Iron in PDB 6udl: Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2700
Enzymatic activity of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2700
All present enzymatic activity of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2700:
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-2700, PDB code: 6udl
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)
|
48.80 /
2.85
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.371,
196.147,
237.222,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
23.8 /
28.7
|
Other elements in 6udl:
The structure of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2700 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-2700
(pdb code 6udl). 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-2700, PDB code: 6udl:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6udl
Go back to
Iron Binding Sites List in 6udl
Iron binding site 1 out
of 4 in the Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2700
 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-2700 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:49.7
occ:1.00
|
FE
|
A:HEM601
|
0.0
|
49.7
|
1.0
|
|
NB
|
A:HEM601
|
2.0
|
48.3
|
1.0
|
|
NA
|
A:HEM601
|
2.0
|
49.2
|
1.0
|
|
NC
|
A:HEM601
|
2.1
|
52.9
|
1.0
|
|
ND
|
A:HEM601
|
2.1
|
49.1
|
1.0
|
|
SG
|
A:CYS457
|
2.7
|
51.7
|
1.0
|
|
C1B
|
A:HEM601
|
3.0
|
48.2
|
1.0
|
|
C4B
|
A:HEM601
|
3.0
|
48.7
|
1.0
|
|
C4A
|
A:HEM601
|
3.1
|
47.4
|
1.0
|
|
C1C
|
A:HEM601
|
3.1
|
52.0
|
1.0
|
|
HB2
|
A:CYS457
|
3.1
|
59.0
|
1.0
|
|
C1A
|
A:HEM601
|
3.1
|
47.4
|
1.0
|
|
C4C
|
A:HEM601
|
3.1
|
54.0
|
1.0
|
|
C1D
|
A:HEM601
|
3.1
|
50.4
|
1.0
|
|
C4D
|
A:HEM601
|
3.1
|
46.9
|
1.0
|
|
CHB
|
A:HEM601
|
3.4
|
48.0
|
1.0
|
|
CB
|
A:CYS457
|
3.4
|
49.0
|
1.0
|
|
CHC
|
A:HEM601
|
3.4
|
51.1
|
1.0
|
|
CHA
|
A:HEM601
|
3.4
|
47.2
|
1.0
|
|
CHD
|
A:HEM601
|
3.4
|
51.9
|
1.0
|
|
HA
|
A:CYS457
|
3.8
|
57.4
|
1.0
|
|
HB1
|
A:ALA317
|
3.8
|
67.8
|
1.0
|
|
H121
|
A:Q4M602
|
4.0
|
52.0
|
1.0
|
|
H
|
A:GLY459
|
4.1
|
59.6
|
1.0
|
|
CA
|
A:CYS457
|
4.2
|
47.6
|
1.0
|
|
C12
|
A:Q4M602
|
4.2
|
52.0
|
1.0
|
|
HB3
|
A:CYS457
|
4.2
|
59.0
|
1.0
|
|
C2B
|
A:HEM601
|
4.3
|
48.5
|
1.0
|
|
C3B
|
A:HEM601
|
4.3
|
47.7
|
1.0
|
|
C2C
|
A:HEM601
|
4.3
|
52.4
|
1.0
|
|
C3A
|
A:HEM601
|
4.3
|
44.7
|
1.0
|
|
C3C
|
A:HEM601
|
4.3
|
53.4
|
1.0
|
|
C2A
|
A:HEM601
|
4.3
|
46.0
|
1.0
|
|
C2D
|
A:HEM601
|
4.3
|
50.2
|
1.0
|
|
C3D
|
A:HEM601
|
4.3
|
47.4
|
1.0
|
|
HG22
|
A:THR321
|
4.4
|
64.1
|
1.0
|
|
HHA
|
A:HEM601
|
4.4
|
47.2
|
1.0
|
|
HHB
|
A:HEM601
|
4.4
|
48.0
|
1.0
|
|
HHC
|
A:HEM601
|
4.4
|
51.1
|
1.0
|
|
HHD
|
A:HEM601
|
4.4
|
51.9
|
1.0
|
|
HD1
|
A:PHE450
|
4.4
|
60.5
|
1.0
|
|
H
|
A:ILE458
|
4.5
|
62.1
|
1.0
|
|
C13
|
A:Q4M602
|
4.6
|
55.3
|
1.0
|
|
C11
|
A:Q4M602
|
4.6
|
55.7
|
1.0
|
|
H111
|
A:Q4M602
|
4.7
|
55.7
|
1.0
|
|
CB
|
A:ALA317
|
4.7
|
56.2
|
1.0
|
|
O14
|
A:Q4M602
|
4.8
|
59.2
|
1.0
|
|
N
|
A:GLY459
|
4.9
|
49.4
|
1.0
|
|
HB3
|
A:ALA317
|
4.9
|
67.8
|
1.0
|
|
HA3
|
A:GLY459
|
4.9
|
62.8
|
1.0
|
|
N
|
A:ILE458
|
4.9
|
51.6
|
1.0
|
|
HB2
|
A:ALA317
|
4.9
|
67.8
|
1.0
|
|
C
|
A:CYS457
|
4.9
|
51.3
|
1.0
|
|
Iron binding site 2 out
of 4 in 6udl
Go back to
Iron Binding Sites List in 6udl
Iron binding site 2 out
of 4 in the Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2700
 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-2700 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe601
b:44.4
occ:1.00
|
FE
|
B:HEM601
|
0.0
|
44.4
|
1.0
|
|
NB
|
B:HEM601
|
2.0
|
44.2
|
1.0
|
|
NC
|
B:HEM601
|
2.0
|
47.2
|
1.0
|
|
NA
|
B:HEM601
|
2.0
|
45.6
|
1.0
|
|
ND
|
B:HEM601
|
2.1
|
47.4
|
1.0
|
|
SG
|
B:CYS457
|
2.7
|
37.4
|
1.0
|
|
C1B
|
B:HEM601
|
3.0
|
45.1
|
1.0
|
|
C4B
|
B:HEM601
|
3.0
|
44.4
|
1.0
|
|
C1C
|
B:HEM601
|
3.1
|
46.1
|
1.0
|
|
C4A
|
B:HEM601
|
3.1
|
44.1
|
1.0
|
|
C4C
|
B:HEM601
|
3.1
|
46.8
|
1.0
|
|
C1A
|
B:HEM601
|
3.1
|
44.1
|
1.0
|
|
C4D
|
B:HEM601
|
3.1
|
47.6
|
1.0
|
|
HB2
|
B:CYS457
|
3.1
|
53.5
|
1.0
|
|
C1D
|
B:HEM601
|
3.1
|
47.6
|
1.0
|
|
CB
|
B:CYS457
|
3.4
|
44.4
|
1.0
|
|
CHC
|
B:HEM601
|
3.4
|
44.4
|
1.0
|
|
CHB
|
B:HEM601
|
3.4
|
43.7
|
1.0
|
|
H121
|
B:Q4M602
|
3.4
|
50.2
|
1.0
|
|
CHA
|
B:HEM601
|
3.4
|
47.2
|
1.0
|
|
CHD
|
B:HEM601
|
3.4
|
46.5
|
1.0
|
|
HA
|
B:CYS457
|
3.7
|
51.0
|
1.0
|
|
HB1
|
B:ALA317
|
4.0
|
57.1
|
1.0
|
|
C12
|
B:Q4M602
|
4.0
|
50.2
|
1.0
|
|
CA
|
B:CYS457
|
4.1
|
42.2
|
1.0
|
|
H
|
B:GLY459
|
4.1
|
54.2
|
1.0
|
|
HB3
|
B:CYS457
|
4.2
|
53.5
|
1.0
|
|
C2B
|
B:HEM601
|
4.3
|
42.2
|
1.0
|
|
C3B
|
B:HEM601
|
4.3
|
41.2
|
1.0
|
|
C2C
|
B:HEM601
|
4.3
|
45.8
|
1.0
|
|
C3C
|
B:HEM601
|
4.3
|
47.4
|
1.0
|
|
C3A
|
B:HEM601
|
4.3
|
42.8
|
1.0
|
|
C2A
|
B:HEM601
|
4.3
|
44.1
|
1.0
|
|
C3D
|
B:HEM601
|
4.3
|
46.0
|
1.0
|
|
C2D
|
B:HEM601
|
4.3
|
47.6
|
1.0
|
|
H111
|
B:Q4M602
|
4.4
|
49.2
|
1.0
|
|
H152
|
B:Q4M602
|
4.4
|
50.3
|
1.0
|
|
HHB
|
B:HEM601
|
4.4
|
43.7
|
1.0
|
|
HHC
|
B:HEM601
|
4.4
|
44.4
|
1.0
|
|
HHA
|
B:HEM601
|
4.4
|
47.2
|
1.0
|
|
HD1
|
B:PHE450
|
4.4
|
52.5
|
1.0
|
|
HHD
|
B:HEM601
|
4.4
|
46.5
|
1.0
|
|
H
|
B:ILE458
|
4.5
|
52.5
|
1.0
|
|
C11
|
B:Q4M602
|
4.5
|
49.2
|
1.0
|
|
HG21
|
B:THR321
|
4.7
|
54.1
|
1.0
|
|
C13
|
B:Q4M602
|
4.8
|
48.4
|
1.0
|
|
O14
|
B:Q4M602
|
4.8
|
51.0
|
1.0
|
|
CB
|
B:ALA317
|
4.9
|
47.3
|
1.0
|
|
C
|
B:CYS457
|
4.9
|
43.3
|
1.0
|
|
N
|
B:ILE458
|
4.9
|
43.6
|
1.0
|
|
N
|
B:GLY459
|
4.9
|
44.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 6udl
Go back to
Iron Binding Sites List in 6udl
Iron binding site 3 out
of 4 in the Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2700
 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-2700 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe601
b:58.6
occ:1.00
|
FE
|
C:HEM601
|
0.0
|
58.6
|
1.0
|
|
ND
|
C:HEM601
|
2.0
|
59.8
|
1.0
|
|
NA
|
C:HEM601
|
2.0
|
53.9
|
1.0
|
|
NC
|
C:HEM601
|
2.0
|
58.3
|
1.0
|
|
NB
|
C:HEM601
|
2.0
|
57.2
|
1.0
|
|
SG
|
C:CYS457
|
2.8
|
65.4
|
1.0
|
|
HG
|
C:CYS457
|
3.0
|
65.4
|
1.0
|
|
C4D
|
C:HEM601
|
3.0
|
59.9
|
1.0
|
|
C1A
|
C:HEM601
|
3.0
|
57.4
|
1.0
|
|
C1D
|
C:HEM601
|
3.0
|
61.0
|
1.0
|
|
C1C
|
C:HEM601
|
3.1
|
59.0
|
1.0
|
|
C4B
|
C:HEM601
|
3.1
|
56.7
|
1.0
|
|
C4C
|
C:HEM601
|
3.1
|
58.7
|
1.0
|
|
C4A
|
C:HEM601
|
3.1
|
54.8
|
1.0
|
|
C1B
|
C:HEM601
|
3.1
|
55.3
|
1.0
|
|
HB2
|
C:CYS457
|
3.3
|
74.0
|
1.0
|
|
CHA
|
C:HEM601
|
3.4
|
59.9
|
1.0
|
|
CHC
|
C:HEM601
|
3.4
|
57.2
|
1.0
|
|
CHD
|
C:HEM601
|
3.4
|
60.8
|
1.0
|
|
CHB
|
C:HEM601
|
3.4
|
55.0
|
1.0
|
|
HB1
|
C:ALA317
|
3.6
|
76.1
|
1.0
|
|
CB
|
C:CYS457
|
3.6
|
61.5
|
1.0
|
|
HA
|
C:CYS457
|
3.8
|
75.1
|
1.0
|
|
H
|
C:GLY459
|
4.1
|
70.4
|
1.0
|
|
C3D
|
C:HEM601
|
4.3
|
63.2
|
1.0
|
|
C2D
|
C:HEM601
|
4.3
|
62.3
|
1.0
|
|
C2A
|
C:HEM601
|
4.3
|
58.5
|
1.0
|
|
C2C
|
C:HEM601
|
4.3
|
58.3
|
1.0
|
|
C3C
|
C:HEM601
|
4.3
|
59.4
|
1.0
|
|
C3A
|
C:HEM601
|
4.3
|
54.5
|
1.0
|
|
C3B
|
C:HEM601
|
4.3
|
52.5
|
1.0
|
|
C2B
|
C:HEM601
|
4.3
|
53.0
|
1.0
|
|
CA
|
C:CYS457
|
4.3
|
62.4
|
1.0
|
|
HHA
|
C:HEM601
|
4.4
|
59.9
|
1.0
|
|
HHC
|
C:HEM601
|
4.4
|
57.2
|
1.0
|
|
HHD
|
C:HEM601
|
4.4
|
60.8
|
1.0
|
|
HHB
|
C:HEM601
|
4.4
|
55.0
|
1.0
|
|
CB
|
C:ALA317
|
4.4
|
63.2
|
1.0
|
|
HB3
|
C:CYS457
|
4.4
|
74.0
|
1.0
|
|
HG21
|
C:THR321
|
4.6
|
72.0
|
1.0
|
|
HB2
|
C:ALA317
|
4.6
|
76.1
|
1.0
|
|
HD1
|
C:PHE450
|
4.6
|
68.7
|
1.0
|
|
HB3
|
C:ALA317
|
4.6
|
76.1
|
1.0
|
|
H
|
C:ILE458
|
4.7
|
74.3
|
1.0
|
|
HA3
|
C:GLY459
|
4.8
|
71.3
|
1.0
|
|
N
|
C:GLY459
|
4.9
|
58.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 6udl
Go back to
Iron Binding Sites List in 6udl
Iron binding site 4 out
of 4 in the Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2700
 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-2700 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe601
b:72.6
occ:1.00
|
FE
|
D:HEM601
|
0.0
|
72.6
|
1.0
|
|
NA
|
D:HEM601
|
2.0
|
68.3
|
1.0
|
|
ND
|
D:HEM601
|
2.0
|
71.7
|
1.0
|
|
NB
|
D:HEM601
|
2.0
|
70.2
|
1.0
|
|
NC
|
D:HEM601
|
2.1
|
71.4
|
1.0
|
|
SG
|
D:CYS457
|
2.9
|
76.3
|
1.0
|
|
C4D
|
D:HEM601
|
3.0
|
72.4
|
1.0
|
|
C1A
|
D:HEM601
|
3.0
|
69.4
|
1.0
|
|
HG
|
D:CYS457
|
3.1
|
91.8
|
1.0
|
|
C4B
|
D:HEM601
|
3.1
|
70.7
|
1.0
|
|
C1B
|
D:HEM601
|
3.1
|
69.9
|
1.0
|
|
C4A
|
D:HEM601
|
3.1
|
68.3
|
1.0
|
|
C1D
|
D:HEM601
|
3.1
|
71.9
|
1.0
|
|
C1C
|
D:HEM601
|
3.1
|
70.0
|
1.0
|
|
C4C
|
D:HEM601
|
3.1
|
72.5
|
1.0
|
|
HB2
|
D:CYS457
|
3.2
|
90.5
|
1.0
|
|
CHA
|
D:HEM601
|
3.4
|
72.0
|
1.0
|
|
CHB
|
D:HEM601
|
3.4
|
69.0
|
1.0
|
|
CHC
|
D:HEM601
|
3.4
|
70.9
|
1.0
|
|
CHD
|
D:HEM601
|
3.4
|
73.0
|
1.0
|
|
CB
|
D:CYS457
|
3.6
|
75.2
|
1.0
|
|
HB1
|
D:ALA317
|
3.9
|
86.6
|
1.0
|
|
HA
|
D:CYS457
|
3.9
|
90.8
|
1.0
|
|
C2A
|
D:HEM601
|
4.3
|
71.9
|
1.0
|
|
C3D
|
D:HEM601
|
4.3
|
73.4
|
1.0
|
|
C2B
|
D:HEM601
|
4.3
|
68.5
|
1.0
|
|
C3B
|
D:HEM601
|
4.3
|
69.9
|
1.0
|
|
C3A
|
D:HEM601
|
4.3
|
70.5
|
1.0
|
|
C2D
|
D:HEM601
|
4.3
|
72.9
|
1.0
|
|
C2C
|
D:HEM601
|
4.3
|
71.3
|
1.0
|
|
C3C
|
D:HEM601
|
4.3
|
72.0
|
1.0
|
|
H
|
D:GLY459
|
4.3
|
91.0
|
1.0
|
|
CA
|
D:CYS457
|
4.3
|
75.5
|
1.0
|
|
HG21
|
D:THR321
|
4.4
|
81.2
|
1.0
|
|
HHA
|
D:HEM601
|
4.4
|
72.0
|
1.0
|
|
HHB
|
D:HEM601
|
4.4
|
69.0
|
1.0
|
|
HB3
|
D:CYS457
|
4.4
|
90.5
|
1.0
|
|
HHC
|
D:HEM601
|
4.4
|
70.9
|
1.0
|
|
HHD
|
D:HEM601
|
4.4
|
73.0
|
1.0
|
|
HD1
|
D:PHE450
|
4.5
|
85.7
|
1.0
|
|
H
|
D:ILE458
|
4.6
|
88.7
|
1.0
|
|
CB
|
D:ALA317
|
4.7
|
72.0
|
1.0
|
|
HB2
|
D:ALA317
|
4.9
|
86.6
|
1.0
|
|
HB3
|
D:ALA317
|
5.0
|
86.6
|
1.0
|
|
Reference:
A.G.Bart,
E.E.Scott.
Designed Duocarmycin Prodrugs For Human Cytochrome P450 1A1 and 2W1 To Be Published.
Page generated: Sun Dec 13 17:15:16 2020
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