Iron in PDB 6jlv: Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan
Enzymatic activity of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan
All present enzymatic activity of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan:
1.14.14.1;
1.6.2.4;
Protein crystallography data
The structure of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan, PDB code: 6jlv
was solved by
J.K.Stanfield,
C.Kasai,
H.Sugimoto,
Y.Shiro,
Y.Watanabe,
O.Shoji,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.22 /
1.22
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.964,
148.732,
63.910,
90.00,
98.38,
90.00
|
R / Rfree (%)
|
13.4 /
15.6
|
Other elements in 6jlv:
The structure of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan
(pdb code 6jlv). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan, PDB code: 6jlv:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6jlv
Go back to
Iron Binding Sites List in 6jlv
Iron binding site 1 out
of 4 in the Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:11.3
occ:0.47
|
FE
|
A:HEM501
|
0.0
|
11.3
|
0.5
|
FE
|
A:HEM501
|
0.0
|
12.1
|
0.5
|
ND
|
A:HEM501
|
1.9
|
11.1
|
0.5
|
ND
|
A:HEM501
|
2.0
|
11.1
|
0.5
|
NA
|
A:HEM501
|
2.0
|
11.4
|
0.5
|
NA
|
A:HEM501
|
2.1
|
10.3
|
0.5
|
NB
|
A:HEM501
|
2.1
|
11.8
|
0.5
|
NC
|
A:HEM501
|
2.1
|
11.3
|
0.5
|
NC
|
A:HEM501
|
2.1
|
11.1
|
0.5
|
NB
|
A:HEM501
|
2.1
|
11.0
|
0.5
|
O
|
A:HOH684
|
2.2
|
18.8
|
1.0
|
SG
|
A:CYS400
|
2.3
|
12.4
|
1.0
|
C1D
|
A:HEM501
|
2.9
|
11.7
|
0.5
|
C4D
|
A:HEM501
|
3.0
|
10.9
|
0.5
|
C1D
|
A:HEM501
|
3.0
|
11.2
|
0.5
|
C4B
|
A:HEM501
|
3.0
|
12.3
|
0.5
|
C4D
|
A:HEM501
|
3.0
|
11.1
|
0.5
|
C4C
|
A:HEM501
|
3.0
|
11.3
|
0.5
|
C1B
|
A:HEM501
|
3.0
|
11.8
|
0.5
|
C4B
|
A:HEM501
|
3.0
|
10.9
|
0.5
|
C4C
|
A:HEM501
|
3.0
|
12.0
|
0.5
|
C1A
|
A:HEM501
|
3.1
|
10.9
|
0.5
|
C1B
|
A:HEM501
|
3.1
|
11.1
|
0.5
|
C4A
|
A:HEM501
|
3.1
|
11.7
|
0.5
|
C1A
|
A:HEM501
|
3.1
|
10.4
|
0.5
|
C1C
|
A:HEM501
|
3.1
|
11.4
|
0.5
|
C1C
|
A:HEM501
|
3.1
|
11.5
|
0.5
|
C4A
|
A:HEM501
|
3.1
|
10.2
|
0.5
|
CB
|
A:CYS400
|
3.3
|
11.4
|
1.0
|
CHD
|
A:HEM501
|
3.4
|
11.4
|
0.5
|
CHD
|
A:HEM501
|
3.4
|
11.4
|
0.5
|
CHB
|
A:HEM501
|
3.4
|
11.8
|
0.5
|
CHA
|
A:HEM501
|
3.4
|
10.4
|
0.5
|
CHC
|
A:HEM501
|
3.4
|
11.8
|
0.5
|
CHA
|
A:HEM501
|
3.5
|
10.8
|
0.5
|
CHC
|
A:HEM501
|
3.5
|
11.1
|
0.5
|
CHB
|
A:HEM501
|
3.5
|
10.4
|
0.5
|
CA
|
A:CYS400
|
4.0
|
10.8
|
1.0
|
O
|
A:ALA264
|
4.2
|
17.5
|
1.0
|
C2D
|
A:HEM501
|
4.2
|
11.3
|
0.5
|
C3D
|
A:HEM501
|
4.2
|
11.4
|
0.5
|
C3C
|
A:HEM501
|
4.3
|
11.5
|
0.5
|
C2C
|
A:HEM501
|
4.3
|
11.2
|
0.5
|
C3C
|
A:HEM501
|
4.3
|
12.2
|
0.5
|
C2B
|
A:HEM501
|
4.3
|
12.1
|
0.5
|
C2C
|
A:HEM501
|
4.3
|
12.0
|
0.5
|
C2A
|
A:HEM501
|
4.3
|
10.7
|
0.5
|
C3A
|
A:HEM501
|
4.3
|
11.5
|
0.5
|
C2D
|
A:HEM501
|
4.3
|
11.4
|
0.5
|
C3B
|
A:HEM501
|
4.3
|
12.5
|
0.5
|
C3A
|
A:HEM501
|
4.3
|
10.5
|
0.5
|
C2B
|
A:HEM501
|
4.3
|
10.9
|
0.5
|
C2A
|
A:HEM501
|
4.3
|
10.3
|
0.5
|
C3D
|
A:HEM501
|
4.3
|
11.0
|
0.5
|
C3B
|
A:HEM501
|
4.3
|
11.0
|
0.5
|
CB
|
A:ALA264
|
4.5
|
18.8
|
1.0
|
N
|
A:GLY402
|
4.7
|
11.3
|
1.0
|
C
|
A:CYS400
|
4.8
|
10.7
|
1.0
|
C
|
A:ALA264
|
4.8
|
17.2
|
1.0
|
N
|
A:ILE401
|
4.9
|
10.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 6jlv
Go back to
Iron Binding Sites List in 6jlv
Iron binding site 2 out
of 4 in the Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:12.1
occ:0.53
|
FE
|
A:HEM501
|
0.0
|
12.1
|
0.5
|
FE
|
A:HEM501
|
0.0
|
11.3
|
0.5
|
ND
|
A:HEM501
|
1.9
|
11.1
|
0.5
|
ND
|
A:HEM501
|
2.0
|
11.1
|
0.5
|
NA
|
A:HEM501
|
2.0
|
10.3
|
0.5
|
NA
|
A:HEM501
|
2.0
|
11.4
|
0.5
|
NC
|
A:HEM501
|
2.0
|
11.3
|
0.5
|
NB
|
A:HEM501
|
2.1
|
11.0
|
0.5
|
NB
|
A:HEM501
|
2.1
|
11.8
|
0.5
|
NC
|
A:HEM501
|
2.1
|
11.1
|
0.5
|
O
|
A:HOH684
|
2.2
|
18.8
|
1.0
|
SG
|
A:CYS400
|
2.3
|
12.4
|
1.0
|
C1D
|
A:HEM501
|
3.0
|
11.2
|
0.5
|
C1D
|
A:HEM501
|
3.0
|
11.7
|
0.5
|
C4D
|
A:HEM501
|
3.0
|
10.9
|
0.5
|
C4D
|
A:HEM501
|
3.0
|
11.1
|
0.5
|
C4C
|
A:HEM501
|
3.0
|
12.0
|
0.5
|
C4B
|
A:HEM501
|
3.0
|
10.9
|
0.5
|
C4B
|
A:HEM501
|
3.0
|
12.3
|
0.5
|
C1B
|
A:HEM501
|
3.1
|
11.1
|
0.5
|
C1A
|
A:HEM501
|
3.1
|
10.4
|
0.5
|
C4C
|
A:HEM501
|
3.1
|
11.3
|
0.5
|
C4A
|
A:HEM501
|
3.1
|
10.2
|
0.5
|
C1A
|
A:HEM501
|
3.1
|
10.9
|
0.5
|
C1B
|
A:HEM501
|
3.1
|
11.8
|
0.5
|
C1C
|
A:HEM501
|
3.1
|
11.5
|
0.5
|
C4A
|
A:HEM501
|
3.1
|
11.7
|
0.5
|
C1C
|
A:HEM501
|
3.1
|
11.4
|
0.5
|
CB
|
A:CYS400
|
3.3
|
11.4
|
1.0
|
CHD
|
A:HEM501
|
3.4
|
11.4
|
0.5
|
CHD
|
A:HEM501
|
3.4
|
11.4
|
0.5
|
CHA
|
A:HEM501
|
3.4
|
10.4
|
0.5
|
CHA
|
A:HEM501
|
3.4
|
10.8
|
0.5
|
CHB
|
A:HEM501
|
3.4
|
10.4
|
0.5
|
CHC
|
A:HEM501
|
3.5
|
11.8
|
0.5
|
CHB
|
A:HEM501
|
3.5
|
11.8
|
0.5
|
CHC
|
A:HEM501
|
3.5
|
11.1
|
0.5
|
CA
|
A:CYS400
|
4.0
|
10.8
|
1.0
|
O
|
A:ALA264
|
4.2
|
17.5
|
1.0
|
C3C
|
A:HEM501
|
4.2
|
12.2
|
0.5
|
C2D
|
A:HEM501
|
4.2
|
11.3
|
0.5
|
C3D
|
A:HEM501
|
4.3
|
11.4
|
0.5
|
C2D
|
A:HEM501
|
4.3
|
11.4
|
0.5
|
C3A
|
A:HEM501
|
4.3
|
10.5
|
0.5
|
C2C
|
A:HEM501
|
4.3
|
12.0
|
0.5
|
C2A
|
A:HEM501
|
4.3
|
10.3
|
0.5
|
C2B
|
A:HEM501
|
4.3
|
10.9
|
0.5
|
C3D
|
A:HEM501
|
4.3
|
11.0
|
0.5
|
C2C
|
A:HEM501
|
4.3
|
11.2
|
0.5
|
C3C
|
A:HEM501
|
4.3
|
11.5
|
0.5
|
C2A
|
A:HEM501
|
4.3
|
10.7
|
0.5
|
C3A
|
A:HEM501
|
4.3
|
11.5
|
0.5
|
C3B
|
A:HEM501
|
4.3
|
11.0
|
0.5
|
C2B
|
A:HEM501
|
4.3
|
12.1
|
0.5
|
C3B
|
A:HEM501
|
4.3
|
12.5
|
0.5
|
CB
|
A:ALA264
|
4.5
|
18.8
|
1.0
|
N
|
A:GLY402
|
4.8
|
11.3
|
1.0
|
C
|
A:CYS400
|
4.8
|
10.7
|
1.0
|
C
|
A:ALA264
|
4.8
|
17.2
|
1.0
|
N
|
A:ILE401
|
4.9
|
10.8
|
1.0
|
|
Iron binding site 3 out
of 4 in 6jlv
Go back to
Iron Binding Sites List in 6jlv
Iron binding site 3 out
of 4 in the Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:11.4
occ:0.41
|
FE
|
B:HEM501
|
0.0
|
11.4
|
0.4
|
FE
|
B:HEM501
|
0.0
|
11.5
|
0.6
|
ND
|
B:HEM501
|
1.9
|
10.7
|
0.4
|
ND
|
B:HEM501
|
1.9
|
10.8
|
0.6
|
NA
|
B:HEM501
|
2.0
|
10.3
|
0.6
|
NA
|
B:HEM501
|
2.0
|
10.8
|
0.4
|
NC
|
B:HEM501
|
2.0
|
10.4
|
0.4
|
NB
|
B:HEM501
|
2.0
|
11.2
|
0.6
|
NB
|
B:HEM501
|
2.1
|
10.8
|
0.4
|
NC
|
B:HEM501
|
2.1
|
11.2
|
0.6
|
O
|
B:HOH624
|
2.2
|
19.2
|
1.0
|
SG
|
B:CYS400
|
2.3
|
12.2
|
1.0
|
C1D
|
B:HEM501
|
2.9
|
10.7
|
0.4
|
C4D
|
B:HEM501
|
3.0
|
10.5
|
0.4
|
C4D
|
B:HEM501
|
3.0
|
11.0
|
0.6
|
C1D
|
B:HEM501
|
3.0
|
10.8
|
0.6
|
C4C
|
B:HEM501
|
3.0
|
10.7
|
0.4
|
C4B
|
B:HEM501
|
3.0
|
11.5
|
0.6
|
C4B
|
B:HEM501
|
3.0
|
11.0
|
0.4
|
C1B
|
B:HEM501
|
3.0
|
11.0
|
0.6
|
C1A
|
B:HEM501
|
3.0
|
10.9
|
0.4
|
C4A
|
B:HEM501
|
3.1
|
10.4
|
0.6
|
C1A
|
B:HEM501
|
3.1
|
9.9
|
0.6
|
C1B
|
B:HEM501
|
3.1
|
11.1
|
0.4
|
C4C
|
B:HEM501
|
3.1
|
11.8
|
0.6
|
C4A
|
B:HEM501
|
3.1
|
11.1
|
0.4
|
C1C
|
B:HEM501
|
3.1
|
10.6
|
0.4
|
C1C
|
B:HEM501
|
3.1
|
11.8
|
0.6
|
CB
|
B:CYS400
|
3.3
|
10.8
|
1.0
|
CHD
|
B:HEM501
|
3.4
|
10.8
|
0.4
|
CHA
|
B:HEM501
|
3.4
|
10.7
|
0.4
|
CHB
|
B:HEM501
|
3.4
|
10.8
|
0.6
|
CHA
|
B:HEM501
|
3.4
|
10.6
|
0.6
|
CHD
|
B:HEM501
|
3.4
|
11.7
|
0.6
|
CHC
|
B:HEM501
|
3.4
|
11.8
|
0.6
|
CHC
|
B:HEM501
|
3.5
|
11.0
|
0.4
|
CHB
|
B:HEM501
|
3.5
|
11.2
|
0.4
|
CA
|
B:CYS400
|
4.0
|
10.8
|
1.0
|
O
|
B:ALA264
|
4.2
|
18.6
|
1.0
|
C2D
|
B:HEM501
|
4.2
|
10.8
|
0.4
|
C3D
|
B:HEM501
|
4.2
|
10.9
|
0.4
|
C3C
|
B:HEM501
|
4.2
|
11.2
|
0.4
|
C2C
|
B:HEM501
|
4.2
|
10.8
|
0.4
|
C2A
|
B:HEM501
|
4.3
|
10.9
|
0.4
|
C2A
|
B:HEM501
|
4.3
|
10.5
|
0.6
|
C3D
|
B:HEM501
|
4.3
|
11.0
|
0.6
|
C3A
|
B:HEM501
|
4.3
|
10.4
|
0.6
|
C3A
|
B:HEM501
|
4.3
|
11.5
|
0.4
|
C2B
|
B:HEM501
|
4.3
|
11.5
|
0.6
|
C2D
|
B:HEM501
|
4.3
|
10.5
|
0.6
|
C2C
|
B:HEM501
|
4.3
|
12.2
|
0.6
|
C3B
|
B:HEM501
|
4.3
|
11.9
|
0.6
|
C2B
|
B:HEM501
|
4.3
|
11.2
|
0.4
|
C3C
|
B:HEM501
|
4.3
|
12.3
|
0.6
|
C3B
|
B:HEM501
|
4.3
|
11.4
|
0.4
|
CB
|
B:ALA264
|
4.5
|
19.6
|
1.0
|
C
|
B:CYS400
|
4.8
|
11.3
|
1.0
|
C
|
B:ALA264
|
4.8
|
17.8
|
1.0
|
N
|
B:GLY402
|
4.8
|
11.5
|
1.0
|
N
|
B:ILE401
|
5.0
|
11.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 6jlv
Go back to
Iron Binding Sites List in 6jlv
Iron binding site 4 out
of 4 in the Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Near-Atomic Resolution Structure of the CYP102A1 Haem Domain with N- Abietoyl-L-Tryptophan within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:11.5
occ:0.59
|
FE
|
B:HEM501
|
0.0
|
11.5
|
0.6
|
FE
|
B:HEM501
|
0.0
|
11.4
|
0.4
|
ND
|
B:HEM501
|
1.9
|
10.8
|
0.6
|
ND
|
B:HEM501
|
2.0
|
10.7
|
0.4
|
NA
|
B:HEM501
|
2.0
|
10.8
|
0.4
|
NB
|
B:HEM501
|
2.0
|
10.8
|
0.4
|
NA
|
B:HEM501
|
2.1
|
10.3
|
0.6
|
NC
|
B:HEM501
|
2.1
|
10.4
|
0.4
|
NC
|
B:HEM501
|
2.1
|
11.2
|
0.6
|
NB
|
B:HEM501
|
2.1
|
11.2
|
0.6
|
O
|
B:HOH624
|
2.2
|
19.2
|
1.0
|
SG
|
B:CYS400
|
2.3
|
12.2
|
1.0
|
C1D
|
B:HEM501
|
3.0
|
10.8
|
0.6
|
C1D
|
B:HEM501
|
3.0
|
10.7
|
0.4
|
C4D
|
B:HEM501
|
3.0
|
11.0
|
0.6
|
C4B
|
B:HEM501
|
3.0
|
11.0
|
0.4
|
C4D
|
B:HEM501
|
3.0
|
10.5
|
0.4
|
C1B
|
B:HEM501
|
3.0
|
11.1
|
0.4
|
C4B
|
B:HEM501
|
3.0
|
11.5
|
0.6
|
C4C
|
B:HEM501
|
3.0
|
11.8
|
0.6
|
C4C
|
B:HEM501
|
3.0
|
10.7
|
0.4
|
C1A
|
B:HEM501
|
3.0
|
10.9
|
0.4
|
C4A
|
B:HEM501
|
3.1
|
11.1
|
0.4
|
C1C
|
B:HEM501
|
3.1
|
11.8
|
0.6
|
C1B
|
B:HEM501
|
3.1
|
11.0
|
0.6
|
C1C
|
B:HEM501
|
3.1
|
10.6
|
0.4
|
C1A
|
B:HEM501
|
3.1
|
9.9
|
0.6
|
C4A
|
B:HEM501
|
3.1
|
10.4
|
0.6
|
CB
|
B:CYS400
|
3.3
|
10.8
|
1.0
|
CHD
|
B:HEM501
|
3.4
|
11.7
|
0.6
|
CHD
|
B:HEM501
|
3.4
|
10.8
|
0.4
|
CHC
|
B:HEM501
|
3.4
|
11.8
|
0.6
|
CHA
|
B:HEM501
|
3.4
|
10.7
|
0.4
|
CHC
|
B:HEM501
|
3.4
|
11.0
|
0.4
|
CHB
|
B:HEM501
|
3.5
|
11.2
|
0.4
|
CHA
|
B:HEM501
|
3.5
|
10.6
|
0.6
|
CHB
|
B:HEM501
|
3.5
|
10.8
|
0.6
|
CA
|
B:CYS400
|
4.0
|
10.8
|
1.0
|
O
|
B:ALA264
|
4.1
|
18.6
|
1.0
|
C2A
|
B:HEM501
|
4.2
|
10.9
|
0.4
|
C2B
|
B:HEM501
|
4.2
|
11.2
|
0.4
|
C2C
|
B:HEM501
|
4.2
|
12.2
|
0.6
|
C3A
|
B:HEM501
|
4.2
|
11.5
|
0.4
|
C3C
|
B:HEM501
|
4.2
|
12.3
|
0.6
|
C3C
|
B:HEM501
|
4.3
|
11.2
|
0.4
|
C3D
|
B:HEM501
|
4.3
|
11.0
|
0.6
|
C2C
|
B:HEM501
|
4.3
|
10.8
|
0.4
|
C2D
|
B:HEM501
|
4.3
|
10.8
|
0.4
|
C2D
|
B:HEM501
|
4.3
|
10.5
|
0.6
|
C3B
|
B:HEM501
|
4.3
|
11.4
|
0.4
|
C3D
|
B:HEM501
|
4.3
|
10.9
|
0.4
|
C2B
|
B:HEM501
|
4.3
|
11.5
|
0.6
|
C3B
|
B:HEM501
|
4.3
|
11.9
|
0.6
|
C2A
|
B:HEM501
|
4.3
|
10.5
|
0.6
|
C3A
|
B:HEM501
|
4.3
|
10.4
|
0.6
|
CB
|
B:ALA264
|
4.5
|
19.6
|
1.0
|
C
|
B:ALA264
|
4.8
|
17.8
|
1.0
|
N
|
B:GLY402
|
4.8
|
11.5
|
1.0
|
C
|
B:CYS400
|
4.8
|
11.3
|
1.0
|
N
|
B:ILE401
|
5.0
|
11.4
|
1.0
|
|
Reference:
O.Shoji,
J.K.Stanfield.
Structure of CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan at 1.22 Angstrom Resolution To Be Published.
Page generated: Tue Aug 6 23:23:52 2024
|