Iron in PDB 2ij5: Crystal Structure of Cytochrome P450 CYP121, P212121 Space Group
Protein crystallography data
The structure of Crystal Structure of Cytochrome P450 CYP121, P212121 Space Group, PDB code: 2ij5
was solved by
A.Roujeinikova,
D.Leys,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.60
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.627,
129.758,
323.757,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.5 /
21
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Cytochrome P450 CYP121, P212121 Space Group
(pdb code 2ij5). 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 Cytochrome P450 CYP121, P212121 Space Group, PDB code: 2ij5:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 2ij5
Go back to
Iron Binding Sites List in 2ij5
Iron binding site 1 out
of 6 in the Crystal Structure of Cytochrome P450 CYP121, P212121 Space Group
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 P450 CYP121, P212121 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe462
b:17.7
occ:1.00
|
FE
|
A:HEM462
|
0.0
|
17.7
|
1.0
|
NC
|
A:HEM462
|
2.0
|
16.9
|
1.0
|
NA
|
A:HEM462
|
2.0
|
17.9
|
1.0
|
ND
|
A:HEM462
|
2.0
|
17.9
|
1.0
|
NB
|
A:HEM462
|
2.0
|
16.7
|
1.0
|
SG
|
A:CYS345
|
2.3
|
18.5
|
1.0
|
O
|
A:HOH2888
|
2.5
|
29.7
|
1.0
|
C4D
|
A:HEM462
|
3.0
|
18.9
|
1.0
|
C4B
|
A:HEM462
|
3.0
|
17.3
|
1.0
|
C1A
|
A:HEM462
|
3.0
|
17.9
|
1.0
|
C1C
|
A:HEM462
|
3.0
|
16.6
|
1.0
|
C4C
|
A:HEM462
|
3.0
|
17.5
|
1.0
|
C4A
|
A:HEM462
|
3.1
|
17.2
|
1.0
|
C1D
|
A:HEM462
|
3.1
|
17.8
|
1.0
|
C1B
|
A:HEM462
|
3.1
|
16.6
|
1.0
|
CHA
|
A:HEM462
|
3.4
|
19.9
|
1.0
|
CHC
|
A:HEM462
|
3.4
|
17.7
|
1.0
|
CB
|
A:CYS345
|
3.4
|
17.9
|
1.0
|
CHD
|
A:HEM462
|
3.4
|
18.3
|
1.0
|
CHB
|
A:HEM462
|
3.5
|
17.7
|
1.0
|
CA
|
A:CYS345
|
4.2
|
17.8
|
1.0
|
C3C
|
A:HEM462
|
4.2
|
17.9
|
1.0
|
C2A
|
A:HEM462
|
4.3
|
16.9
|
1.0
|
C3A
|
A:HEM462
|
4.3
|
16.8
|
1.0
|
C2C
|
A:HEM462
|
4.3
|
17.4
|
1.0
|
C3D
|
A:HEM462
|
4.3
|
20.2
|
1.0
|
C3B
|
A:HEM462
|
4.3
|
15.3
|
1.0
|
C2B
|
A:HEM462
|
4.3
|
15.1
|
1.0
|
C2D
|
A:HEM462
|
4.3
|
18.7
|
1.0
|
O
|
A:HOH3104
|
4.4
|
50.8
|
1.0
|
OG
|
A:SER237
|
4.5
|
16.2
|
1.0
|
CD
|
A:PRO346
|
4.7
|
19.7
|
1.0
|
CB
|
A:SER237
|
4.8
|
16.5
|
1.0
|
C
|
A:CYS345
|
4.8
|
18.2
|
1.0
|
N
|
A:GLY347
|
4.9
|
18.6
|
1.0
|
|
Iron binding site 2 out
of 6 in 2ij5
Go back to
Iron Binding Sites List in 2ij5
Iron binding site 2 out
of 6 in the Crystal Structure of Cytochrome P450 CYP121, P212121 Space Group
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 P450 CYP121, P212121 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe462
b:23.9
occ:1.00
|
FE
|
B:HEM462
|
0.0
|
23.9
|
1.0
|
NA
|
B:HEM462
|
2.0
|
19.9
|
1.0
|
NC
|
B:HEM462
|
2.0
|
23.6
|
1.0
|
NB
|
B:HEM462
|
2.1
|
22.9
|
1.0
|
ND
|
B:HEM462
|
2.1
|
21.7
|
1.0
|
SG
|
B:CYS345
|
2.3
|
26.6
|
1.0
|
O
|
B:HOH3010
|
2.4
|
41.0
|
1.0
|
C1C
|
B:HEM462
|
3.0
|
22.9
|
1.0
|
C4A
|
B:HEM462
|
3.0
|
19.6
|
1.0
|
C4D
|
B:HEM462
|
3.0
|
22.2
|
1.0
|
C1A
|
B:HEM462
|
3.0
|
20.6
|
1.0
|
C4C
|
B:HEM462
|
3.1
|
25.3
|
1.0
|
C4B
|
B:HEM462
|
3.1
|
22.0
|
1.0
|
C1B
|
B:HEM462
|
3.1
|
20.5
|
1.0
|
C1D
|
B:HEM462
|
3.1
|
22.1
|
1.0
|
CB
|
B:CYS345
|
3.4
|
28.5
|
1.0
|
CHC
|
B:HEM462
|
3.4
|
23.4
|
1.0
|
CHA
|
B:HEM462
|
3.4
|
23.0
|
1.0
|
CHB
|
B:HEM462
|
3.4
|
20.8
|
1.0
|
CHD
|
B:HEM462
|
3.5
|
24.1
|
1.0
|
CA
|
B:CYS345
|
4.2
|
28.0
|
1.0
|
C3A
|
B:HEM462
|
4.2
|
19.3
|
1.0
|
C3C
|
B:HEM462
|
4.3
|
26.7
|
1.0
|
C2A
|
B:HEM462
|
4.3
|
19.7
|
1.0
|
C2C
|
B:HEM462
|
4.3
|
24.9
|
1.0
|
C3D
|
B:HEM462
|
4.3
|
23.8
|
1.0
|
C2D
|
B:HEM462
|
4.3
|
21.6
|
1.0
|
C2B
|
B:HEM462
|
4.3
|
21.5
|
1.0
|
C3B
|
B:HEM462
|
4.3
|
22.0
|
1.0
|
OG
|
B:SER237
|
4.5
|
21.8
|
1.0
|
CB
|
B:SER237
|
4.7
|
22.0
|
1.0
|
O
|
B:HOH3009
|
4.8
|
49.2
|
1.0
|
CD
|
B:PRO346
|
4.8
|
29.9
|
1.0
|
C
|
B:CYS345
|
4.9
|
29.0
|
1.0
|
N
|
B:GLY347
|
4.9
|
31.4
|
1.0
|
|
Iron binding site 3 out
of 6 in 2ij5
Go back to
Iron Binding Sites List in 2ij5
Iron binding site 3 out
of 6 in the Crystal Structure of Cytochrome P450 CYP121, P212121 Space Group
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 P450 CYP121, P212121 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe462
b:21.1
occ:1.00
|
FE
|
C:HEM462
|
0.0
|
21.1
|
1.0
|
NB
|
C:HEM462
|
2.0
|
18.6
|
1.0
|
ND
|
C:HEM462
|
2.0
|
19.7
|
1.0
|
NC
|
C:HEM462
|
2.1
|
18.3
|
1.0
|
NA
|
C:HEM462
|
2.1
|
19.5
|
1.0
|
SG
|
C:CYS345
|
2.3
|
21.8
|
1.0
|
O
|
C:HOH2916
|
2.6
|
32.8
|
1.0
|
C1C
|
C:HEM462
|
3.0
|
20.0
|
1.0
|
C4B
|
C:HEM462
|
3.0
|
19.2
|
1.0
|
C1D
|
C:HEM462
|
3.1
|
18.8
|
1.0
|
C4D
|
C:HEM462
|
3.1
|
20.2
|
1.0
|
C4A
|
C:HEM462
|
3.1
|
18.4
|
1.0
|
C4C
|
C:HEM462
|
3.1
|
19.5
|
1.0
|
C1A
|
C:HEM462
|
3.1
|
19.3
|
1.0
|
C1B
|
C:HEM462
|
3.1
|
17.8
|
1.0
|
CHC
|
C:HEM462
|
3.4
|
18.6
|
1.0
|
CB
|
C:CYS345
|
3.4
|
20.6
|
1.0
|
CHB
|
C:HEM462
|
3.4
|
17.2
|
1.0
|
CHA
|
C:HEM462
|
3.4
|
20.3
|
1.0
|
CHD
|
C:HEM462
|
3.4
|
19.2
|
1.0
|
CA
|
C:CYS345
|
4.1
|
21.4
|
1.0
|
C3B
|
C:HEM462
|
4.3
|
18.3
|
1.0
|
C2C
|
C:HEM462
|
4.3
|
19.6
|
1.0
|
C3A
|
C:HEM462
|
4.3
|
18.6
|
1.0
|
C3C
|
C:HEM462
|
4.3
|
21.2
|
1.0
|
C2A
|
C:HEM462
|
4.3
|
17.1
|
1.0
|
C2D
|
C:HEM462
|
4.3
|
21.0
|
1.0
|
C3D
|
C:HEM462
|
4.3
|
23.3
|
1.0
|
C2B
|
C:HEM462
|
4.3
|
17.9
|
1.0
|
OG
|
C:SER237
|
4.5
|
19.7
|
1.0
|
CB
|
C:SER237
|
4.8
|
19.4
|
1.0
|
C
|
C:CYS345
|
4.9
|
22.4
|
1.0
|
CD
|
C:PRO346
|
4.9
|
23.7
|
1.0
|
N
|
C:GLY347
|
4.9
|
23.6
|
1.0
|
|
Iron binding site 4 out
of 6 in 2ij5
Go back to
Iron Binding Sites List in 2ij5
Iron binding site 4 out
of 6 in the Crystal Structure of Cytochrome P450 CYP121, P212121 Space Group
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 P450 CYP121, P212121 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe462
b:19.1
occ:1.00
|
FE
|
D:HEM462
|
0.0
|
19.1
|
1.0
|
NA
|
D:HEM462
|
2.0
|
15.8
|
1.0
|
NB
|
D:HEM462
|
2.0
|
17.0
|
1.0
|
ND
|
D:HEM462
|
2.1
|
18.4
|
1.0
|
NC
|
D:HEM462
|
2.1
|
18.9
|
1.0
|
SG
|
D:CYS345
|
2.3
|
20.0
|
1.0
|
O
|
D:HOH2971
|
2.8
|
31.0
|
1.0
|
C4A
|
D:HEM462
|
3.0
|
17.1
|
1.0
|
C4C
|
D:HEM462
|
3.0
|
20.0
|
1.0
|
C1A
|
D:HEM462
|
3.1
|
16.7
|
1.0
|
C1C
|
D:HEM462
|
3.1
|
17.9
|
1.0
|
C4D
|
D:HEM462
|
3.1
|
20.6
|
1.0
|
C1D
|
D:HEM462
|
3.1
|
20.0
|
1.0
|
C4B
|
D:HEM462
|
3.1
|
17.0
|
1.0
|
C1B
|
D:HEM462
|
3.1
|
16.6
|
1.0
|
CB
|
D:CYS345
|
3.4
|
19.7
|
1.0
|
CHC
|
D:HEM462
|
3.4
|
17.9
|
1.0
|
CHA
|
D:HEM462
|
3.4
|
19.2
|
1.0
|
CHB
|
D:HEM462
|
3.4
|
18.1
|
1.0
|
CHD
|
D:HEM462
|
3.5
|
18.6
|
1.0
|
CA
|
D:CYS345
|
4.1
|
19.6
|
1.0
|
C3C
|
D:HEM462
|
4.2
|
20.0
|
1.0
|
C2C
|
D:HEM462
|
4.3
|
19.1
|
1.0
|
C3A
|
D:HEM462
|
4.3
|
17.5
|
1.0
|
C2A
|
D:HEM462
|
4.3
|
16.0
|
1.0
|
C3B
|
D:HEM462
|
4.3
|
17.7
|
1.0
|
C3D
|
D:HEM462
|
4.3
|
18.9
|
1.0
|
C2D
|
D:HEM462
|
4.3
|
19.5
|
1.0
|
C2B
|
D:HEM462
|
4.3
|
16.3
|
1.0
|
OG
|
D:SER237
|
4.5
|
18.2
|
1.0
|
CD
|
D:PRO346
|
4.7
|
21.0
|
1.0
|
CB
|
D:SER237
|
4.8
|
17.3
|
1.0
|
N
|
D:GLY347
|
4.8
|
20.2
|
1.0
|
C
|
D:CYS345
|
4.9
|
19.8
|
1.0
|
O
|
D:HOH3168
|
5.0
|
39.2
|
1.0
|
N
|
D:PRO346
|
5.0
|
20.7
|
1.0
|
|
Iron binding site 5 out
of 6 in 2ij5
Go back to
Iron Binding Sites List in 2ij5
Iron binding site 5 out
of 6 in the Crystal Structure of Cytochrome P450 CYP121, P212121 Space Group
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 Cytochrome P450 CYP121, P212121 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe462
b:16.2
occ:1.00
|
FE
|
E:HEM462
|
0.0
|
16.2
|
1.0
|
NB
|
E:HEM462
|
2.0
|
15.0
|
1.0
|
ND
|
E:HEM462
|
2.0
|
15.6
|
1.0
|
NC
|
E:HEM462
|
2.0
|
13.2
|
1.0
|
NA
|
E:HEM462
|
2.1
|
15.0
|
1.0
|
SG
|
E:CYS345
|
2.3
|
17.4
|
1.0
|
O
|
E:HOH3017
|
2.6
|
32.1
|
1.0
|
C4B
|
E:HEM462
|
3.0
|
14.8
|
1.0
|
C1C
|
E:HEM462
|
3.0
|
14.4
|
1.0
|
C4C
|
E:HEM462
|
3.0
|
14.8
|
1.0
|
C4D
|
E:HEM462
|
3.1
|
15.5
|
1.0
|
C1A
|
E:HEM462
|
3.1
|
16.2
|
1.0
|
C1D
|
E:HEM462
|
3.1
|
15.8
|
1.0
|
C4A
|
E:HEM462
|
3.1
|
15.1
|
1.0
|
C1B
|
E:HEM462
|
3.1
|
12.7
|
1.0
|
CHC
|
E:HEM462
|
3.3
|
15.3
|
1.0
|
CB
|
E:CYS345
|
3.4
|
17.7
|
1.0
|
CHA
|
E:HEM462
|
3.4
|
17.7
|
1.0
|
CHB
|
E:HEM462
|
3.4
|
15.4
|
1.0
|
CHD
|
E:HEM462
|
3.5
|
16.3
|
1.0
|
CA
|
E:CYS345
|
4.1
|
17.0
|
1.0
|
C3C
|
E:HEM462
|
4.2
|
16.8
|
1.0
|
C2C
|
E:HEM462
|
4.3
|
15.8
|
1.0
|
C3B
|
E:HEM462
|
4.3
|
15.2
|
1.0
|
C2A
|
E:HEM462
|
4.3
|
14.9
|
1.0
|
C3A
|
E:HEM462
|
4.3
|
15.5
|
1.0
|
C2D
|
E:HEM462
|
4.3
|
17.3
|
1.0
|
C3D
|
E:HEM462
|
4.3
|
15.7
|
1.0
|
C2B
|
E:HEM462
|
4.3
|
13.9
|
1.0
|
OG
|
E:SER237
|
4.6
|
15.1
|
1.0
|
CD
|
E:PRO346
|
4.7
|
16.8
|
1.0
|
CB
|
E:SER237
|
4.8
|
15.0
|
1.0
|
C
|
E:CYS345
|
4.9
|
17.0
|
1.0
|
N
|
E:GLY347
|
4.9
|
16.3
|
1.0
|
CE
|
E:MET86
|
5.0
|
25.2
|
0.3
|
|
Iron binding site 6 out
of 6 in 2ij5
Go back to
Iron Binding Sites List in 2ij5
Iron binding site 6 out
of 6 in the Crystal Structure of Cytochrome P450 CYP121, P212121 Space Group
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 Cytochrome P450 CYP121, P212121 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe462
b:19.2
occ:1.00
|
FE
|
F:HEM462
|
0.0
|
19.2
|
1.0
|
ND
|
F:HEM462
|
2.0
|
18.0
|
1.0
|
NA
|
F:HEM462
|
2.0
|
17.2
|
1.0
|
NB
|
F:HEM462
|
2.1
|
18.1
|
1.0
|
NC
|
F:HEM462
|
2.1
|
17.9
|
1.0
|
SG
|
F:CYS345
|
2.3
|
19.1
|
1.0
|
O
|
F:HOH3059
|
2.5
|
33.4
|
1.0
|
C1D
|
F:HEM462
|
3.0
|
18.5
|
1.0
|
C4B
|
F:HEM462
|
3.0
|
16.3
|
1.0
|
C1A
|
F:HEM462
|
3.0
|
18.4
|
1.0
|
C4D
|
F:HEM462
|
3.1
|
18.6
|
1.0
|
C1C
|
F:HEM462
|
3.1
|
18.1
|
1.0
|
C4C
|
F:HEM462
|
3.1
|
17.4
|
1.0
|
C4A
|
F:HEM462
|
3.1
|
17.3
|
1.0
|
C1B
|
F:HEM462
|
3.1
|
15.7
|
1.0
|
CB
|
F:CYS345
|
3.3
|
18.9
|
1.0
|
CHC
|
F:HEM462
|
3.4
|
16.9
|
1.0
|
CHA
|
F:HEM462
|
3.4
|
20.1
|
1.0
|
CHD
|
F:HEM462
|
3.4
|
19.3
|
1.0
|
CHB
|
F:HEM462
|
3.4
|
17.7
|
1.0
|
CA
|
F:CYS345
|
4.1
|
18.7
|
1.0
|
C3C
|
F:HEM462
|
4.3
|
18.8
|
1.0
|
C2D
|
F:HEM462
|
4.3
|
20.4
|
1.0
|
C3B
|
F:HEM462
|
4.3
|
16.9
|
1.0
|
C3D
|
F:HEM462
|
4.3
|
22.0
|
1.0
|
C2A
|
F:HEM462
|
4.3
|
17.8
|
1.0
|
C2C
|
F:HEM462
|
4.3
|
19.3
|
1.0
|
C2B
|
F:HEM462
|
4.3
|
15.3
|
1.0
|
C3A
|
F:HEM462
|
4.3
|
17.8
|
1.0
|
O
|
F:HOH3185
|
4.4
|
44.2
|
1.0
|
OG
|
F:SER237
|
4.6
|
18.4
|
1.0
|
CD
|
F:PRO346
|
4.7
|
20.4
|
1.0
|
CB
|
F:SER237
|
4.8
|
16.3
|
1.0
|
C
|
F:CYS345
|
4.9
|
18.5
|
1.0
|
N
|
F:GLY347
|
4.9
|
18.8
|
1.0
|
|
Reference:
H.E.Seward,
A.Roujeinikova,
K.J.Mclean,
A.W.Munro,
D.Leys.
Crystal Structure of the Mycobacterium Tuberculosis P450 CYP121-Fluconazole Complex Reveals New Azole Drug-P450 Binding Mode. J.Biol.Chem. V. 281 39437 2006.
ISSN: ISSN 0021-9258
PubMed: 17028183
DOI: 10.1074/JBC.M607665200
Page generated: Sat Aug 3 23:21:42 2024
|