Iron in PDB 3me6: Crystal Structure of Cytochrome 2B4 in Complex with the Anti-Platelet Drug Clopidogrel
Enzymatic activity of Crystal Structure of Cytochrome 2B4 in Complex with the Anti-Platelet Drug Clopidogrel
All present enzymatic activity of Crystal Structure of Cytochrome 2B4 in Complex with the Anti-Platelet Drug Clopidogrel:
1.14.14.1;
Protein crystallography data
The structure of Crystal Structure of Cytochrome 2B4 in Complex with the Anti-Platelet Drug Clopidogrel, PDB code: 3me6
was solved by
S.C.Gay,
A.G.Roberts,
K.Maekawa,
J.C.Talakad,
W.X.Hong,
Q.Zhang,
C.D.Stout,
J.R.Halpert,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
76.75 /
3.10
|
Space group
|
P 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
234.490,
234.490,
57.320,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.8 /
23.4
|
Other elements in 3me6:
The structure of Crystal Structure of Cytochrome 2B4 in Complex with the Anti-Platelet Drug Clopidogrel also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Cytochrome 2B4 in Complex with the Anti-Platelet Drug Clopidogrel
(pdb code 3me6). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of Cytochrome 2B4 in Complex with the Anti-Platelet Drug Clopidogrel, PDB code: 3me6:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3me6
Go back to
Iron Binding Sites List in 3me6
Iron binding site 1 out
of 4 in the Crystal Structure of Cytochrome 2B4 in Complex with the Anti-Platelet Drug Clopidogrel
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 Cytochrome 2B4 in Complex with the Anti-Platelet Drug Clopidogrel within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:29.2
occ:1.00
|
FE
|
A:HEM500
|
0.0
|
29.2
|
1.0
|
NA
|
A:HEM500
|
2.0
|
30.5
|
1.0
|
NB
|
A:HEM500
|
2.0
|
31.9
|
1.0
|
NC
|
A:HEM500
|
2.1
|
31.2
|
1.0
|
ND
|
A:HEM500
|
2.1
|
31.5
|
1.0
|
SG
|
A:CYS436
|
2.3
|
26.1
|
1.0
|
C4A
|
A:HEM500
|
3.0
|
31.5
|
1.0
|
C1B
|
A:HEM500
|
3.0
|
32.9
|
1.0
|
C1A
|
A:HEM500
|
3.0
|
30.2
|
1.0
|
C4B
|
A:HEM500
|
3.1
|
31.8
|
1.0
|
C4D
|
A:HEM500
|
3.1
|
30.9
|
1.0
|
C1D
|
A:HEM500
|
3.1
|
31.4
|
1.0
|
C1C
|
A:HEM500
|
3.1
|
30.8
|
1.0
|
C4C
|
A:HEM500
|
3.1
|
31.7
|
1.0
|
CB
|
A:CYS436
|
3.2
|
27.2
|
1.0
|
CAD
|
A:CGE501
|
3.3
|
98.9
|
1.0
|
CHB
|
A:HEM500
|
3.3
|
33.5
|
1.0
|
CHA
|
A:HEM500
|
3.4
|
30.0
|
1.0
|
CHC
|
A:HEM500
|
3.5
|
32.3
|
1.0
|
CHD
|
A:HEM500
|
3.5
|
32.3
|
1.0
|
CAE
|
A:CGE501
|
3.6
|
98.5
|
1.0
|
CA
|
A:CYS436
|
4.1
|
27.6
|
1.0
|
C3A
|
A:HEM500
|
4.2
|
31.1
|
1.0
|
C2A
|
A:HEM500
|
4.2
|
31.1
|
1.0
|
C2B
|
A:HEM500
|
4.3
|
32.3
|
1.0
|
C3B
|
A:HEM500
|
4.3
|
32.8
|
1.0
|
C3D
|
A:HEM500
|
4.3
|
28.4
|
1.0
|
C2D
|
A:HEM500
|
4.3
|
28.4
|
1.0
|
C2C
|
A:HEM500
|
4.3
|
28.9
|
1.0
|
C3C
|
A:HEM500
|
4.3
|
30.1
|
1.0
|
CAG
|
A:CGE501
|
4.5
|
98.1
|
1.0
|
N
|
A:GLY438
|
4.7
|
30.2
|
1.0
|
C
|
A:CYS436
|
4.8
|
27.2
|
1.0
|
CB
|
A:ALA298
|
4.8
|
48.8
|
1.0
|
N
|
A:LEU437
|
4.8
|
27.8
|
1.0
|
CAH
|
A:CGE501
|
4.9
|
98.3
|
1.0
|
CA
|
A:GLY438
|
5.0
|
30.4
|
1.0
|
|
Iron binding site 2 out
of 4 in 3me6
Go back to
Iron Binding Sites List in 3me6
Iron binding site 2 out
of 4 in the Crystal Structure of Cytochrome 2B4 in Complex with the Anti-Platelet Drug Clopidogrel
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 Cytochrome 2B4 in Complex with the Anti-Platelet Drug Clopidogrel within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe500
b:25.8
occ:1.00
|
FE
|
B:HEM500
|
0.0
|
25.8
|
1.0
|
NA
|
B:HEM500
|
1.9
|
26.4
|
1.0
|
NC
|
B:HEM500
|
2.0
|
27.8
|
1.0
|
NB
|
B:HEM500
|
2.1
|
28.5
|
1.0
|
ND
|
B:HEM500
|
2.1
|
29.2
|
1.0
|
SG
|
B:CYS436
|
2.4
|
23.2
|
1.0
|
C4A
|
B:HEM500
|
2.9
|
27.2
|
1.0
|
C1B
|
B:HEM500
|
3.0
|
28.7
|
1.0
|
C1A
|
B:HEM500
|
3.0
|
27.5
|
1.0
|
C4C
|
B:HEM500
|
3.0
|
28.5
|
1.0
|
C1D
|
B:HEM500
|
3.1
|
28.6
|
1.0
|
C1C
|
B:HEM500
|
3.1
|
28.7
|
1.0
|
C4D
|
B:HEM500
|
3.1
|
28.6
|
1.0
|
C4B
|
B:HEM500
|
3.2
|
28.6
|
1.0
|
CHB
|
B:HEM500
|
3.3
|
28.5
|
1.0
|
CB
|
B:CYS436
|
3.3
|
25.8
|
1.0
|
CAE
|
B:CGE501
|
3.4
|
0.2
|
1.0
|
CHD
|
B:HEM500
|
3.4
|
29.0
|
1.0
|
CHA
|
B:HEM500
|
3.5
|
28.2
|
1.0
|
CAD
|
B:CGE501
|
3.5
|
0.3
|
1.0
|
CHC
|
B:HEM500
|
3.6
|
29.3
|
1.0
|
C3A
|
B:HEM500
|
4.1
|
29.0
|
1.0
|
CA
|
B:CYS436
|
4.2
|
26.1
|
1.0
|
C2A
|
B:HEM500
|
4.2
|
29.3
|
1.0
|
C3C
|
B:HEM500
|
4.3
|
27.4
|
1.0
|
C2B
|
B:HEM500
|
4.3
|
28.0
|
1.0
|
C2C
|
B:HEM500
|
4.3
|
27.7
|
1.0
|
C2D
|
B:HEM500
|
4.3
|
25.9
|
1.0
|
C3D
|
B:HEM500
|
4.3
|
25.9
|
1.0
|
C3B
|
B:HEM500
|
4.4
|
28.1
|
1.0
|
CAH
|
B:CGE501
|
4.7
|
0.1
|
1.0
|
N
|
B:GLY438
|
4.8
|
28.8
|
1.0
|
CAG
|
B:CGE501
|
4.8
|
0.1
|
1.0
|
CB
|
B:ALA298
|
4.8
|
47.8
|
1.0
|
N
|
B:LEU437
|
5.0
|
26.7
|
1.0
|
C
|
B:CYS436
|
5.0
|
26.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 3me6
Go back to
Iron Binding Sites List in 3me6
Iron binding site 3 out
of 4 in the Crystal Structure of Cytochrome 2B4 in Complex with the Anti-Platelet Drug Clopidogrel
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 Cytochrome 2B4 in Complex with the Anti-Platelet Drug Clopidogrel within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe500
b:23.7
occ:1.00
|
FE
|
C:HEM500
|
0.0
|
23.7
|
1.0
|
NA
|
C:HEM500
|
1.9
|
25.4
|
1.0
|
ND
|
C:HEM500
|
2.1
|
27.4
|
1.0
|
NB
|
C:HEM500
|
2.1
|
27.2
|
1.0
|
NC
|
C:HEM500
|
2.1
|
26.3
|
1.0
|
SG
|
C:CYS436
|
2.5
|
23.1
|
1.0
|
C4A
|
C:HEM500
|
2.9
|
26.7
|
1.0
|
C1A
|
C:HEM500
|
3.0
|
28.0
|
1.0
|
C1B
|
C:HEM500
|
3.0
|
28.7
|
1.0
|
C1D
|
C:HEM500
|
3.1
|
27.8
|
1.0
|
C4D
|
C:HEM500
|
3.1
|
27.6
|
1.0
|
C4C
|
C:HEM500
|
3.1
|
26.8
|
1.0
|
C4B
|
C:HEM500
|
3.1
|
26.8
|
1.0
|
C1C
|
C:HEM500
|
3.2
|
26.9
|
1.0
|
CB
|
C:CYS436
|
3.2
|
25.2
|
1.0
|
CHB
|
C:HEM500
|
3.3
|
29.9
|
1.0
|
CAD
|
C:CGE501
|
3.4
|
0.1
|
1.0
|
CHA
|
C:HEM500
|
3.4
|
27.0
|
1.0
|
CHD
|
C:HEM500
|
3.4
|
28.1
|
1.0
|
CAE
|
C:CGE501
|
3.5
|
0.7
|
1.0
|
CHC
|
C:HEM500
|
3.6
|
27.8
|
1.0
|
CA
|
C:CYS436
|
4.1
|
25.5
|
1.0
|
C3A
|
C:HEM500
|
4.2
|
28.4
|
1.0
|
C2A
|
C:HEM500
|
4.2
|
30.3
|
1.0
|
C2B
|
C:HEM500
|
4.3
|
26.9
|
1.0
|
C2D
|
C:HEM500
|
4.3
|
25.9
|
1.0
|
C3D
|
C:HEM500
|
4.3
|
26.7
|
1.0
|
C3B
|
C:HEM500
|
4.3
|
27.6
|
1.0
|
C3C
|
C:HEM500
|
4.4
|
23.9
|
1.0
|
C2C
|
C:HEM500
|
4.4
|
24.1
|
1.0
|
CAG
|
C:CGE501
|
4.7
|
0.5
|
1.0
|
C
|
C:CYS436
|
4.9
|
25.8
|
1.0
|
CAH
|
C:CGE501
|
4.9
|
0.3
|
1.0
|
N
|
C:LEU437
|
4.9
|
26.8
|
1.0
|
N
|
C:GLY438
|
4.9
|
29.6
|
1.0
|
CB
|
C:ALA298
|
4.9
|
46.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 3me6
Go back to
Iron Binding Sites List in 3me6
Iron binding site 4 out
of 4 in the Crystal Structure of Cytochrome 2B4 in Complex with the Anti-Platelet Drug Clopidogrel
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 Cytochrome 2B4 in Complex with the Anti-Platelet Drug Clopidogrel within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe500
b:24.4
occ:1.00
|
FE
|
D:HEM500
|
0.0
|
24.4
|
1.0
|
NA
|
D:HEM500
|
2.0
|
25.9
|
1.0
|
ND
|
D:HEM500
|
2.0
|
27.4
|
1.0
|
NB
|
D:HEM500
|
2.1
|
27.4
|
1.0
|
NC
|
D:HEM500
|
2.1
|
24.0
|
1.0
|
SG
|
D:CYS436
|
2.3
|
22.6
|
1.0
|
C4A
|
D:HEM500
|
3.0
|
26.4
|
1.0
|
C1A
|
D:HEM500
|
3.0
|
27.3
|
1.0
|
C1B
|
D:HEM500
|
3.1
|
28.1
|
1.0
|
C4D
|
D:HEM500
|
3.1
|
27.4
|
1.0
|
C1D
|
D:HEM500
|
3.1
|
26.9
|
1.0
|
C1C
|
D:HEM500
|
3.1
|
23.3
|
1.0
|
C4B
|
D:HEM500
|
3.1
|
27.6
|
1.0
|
C4C
|
D:HEM500
|
3.1
|
22.2
|
1.0
|
CAD
|
D:CGE501
|
3.2
|
0.8
|
1.0
|
CB
|
D:CYS436
|
3.2
|
25.9
|
1.0
|
CHB
|
D:HEM500
|
3.4
|
27.2
|
1.0
|
CHA
|
D:HEM500
|
3.4
|
27.1
|
1.0
|
CHD
|
D:HEM500
|
3.5
|
23.8
|
1.0
|
CHC
|
D:HEM500
|
3.5
|
26.1
|
1.0
|
CAE
|
D:CGE501
|
3.6
|
0.5
|
1.0
|
CA
|
D:CYS436
|
4.0
|
26.7
|
1.0
|
C3A
|
D:HEM500
|
4.2
|
27.5
|
1.0
|
C2A
|
D:HEM500
|
4.3
|
28.4
|
1.0
|
C2D
|
D:HEM500
|
4.3
|
26.1
|
1.0
|
C3D
|
D:HEM500
|
4.3
|
26.2
|
1.0
|
C2B
|
D:HEM500
|
4.3
|
29.4
|
1.0
|
C3B
|
D:HEM500
|
4.3
|
29.3
|
1.0
|
C2C
|
D:HEM500
|
4.3
|
19.4
|
1.0
|
C3C
|
D:HEM500
|
4.3
|
18.9
|
1.0
|
CAG
|
D:CGE501
|
4.4
|
0.4
|
1.0
|
N
|
D:GLY438
|
4.8
|
32.3
|
1.0
|
N
|
D:LEU437
|
4.8
|
28.3
|
1.0
|
C
|
D:CYS436
|
4.8
|
27.4
|
1.0
|
CAH
|
D:CGE501
|
4.9
|
0.3
|
1.0
|
CB
|
D:ALA298
|
4.9
|
48.8
|
1.0
|
|
Reference:
S.C.Gay,
A.G.Roberts,
K.Maekawa,
J.C.Talakad,
W.X.Hong,
Q.Zhang,
C.D.Stout,
J.R.Halpert.
Structures of Cytochrome P450 2B4 Complexed with the Antiplatelet Drugs Ticlopidine and Clopidogrel. Biochemistry V. 49 8709 2010.
ISSN: ISSN 0006-2960
PubMed: 20815363
DOI: 10.1021/BI100914Z
Page generated: Sun Aug 4 14:46:52 2024
|