Iron in PDB 6udm: Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726
Enzymatic activity of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726
All present enzymatic activity of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726:
1.14.14.1;
4.2.1.152;
Protein crystallography data
The structure of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726, PDB code: 6udm
was solved by
A.G.Bart,
E.E.Scott,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
39.64 /
3.08
|
|
Space group
|
P 31 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
241.281,
241.281,
125.298,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
20.9 /
22.1
|
Other elements in 6udm:
The structure of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726 also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726
(pdb code 6udm). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726, PDB code: 6udm:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6udm
Go back to
Iron Binding Sites List in 6udm
Iron binding site 1 out
of 4 in the Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:65.8
occ:1.00
|
FE
|
A:HEM601
|
0.0
|
65.8
|
1.0
|
|
ND
|
A:HEM601
|
2.0
|
66.4
|
1.0
|
|
NB
|
A:HEM601
|
2.0
|
64.2
|
1.0
|
|
NC
|
A:HEM601
|
2.0
|
67.8
|
1.0
|
|
NA
|
A:HEM601
|
2.1
|
65.3
|
1.0
|
|
SG
|
A:CYS457
|
2.7
|
64.2
|
1.0
|
|
C4D
|
A:HEM601
|
3.0
|
67.6
|
1.0
|
|
C1C
|
A:HEM601
|
3.1
|
67.7
|
1.0
|
|
C4B
|
A:HEM601
|
3.1
|
64.6
|
1.0
|
|
C1D
|
A:HEM601
|
3.1
|
68.8
|
1.0
|
|
C4C
|
A:HEM601
|
3.1
|
69.4
|
1.0
|
|
C1A
|
A:HEM601
|
3.1
|
66.0
|
1.0
|
|
C1B
|
A:HEM601
|
3.1
|
64.3
|
1.0
|
|
C4A
|
A:HEM601
|
3.1
|
64.3
|
1.0
|
|
HB2
|
A:CYS457
|
3.2
|
79.3
|
1.0
|
|
CHC
|
A:HEM601
|
3.4
|
66.4
|
1.0
|
|
CHA
|
A:HEM601
|
3.4
|
67.6
|
1.0
|
|
CHD
|
A:HEM601
|
3.4
|
70.2
|
1.0
|
|
CHB
|
A:HEM601
|
3.5
|
64.0
|
1.0
|
|
CB
|
A:CYS457
|
3.5
|
66.1
|
1.0
|
|
HB1
|
A:ALA317
|
3.7
|
86.5
|
1.0
|
|
HA
|
A:CYS457
|
3.8
|
81.8
|
1.0
|
|
H
|
A:GLY459
|
4.1
|
83.6
|
1.0
|
|
H121
|
A:Q4P602
|
4.1
|
68.3
|
1.0
|
|
H111
|
A:Q4P602
|
4.1
|
69.3
|
1.0
|
|
CA
|
A:CYS457
|
4.2
|
68.2
|
1.0
|
|
HG23
|
A:THR321
|
4.2
|
82.0
|
1.0
|
|
C2C
|
A:HEM601
|
4.3
|
68.5
|
1.0
|
|
C3C
|
A:HEM601
|
4.3
|
69.2
|
1.0
|
|
C3D
|
A:HEM601
|
4.3
|
69.8
|
1.0
|
|
C2D
|
A:HEM601
|
4.3
|
69.8
|
1.0
|
|
HB3
|
A:CYS457
|
4.3
|
79.3
|
1.0
|
|
C3B
|
A:HEM601
|
4.3
|
63.3
|
1.0
|
|
C2A
|
A:HEM601
|
4.3
|
64.7
|
1.0
|
|
C2B
|
A:HEM601
|
4.3
|
63.4
|
1.0
|
|
C3A
|
A:HEM601
|
4.3
|
64.2
|
1.0
|
|
C12
|
A:Q4P602
|
4.3
|
68.3
|
1.0
|
|
C11
|
A:Q4P602
|
4.3
|
69.3
|
1.0
|
|
HHA
|
A:HEM601
|
4.4
|
67.6
|
1.0
|
|
HHC
|
A:HEM601
|
4.4
|
66.4
|
1.0
|
|
HHD
|
A:HEM601
|
4.4
|
70.2
|
1.0
|
|
HD1
|
A:PHE450
|
4.4
|
75.4
|
1.0
|
|
HHB
|
A:HEM601
|
4.4
|
64.0
|
1.0
|
|
H
|
A:ILE458
|
4.5
|
84.3
|
1.0
|
|
CB
|
A:ALA317
|
4.5
|
72.1
|
1.0
|
|
HB3
|
A:ALA317
|
4.7
|
86.5
|
1.0
|
|
HB2
|
A:ALA317
|
4.7
|
86.5
|
1.0
|
|
N
|
A:GLY459
|
4.9
|
69.7
|
1.0
|
|
N
|
A:ILE458
|
4.9
|
70.2
|
1.0
|
|
C
|
A:CYS457
|
5.0
|
69.0
|
1.0
|
|
HA3
|
A:GLY459
|
5.0
|
83.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 6udm
Go back to
Iron Binding Sites List in 6udm
Iron binding site 2 out
of 4 in the Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe601
b:0.4
occ:1.00
|
FE
|
B:HEM601
|
0.0
|
0.4
|
1.0
|
|
NB
|
B:HEM601
|
2.0
|
68.7
|
1.0
|
|
NA
|
B:HEM601
|
2.0
|
70.1
|
1.0
|
|
ND
|
B:HEM601
|
2.0
|
70.6
|
1.0
|
|
NC
|
B:HEM601
|
2.0
|
71.4
|
1.0
|
|
SG
|
B:CYS457
|
2.7
|
67.6
|
1.0
|
|
C1A
|
B:HEM601
|
3.0
|
69.0
|
1.0
|
|
C4B
|
B:HEM601
|
3.0
|
68.9
|
1.0
|
|
C4D
|
B:HEM601
|
3.0
|
69.8
|
1.0
|
|
C1C
|
B:HEM601
|
3.1
|
70.5
|
1.0
|
|
C1B
|
B:HEM601
|
3.1
|
68.0
|
1.0
|
|
C4A
|
B:HEM601
|
3.1
|
68.5
|
1.0
|
|
C4C
|
B:HEM601
|
3.1
|
71.8
|
1.0
|
|
C1D
|
B:HEM601
|
3.1
|
71.2
|
1.0
|
|
HB2
|
B:CYS457
|
3.1
|
81.7
|
1.0
|
|
CHA
|
B:HEM601
|
3.4
|
69.5
|
1.0
|
|
CHC
|
B:HEM601
|
3.4
|
70.0
|
1.0
|
|
CHB
|
B:HEM601
|
3.4
|
67.5
|
1.0
|
|
CHD
|
B:HEM601
|
3.4
|
71.8
|
1.0
|
|
CB
|
B:CYS457
|
3.5
|
68.1
|
1.0
|
|
HB1
|
B:ALA317
|
3.7
|
86.2
|
1.0
|
|
HA
|
B:CYS457
|
3.8
|
80.3
|
1.0
|
|
H121
|
B:Q4P602
|
4.0
|
71.0
|
1.0
|
|
H111
|
B:Q4P602
|
4.1
|
70.4
|
1.0
|
|
HG21
|
B:THR321
|
4.1
|
82.8
|
1.0
|
|
CA
|
B:CYS457
|
4.2
|
67.0
|
1.0
|
|
C12
|
B:Q4P602
|
4.2
|
71.0
|
1.0
|
|
H
|
B:GLY459
|
4.2
|
81.1
|
1.0
|
|
C11
|
B:Q4P602
|
4.3
|
70.4
|
1.0
|
|
C2A
|
B:HEM601
|
4.3
|
66.2
|
1.0
|
|
C3D
|
B:HEM601
|
4.3
|
69.2
|
1.0
|
|
C3B
|
B:HEM601
|
4.3
|
65.9
|
1.0
|
|
HB3
|
B:CYS457
|
4.3
|
81.7
|
1.0
|
|
C2C
|
B:HEM601
|
4.3
|
69.5
|
1.0
|
|
C2B
|
B:HEM601
|
4.3
|
65.9
|
1.0
|
|
C3A
|
B:HEM601
|
4.3
|
66.1
|
1.0
|
|
C2D
|
B:HEM601
|
4.3
|
70.1
|
1.0
|
|
C3C
|
B:HEM601
|
4.3
|
70.1
|
1.0
|
|
HHA
|
B:HEM601
|
4.4
|
69.5
|
1.0
|
|
HHC
|
B:HEM601
|
4.4
|
70.0
|
1.0
|
|
HHB
|
B:HEM601
|
4.4
|
67.5
|
1.0
|
|
HHD
|
B:HEM601
|
4.4
|
71.8
|
1.0
|
|
H
|
B:ILE458
|
4.5
|
80.6
|
1.0
|
|
CB
|
B:ALA317
|
4.5
|
71.8
|
1.0
|
|
HD1
|
B:PHE450
|
4.5
|
77.4
|
1.0
|
|
HB2
|
B:ALA317
|
4.7
|
86.2
|
1.0
|
|
HB3
|
B:ALA317
|
4.7
|
86.2
|
1.0
|
|
N
|
B:ILE458
|
5.0
|
67.2
|
1.0
|
|
C
|
B:CYS457
|
5.0
|
66.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 6udm
Go back to
Iron Binding Sites List in 6udm
Iron binding site 3 out
of 4 in the Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe601
b:58.1
occ:1.00
|
FE
|
C:HEM601
|
0.0
|
58.1
|
1.0
|
|
NC
|
C:HEM601
|
2.0
|
61.4
|
1.0
|
|
NB
|
C:HEM601
|
2.0
|
62.5
|
1.0
|
|
ND
|
C:HEM601
|
2.0
|
64.0
|
1.0
|
|
NA
|
C:HEM601
|
2.1
|
63.6
|
1.0
|
|
SG
|
C:CYS457
|
2.7
|
62.8
|
1.0
|
|
C1C
|
C:HEM601
|
3.0
|
62.1
|
1.0
|
|
C4C
|
C:HEM601
|
3.0
|
63.0
|
1.0
|
|
C4B
|
C:HEM601
|
3.0
|
62.2
|
1.0
|
|
C1D
|
C:HEM601
|
3.1
|
64.7
|
1.0
|
|
C1B
|
C:HEM601
|
3.1
|
63.0
|
1.0
|
|
C4D
|
C:HEM601
|
3.1
|
64.2
|
1.0
|
|
C1A
|
C:HEM601
|
3.1
|
64.0
|
1.0
|
|
C4A
|
C:HEM601
|
3.1
|
63.2
|
1.0
|
|
HB2
|
C:CYS457
|
3.2
|
77.8
|
1.0
|
|
CHC
|
C:HEM601
|
3.4
|
62.3
|
1.0
|
|
CHD
|
C:HEM601
|
3.4
|
64.7
|
1.0
|
|
CHB
|
C:HEM601
|
3.4
|
63.0
|
1.0
|
|
CHA
|
C:HEM601
|
3.4
|
64.3
|
1.0
|
|
CB
|
C:CYS457
|
3.5
|
64.8
|
1.0
|
|
HB1
|
C:ALA317
|
3.7
|
82.4
|
1.0
|
|
HA
|
C:CYS457
|
3.8
|
78.5
|
1.0
|
|
H121
|
C:Q4P602
|
3.9
|
68.4
|
1.0
|
|
H
|
C:GLY459
|
4.1
|
79.7
|
1.0
|
|
HG22
|
C:THR321
|
4.2
|
80.2
|
1.0
|
|
CA
|
C:CYS457
|
4.2
|
65.4
|
1.0
|
|
C2C
|
C:HEM601
|
4.3
|
62.6
|
1.0
|
|
C3C
|
C:HEM601
|
4.3
|
63.0
|
1.0
|
|
C3B
|
C:HEM601
|
4.3
|
61.8
|
1.0
|
|
C2B
|
C:HEM601
|
4.3
|
61.9
|
1.0
|
|
C12
|
C:Q4P602
|
4.3
|
68.4
|
1.0
|
|
C2D
|
C:HEM601
|
4.3
|
65.9
|
1.0
|
|
C3D
|
C:HEM601
|
4.3
|
66.4
|
1.0
|
|
C2A
|
C:HEM601
|
4.3
|
65.0
|
1.0
|
|
C3A
|
C:HEM601
|
4.3
|
64.2
|
1.0
|
|
HB3
|
C:CYS457
|
4.3
|
77.8
|
1.0
|
|
HHC
|
C:HEM601
|
4.4
|
62.3
|
1.0
|
|
HHD
|
C:HEM601
|
4.4
|
64.7
|
1.0
|
|
HHA
|
C:HEM601
|
4.4
|
64.3
|
1.0
|
|
H
|
C:ILE458
|
4.4
|
77.9
|
1.0
|
|
HHB
|
C:HEM601
|
4.4
|
63.0
|
1.0
|
|
H111
|
C:Q4P602
|
4.5
|
68.6
|
1.0
|
|
CB
|
C:ALA317
|
4.5
|
68.7
|
1.0
|
|
C11
|
C:Q4P602
|
4.6
|
68.6
|
1.0
|
|
HD1
|
C:PHE450
|
4.6
|
76.4
|
1.0
|
|
HB2
|
C:ALA317
|
4.7
|
82.4
|
1.0
|
|
HB3
|
C:ALA317
|
4.7
|
82.4
|
1.0
|
|
N
|
C:ILE458
|
4.9
|
64.9
|
1.0
|
|
N
|
C:GLY459
|
4.9
|
66.4
|
1.0
|
|
C13
|
C:Q4P602
|
5.0
|
71.3
|
1.0
|
|
C
|
C:CYS457
|
5.0
|
65.8
|
1.0
|
|
Iron binding site 4 out
of 4 in 6udm
Go back to
Iron Binding Sites List in 6udm
Iron binding site 4 out
of 4 in the Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe601
b:65.5
occ:1.00
|
FE
|
D:HEM601
|
0.0
|
65.5
|
1.0
|
|
NB
|
D:HEM601
|
2.0
|
68.5
|
1.0
|
|
NA
|
D:HEM601
|
2.0
|
69.4
|
1.0
|
|
ND
|
D:HEM601
|
2.1
|
71.4
|
1.0
|
|
NC
|
D:HEM601
|
2.1
|
71.8
|
1.0
|
|
SG
|
D:CYS457
|
2.8
|
72.3
|
1.0
|
|
HG
|
D:CYS457
|
2.9
|
72.3
|
1.0
|
|
C1B
|
D:HEM601
|
3.1
|
69.0
|
1.0
|
|
C4B
|
D:HEM601
|
3.1
|
68.9
|
1.0
|
|
C4A
|
D:HEM601
|
3.1
|
68.8
|
1.0
|
|
C1A
|
D:HEM601
|
3.1
|
71.3
|
1.0
|
|
C1C
|
D:HEM601
|
3.1
|
71.0
|
1.0
|
|
C4D
|
D:HEM601
|
3.1
|
72.4
|
1.0
|
|
C4C
|
D:HEM601
|
3.1
|
73.1
|
1.0
|
|
C1D
|
D:HEM601
|
3.1
|
72.1
|
1.0
|
|
HB2
|
D:CYS457
|
3.3
|
86.8
|
1.0
|
|
CHB
|
D:HEM601
|
3.4
|
68.8
|
1.0
|
|
CHC
|
D:HEM601
|
3.4
|
69.8
|
1.0
|
|
CHA
|
D:HEM601
|
3.4
|
72.9
|
1.0
|
|
CHD
|
D:HEM601
|
3.5
|
73.1
|
1.0
|
|
CB
|
D:CYS457
|
3.6
|
72.3
|
1.0
|
|
HB1
|
D:ALA317
|
3.7
|
94.7
|
1.0
|
|
HA
|
D:CYS457
|
3.9
|
87.9
|
1.0
|
|
H
|
D:GLY459
|
4.1
|
88.2
|
1.0
|
|
HG21
|
D:THR321
|
4.2
|
89.9
|
1.0
|
|
H121
|
D:Q4P602
|
4.2
|
76.7
|
1.0
|
|
H111
|
D:Q4P602
|
4.3
|
77.3
|
1.0
|
|
C2B
|
D:HEM601
|
4.3
|
67.8
|
1.0
|
|
C3A
|
D:HEM601
|
4.3
|
69.0
|
1.0
|
|
C3B
|
D:HEM601
|
4.3
|
68.3
|
1.0
|
|
C2A
|
D:HEM601
|
4.3
|
70.4
|
1.0
|
|
C2C
|
D:HEM601
|
4.3
|
72.1
|
1.0
|
|
C3C
|
D:HEM601
|
4.3
|
73.4
|
1.0
|
|
C3D
|
D:HEM601
|
4.3
|
73.9
|
1.0
|
|
C2D
|
D:HEM601
|
4.3
|
73.5
|
1.0
|
|
C12
|
D:Q4P602
|
4.3
|
76.7
|
1.0
|
|
CA
|
D:CYS457
|
4.3
|
73.2
|
1.0
|
|
C11
|
D:Q4P602
|
4.4
|
77.3
|
1.0
|
|
HB3
|
D:CYS457
|
4.4
|
86.8
|
1.0
|
|
HHB
|
D:HEM601
|
4.4
|
68.8
|
1.0
|
|
HHA
|
D:HEM601
|
4.4
|
72.9
|
1.0
|
|
HHC
|
D:HEM601
|
4.4
|
69.8
|
1.0
|
|
HHD
|
D:HEM601
|
4.4
|
73.1
|
1.0
|
|
HD1
|
D:PHE450
|
4.5
|
80.0
|
1.0
|
|
H
|
D:ILE458
|
4.5
|
88.7
|
1.0
|
|
CB
|
D:ALA317
|
4.6
|
78.9
|
1.0
|
|
HB3
|
D:ALA317
|
4.7
|
94.7
|
1.0
|
|
HB2
|
D:ALA317
|
4.8
|
94.7
|
1.0
|
|
N
|
D:GLY459
|
4.9
|
73.5
|
1.0
|
|
HA3
|
D:GLY459
|
5.0
|
88.4
|
1.0
|
|
N
|
D:ILE458
|
5.0
|
74.0
|
1.0
|
|
Reference:
A.G.Bart,
E.E.Scott.
Designed Duocarmycin Prodrugs For Human Cytochrome P450 1A1 and 2W1 To Be Published.
Page generated: Wed Aug 7 12:16:54 2024
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