLY250
|
3.9
|
16.3
|
1.0
|
|
CA
|
C:CYS359
|
4.2
|
18.2
|
1.0
|
|
C2C
|
C:HEM501
|
4.2
|
14.4
|
1.0
|
|
C3C
|
C:HEM501
|
4.3
|
19.1
|
1.0
|
|
C3D
|
C:HEM501
|
4.3
|
17.7
|
1.0
|
|
C2B
|
C:HEM501
|
4.3
|
14.4
|
1.0
|
|
C2A
|
C:HEM501
|
4.3
|
17.5
|
1.0
|
|
C2D
|
C:HEM501
|
4.3
|
16.2
|
1.0
|
|
C3B
|
C:HEM501
|
4.3
|
14.7
|
1.0
|
|
C3A
|
C:HEM501
|
4.3
|
19.8
|
1.0
|
|
C
|
C:GLY250
|
4.7
|
23.4
|
1.0
|
|
N
|
C:GLY361
|
4.8
|
14.6
|
1.0
|
|
CD
|
C:PRO360
|
4.9
|
14.7
|
1.0
|
|
C
|
C:CYS359
|
5.0
|
20.4
|
1.0
|
|
Iron binding site 4 out
of 6 in 5kyo
Go back to
Iron Binding Sites List in 5kyo
Iron binding site 4 out
of 6 in the Crystal Structure of CYP101J2
 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 CYP101J2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:19.4
occ:1.00
|
FE
|
D:HEM501
|
0.0
|
19.4
|
1.0
|
|
NC
|
D:HEM501
|
2.1
|
17.0
|
1.0
|
|
NB
|
D:HEM501
|
2.1
|
17.8
|
1.0
|
|
NA
|
D:HEM501
|
2.1
|
18.8
|
1.0
|
|
ND
|
D:HEM501
|
2.1
|
19.4
|
1.0
|
|
SG
|
D:CYS359
|
2.5
|
22.0
|
1.0
|
|
O
|
D:HOH659
|
2.7
|
35.0
|
1.0
|
|
C4B
|
D:HEM501
|
3.1
|
18.7
|
1.0
|
|
C1C
|
D:HEM501
|
3.1
|
16.3
|
1.0
|
|
C4C
|
D:HEM501
|
3.1
|
23.5
|
1.0
|
|
C1B
|
D:HEM501
|
3.1
|
22.6
|
1.0
|
|
C4A
|
D:HEM501
|
3.1
|
20.2
|
1.0
|
|
C1A
|
D:HEM501
|
3.1
|
17.6
|
1.0
|
|
C4D
|
D:HEM501
|
3.1
|
17.6
|
1.0
|
|
C1D
|
D:HEM501
|
3.1
|
19.4
|
1.0
|
|
CHC
|
D:HEM501
|
3.4
|
16.3
|
1.0
|
|
CHB
|
D:HEM501
|
3.5
|
22.5
|
1.0
|
|
CHD
|
D:HEM501
|
3.5
|
17.7
|
1.0
|
|
CHA
|
D:HEM501
|
3.5
|
16.1
|
1.0
|
|
CB
|
D:CYS359
|
3.5
|
23.1
|
1.0
|
|
O
|
D:GLY250
|
4.0
|
19.4
|
1.0
|
|
C3B
|
D:HEM501
|
4.3
|
16.2
|
1.0
|
|
C2C
|
D:HEM501
|
4.3
|
16.4
|
1.0
|
|
C3C
|
D:HEM501
|
4.3
|
16.4
|
1.0
|
|
C2B
|
D:HEM501
|
4.3
|
22.4
|
1.0
|
|
CA
|
D:CYS359
|
4.3
|
22.0
|
1.0
|
|
C3A
|
D:HEM501
|
4.3
|
17.6
|
1.0
|
|
C2A
|
D:HEM501
|
4.3
|
16.0
|
1.0
|
|
C3D
|
D:HEM501
|
4.3
|
24.2
|
1.0
|
|
C2D
|
D:HEM501
|
4.4
|
19.3
|
1.0
|
|
O
|
D:HOH799
|
4.4
|
36.4
|
1.0
|
|
O
|
D:HOH821
|
4.6
|
52.1
|
1.0
|
|
C
|
D:GLY250
|
4.8
|
23.5
|
1.0
|
|
N
|
D:GLY361
|
4.9
|
18.3
|
1.0
|
|
CG2
|
D:THR254
|
5.0
|
16.3
|
1.0
|
|
CD
|
D:PRO360
|
5.0
|
17.6
|
1.0
|
|
Iron binding site 5 out
of 6 in 5kyo
Go back to
Iron Binding Sites List in 5kyo
Iron binding site 5 out
of 6 in the Crystal Structure of CYP101J2
 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 CYP101J2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe501
b:17.5
occ:1.00
|
FE
|
E:HEM501
|
0.0
|
17.5
|
1.0
|
|
NB
|
E:HEM501
|
2.0
|
19.4
|
1.0
|
|
NA
|
E:HEM501
|
2.1
|
16.1
|
1.0
|
|
NC
|
E:HEM501
|
2.1
|
16.3
|
1.0
|
|
ND
|
E:HEM501
|
2.1
|
16.2
|
1.0
|
|
SG
|
E:CYS359
|
2.5
|
20.0
|
1.0
|
|
O
|
E:HOH629
|
2.7
|
22.4
|
1.0
|
|
C4B
|
E:HEM501
|
3.0
|
21.9
|
1.0
|
|
C1C
|
E:HEM501
|
3.1
|
16.3
|
1.0
|
|
C4A
|
E:HEM501
|
3.1
|
17.8
|
1.0
|
|
C1A
|
E:HEM501
|
3.1
|
18.4
|
1.0
|
|
C4D
|
E:HEM501
|
3.1
|
19.2
|
1.0
|
|
C1D
|
E:HEM501
|
3.1
|
16.2
|
1.0
|
|
C1B
|
E:HEM501
|
3.1
|
16.1
|
1.0
|
|
C4C
|
E:HEM501
|
3.1
|
18.8
|
1.0
|
|
CHC
|
E:HEM501
|
3.4
|
16.3
|
1.0
|
|
CHA
|
E:HEM501
|
3.4
|
16.0
|
1.0
|
|
CB
|
E:CYS359
|
3.4
|
21.2
|
1.0
|
|
CHB
|
E:HEM501
|
3.4
|
21.4
|
1.0
|
|
CHD
|
E:HEM501
|
3.4
|
16.3
|
1.0
|
|
O
|
E:GLY250
|
4.0
|
20.8
|
1.0
|
|
O
|
E:HOH782
|
4.2
|
38.5
|
1.0
|
|
CA
|
E:CYS359
|
4.2
|
19.4
|
1.0
|
|
C3B
|
E:HEM501
|
4.3
|
16.2
|
1.0
|
|
C3A
|
E:HEM501
|
4.3
|
15.9
|
1.0
|
|
C2C
|
E:HEM501
|
4.3
|
16.4
|
1.0
|
|
C2A
|
E:HEM501
|
4.3
|
18.5
|
1.0
|
|
C2B
|
E:HEM501
|
4.3
|
16.1
|
1.0
|
|
C3D
|
E:HEM501
|
4.3
|
20.5
|
1.0
|
|
C3C
|
E:HEM501
|
4.3
|
20.4
|
1.0
|
|
C2D
|
E:HEM501
|
4.3
|
16.2
|
1.0
|
|
C
|
E:GLY250
|
4.7
|
22.8
|
1.0
|
|
N
|
E:GLY361
|
4.9
|
17.1
|
1.0
|
|
CD
|
E:PRO360
|
4.9
|
16.0
|
1.0
|
|
CG2
|
E:THR254
|
4.9
|
16.3
|
1.0
|
|
Iron binding site 6 out
of 6 in 5kyo
Go back to
Iron Binding Sites List in 5kyo
Iron binding site 6 out
of 6 in the Crystal Structure of CYP101J2
 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 CYP101J2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe501
b:19.2
occ:1.00
|
FE
|
F:HEM501
|
0.0
|
19.2
|
1.0
|
|
NB
|
F:HEM501
|
2.1
|
18.0
|
1.0
|
|
NA
|
F:HEM501
|
2.1
|
16.4
|
1.0
|
|
NC
|
F:HEM501
|
2.1
|
26.9
|
1.0
|
|
ND
|
F:HEM501
|
2.1
|
18.6
|
1.0
|
|
SG
|
F:CYS359
|
2.4
|
22.2
|
1.0
|
|
O
|
F:HOH615
|
2.6
|
30.0
|
1.0
|
|
C1C
|
F:HEM501
|
3.1
|
16.6
|
1.0
|
|
C1D
|
F:HEM501
|
3.1
|
16.6
|
1.0
|
|
C4A
|
F:HEM501
|
3.1
|
16.3
|
1.0
|
|
C4B
|
F:HEM501
|
3.1
|
20.3
|
1.0
|
|
C1B
|
F:HEM501
|
3.1
|
19.0
|
1.0
|
|
C4C
|
F:HEM501
|
3.1
|
16.7
|
1.0
|
|
C1A
|
F:HEM501
|
3.1
|
16.3
|
1.0
|
|
C4D
|
F:HEM501
|
3.1
|
23.5
|
1.0
|
|
CB
|
F:CYS359
|
3.3
|
24.1
|
1.0
|
|
CHC
|
F:HEM501
|
3.4
|
20.3
|
1.0
|
|
CHD
|
F:HEM501
|
3.4
|
16.6
|
1.0
|
|
CHB
|
F:HEM501
|
3.5
|
20.1
|
1.0
|
|
CHA
|
F:HEM501
|
3.5
|
16.3
|
1.0
|
|
O
|
F:GLY250
|
4.1
|
19.4
|
1.0
|
|
CA
|
F:CYS359
|
4.1
|
18.0
|
1.0
|
|
C2C
|
F:HEM501
|
4.3
|
16.7
|
1.0
|
|
C3C
|
F:HEM501
|
4.3
|
16.7
|
1.0
|
|
C2B
|
F:HEM501
|
4.3
|
19.2
|
1.0
|
|
C3A
|
F:HEM501
|
4.3
|
16.2
|
1.0
|
|
C3B
|
F:HEM501
|
4.3
|
16.5
|
1.0
|
|
C2A
|
F:HEM501
|
4.3
|
16.2
|
1.0
|
|
C2D
|
F:HEM501
|
4.3
|
16.6
|
1.0
|
|
C3D
|
F:HEM501
|
4.3
|
22.4
|
1.0
|
|
O
|
F:HOH777
|
4.7
|
31.7
|
1.0
|
|
N
|
F:GLY361
|
4.8
|
22.2
|
1.0
|
|
C
|
F:GLY250
|
4.8
|
20.1
|
1.0
|
|
O
|
F:HOH785
|
4.8
|
40.2
|
1.0
|
|
C
|
F:CYS359
|
4.9
|
20.1
|
1.0
|
|
Reference:
B.Unterweger,
N.Drinkwater,
P.Johanesen,
D.Lyras,
G.J.Dumsday,
S.Mcgowan.
X-Ray Crystal Structure of Cytochrome P450 Monooxygenase CYP101J2 From Sphingobium Yanoikuyae Strain B2. Proteins V. 85 945 2017.
ISSN: ESSN 1097-0134
PubMed: 27936485
DOI: 10.1002/PROT.25227
Page generated: Tue Aug 6 04:01:16 2024
|
