Iron in PDB 3ejd: Crystal Structure of P450BIOI in Complex with Hexadec-9Z-Enoic Acid Ligated Acyl Carrier Protein
Protein crystallography data
The structure of Crystal Structure of P450BIOI in Complex with Hexadec-9Z-Enoic Acid Ligated Acyl Carrier Protein, PDB code: 3ejd
was solved by
M.J.Cryle,
I.Schlichting,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.10
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.300,
92.100,
107.700,
109.00,
89.20,
90.10
|
R / Rfree (%)
|
24.1 /
28.5
|
Other elements in 3ejd:
The structure of Crystal Structure of P450BIOI in Complex with Hexadec-9Z-Enoic Acid Ligated Acyl Carrier Protein also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of P450BIOI in Complex with Hexadec-9Z-Enoic Acid Ligated Acyl Carrier Protein
(pdb code 3ejd). 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 P450BIOI in Complex with Hexadec-9Z-Enoic Acid Ligated Acyl Carrier Protein, PDB code: 3ejd:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3ejd
Go back to
Iron Binding Sites List in 3ejd
Iron binding site 1 out
of 4 in the Crystal Structure of P450BIOI in Complex with Hexadec-9Z-Enoic Acid Ligated Acyl Carrier Protein
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 P450BIOI in Complex with Hexadec-9Z-Enoic Acid Ligated Acyl Carrier Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe405
b:16.0
occ:1.00
|
FE
|
B:HEM405
|
0.0
|
16.0
|
1.0
|
NB
|
B:HEM405
|
2.0
|
14.7
|
1.0
|
NC
|
B:HEM405
|
2.1
|
15.3
|
1.0
|
ND
|
B:HEM405
|
2.1
|
14.7
|
1.0
|
NA
|
B:HEM405
|
2.1
|
13.6
|
1.0
|
SG
|
B:CYS344
|
2.3
|
20.6
|
1.0
|
C4B
|
B:HEM405
|
3.1
|
15.3
|
1.0
|
C1B
|
B:HEM405
|
3.1
|
15.0
|
1.0
|
C4C
|
B:HEM405
|
3.1
|
15.4
|
1.0
|
C1D
|
B:HEM405
|
3.1
|
15.5
|
1.0
|
C1C
|
B:HEM405
|
3.1
|
15.3
|
1.0
|
C4D
|
B:HEM405
|
3.1
|
13.8
|
1.0
|
C4A
|
B:HEM405
|
3.1
|
14.6
|
1.0
|
C1A
|
B:HEM405
|
3.1
|
14.0
|
1.0
|
CB
|
B:CYS344
|
3.3
|
21.3
|
1.0
|
CHD
|
B:HEM405
|
3.4
|
15.5
|
1.0
|
CHC
|
B:HEM405
|
3.4
|
15.6
|
1.0
|
CHB
|
B:HEM405
|
3.4
|
14.9
|
1.0
|
CHA
|
B:HEM405
|
3.5
|
14.4
|
1.0
|
CA
|
B:CYS344
|
3.9
|
21.1
|
1.0
|
C8
|
A:ZMQ99
|
4.2
|
36.8
|
1.0
|
C7
|
A:ZMQ99
|
4.3
|
35.7
|
1.0
|
C3B
|
B:HEM405
|
4.3
|
16.0
|
1.0
|
C2B
|
B:HEM405
|
4.3
|
15.0
|
1.0
|
C3C
|
B:HEM405
|
4.3
|
15.7
|
1.0
|
C2C
|
B:HEM405
|
4.3
|
16.3
|
1.0
|
C2D
|
B:HEM405
|
4.3
|
15.1
|
1.0
|
C3D
|
B:HEM405
|
4.3
|
15.2
|
1.0
|
C3A
|
B:HEM405
|
4.3
|
14.2
|
1.0
|
C2A
|
B:HEM405
|
4.3
|
14.4
|
1.0
|
N
|
B:LEU345
|
4.5
|
21.1
|
1.0
|
C
|
B:CYS344
|
4.6
|
21.1
|
1.0
|
N
|
B:GLY346
|
4.7
|
20.9
|
1.0
|
CB
|
B:ALA234
|
4.9
|
28.7
|
1.0
|
|
Iron binding site 2 out
of 4 in 3ejd
Go back to
Iron Binding Sites List in 3ejd
Iron binding site 2 out
of 4 in the Crystal Structure of P450BIOI in Complex with Hexadec-9Z-Enoic Acid Ligated Acyl Carrier Protein
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 P450BIOI in Complex with Hexadec-9Z-Enoic Acid Ligated Acyl Carrier Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe405
b:17.6
occ:1.00
|
FE
|
D:HEM405
|
0.0
|
17.6
|
1.0
|
NB
|
D:HEM405
|
2.0
|
15.2
|
1.0
|
NA
|
D:HEM405
|
2.1
|
15.9
|
1.0
|
ND
|
D:HEM405
|
2.1
|
15.2
|
1.0
|
NC
|
D:HEM405
|
2.1
|
16.2
|
1.0
|
SG
|
D:CYS344
|
2.4
|
21.1
|
1.0
|
C1B
|
D:HEM405
|
3.1
|
17.3
|
1.0
|
C4A
|
D:HEM405
|
3.1
|
16.6
|
1.0
|
C4B
|
D:HEM405
|
3.1
|
16.9
|
1.0
|
C1A
|
D:HEM405
|
3.1
|
15.4
|
1.0
|
C1D
|
D:HEM405
|
3.1
|
16.4
|
1.0
|
C4D
|
D:HEM405
|
3.1
|
15.1
|
1.0
|
C4C
|
D:HEM405
|
3.1
|
16.9
|
1.0
|
C1C
|
D:HEM405
|
3.1
|
16.7
|
1.0
|
CB
|
D:CYS344
|
3.3
|
21.1
|
1.0
|
CHB
|
D:HEM405
|
3.4
|
16.4
|
1.0
|
CHA
|
D:HEM405
|
3.5
|
15.8
|
1.0
|
CHC
|
D:HEM405
|
3.5
|
16.7
|
1.0
|
CHD
|
D:HEM405
|
3.5
|
16.3
|
1.0
|
C8
|
C:ZMQ99
|
3.8
|
35.5
|
1.0
|
CA
|
D:CYS344
|
3.9
|
21.1
|
1.0
|
C2B
|
D:HEM405
|
4.3
|
16.9
|
1.0
|
C3B
|
D:HEM405
|
4.3
|
17.2
|
1.0
|
C3A
|
D:HEM405
|
4.3
|
15.7
|
1.0
|
C2A
|
D:HEM405
|
4.3
|
16.7
|
1.0
|
C3C
|
D:HEM405
|
4.3
|
17.2
|
1.0
|
C2C
|
D:HEM405
|
4.3
|
17.2
|
1.0
|
C7
|
C:ZMQ99
|
4.3
|
35.7
|
1.0
|
C3D
|
D:HEM405
|
4.3
|
15.4
|
1.0
|
C2D
|
D:HEM405
|
4.3
|
16.2
|
1.0
|
N
|
D:LEU345
|
4.4
|
21.1
|
1.0
|
C
|
D:CYS344
|
4.6
|
21.0
|
1.0
|
N
|
D:GLY346
|
4.7
|
20.9
|
1.0
|
C9
|
C:ZMQ99
|
4.8
|
35.2
|
1.0
|
CB
|
D:ALA234
|
4.9
|
28.7
|
1.0
|
|
Iron binding site 3 out
of 4 in 3ejd
Go back to
Iron Binding Sites List in 3ejd
Iron binding site 3 out
of 4 in the Crystal Structure of P450BIOI in Complex with Hexadec-9Z-Enoic Acid Ligated Acyl Carrier Protein
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 P450BIOI in Complex with Hexadec-9Z-Enoic Acid Ligated Acyl Carrier Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe405
b:20.7
occ:1.00
|
FE
|
F:HEM405
|
0.0
|
20.7
|
1.0
|
NA
|
F:HEM405
|
2.1
|
21.0
|
1.0
|
NB
|
F:HEM405
|
2.1
|
21.5
|
1.0
|
ND
|
F:HEM405
|
2.1
|
20.4
|
1.0
|
NC
|
F:HEM405
|
2.1
|
21.6
|
1.0
|
SG
|
F:CYS344
|
2.4
|
21.6
|
1.0
|
C1A
|
F:HEM405
|
3.1
|
19.8
|
1.0
|
C4A
|
F:HEM405
|
3.1
|
20.4
|
1.0
|
C1B
|
F:HEM405
|
3.1
|
21.4
|
1.0
|
C4C
|
F:HEM405
|
3.1
|
20.8
|
1.0
|
C4D
|
F:HEM405
|
3.1
|
20.4
|
1.0
|
C4B
|
F:HEM405
|
3.1
|
21.9
|
1.0
|
C1D
|
F:HEM405
|
3.1
|
21.1
|
1.0
|
C1C
|
F:HEM405
|
3.1
|
21.1
|
1.0
|
CB
|
F:CYS344
|
3.4
|
21.4
|
1.0
|
CHA
|
F:HEM405
|
3.4
|
20.1
|
1.0
|
CHB
|
F:HEM405
|
3.4
|
20.6
|
1.0
|
CHD
|
F:HEM405
|
3.4
|
20.9
|
1.0
|
CHC
|
F:HEM405
|
3.5
|
21.9
|
1.0
|
CA
|
F:CYS344
|
4.0
|
21.2
|
1.0
|
C7
|
E:ZMQ99
|
4.0
|
35.3
|
1.0
|
C2A
|
F:HEM405
|
4.3
|
19.9
|
1.0
|
C3A
|
F:HEM405
|
4.3
|
20.3
|
1.0
|
C3C
|
F:HEM405
|
4.3
|
21.4
|
1.0
|
C2B
|
F:HEM405
|
4.3
|
21.3
|
1.0
|
C3B
|
F:HEM405
|
4.3
|
21.8
|
1.0
|
C2C
|
F:HEM405
|
4.3
|
21.5
|
1.0
|
C3D
|
F:HEM405
|
4.3
|
20.6
|
1.0
|
C2D
|
F:HEM405
|
4.3
|
20.2
|
1.0
|
N
|
F:LEU345
|
4.5
|
21.1
|
1.0
|
C8
|
E:ZMQ99
|
4.6
|
35.1
|
1.0
|
C
|
F:CYS344
|
4.6
|
21.1
|
1.0
|
N
|
F:GLY346
|
4.8
|
20.9
|
1.0
|
C9
|
E:ZMQ99
|
4.9
|
35.1
|
1.0
|
CB
|
F:ALA234
|
4.9
|
28.7
|
1.0
|
C6
|
E:ZMQ99
|
5.0
|
35.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 3ejd
Go back to
Iron Binding Sites List in 3ejd
Iron binding site 4 out
of 4 in the Crystal Structure of P450BIOI in Complex with Hexadec-9Z-Enoic Acid Ligated Acyl Carrier Protein
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 P450BIOI in Complex with Hexadec-9Z-Enoic Acid Ligated Acyl Carrier Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Fe405
b:18.7
occ:1.00
|
FE
|
H:HEM405
|
0.0
|
18.7
|
1.0
|
NA
|
H:HEM405
|
2.0
|
16.7
|
1.0
|
NC
|
H:HEM405
|
2.0
|
16.4
|
1.0
|
NB
|
H:HEM405
|
2.1
|
17.7
|
1.0
|
ND
|
H:HEM405
|
2.1
|
16.5
|
1.0
|
SG
|
H:CYS344
|
2.4
|
20.6
|
1.0
|
C4A
|
H:HEM405
|
3.1
|
17.8
|
1.0
|
C1C
|
H:HEM405
|
3.1
|
17.0
|
1.0
|
C4B
|
H:HEM405
|
3.1
|
17.8
|
1.0
|
C4C
|
H:HEM405
|
3.1
|
17.5
|
1.0
|
C1A
|
H:HEM405
|
3.1
|
16.9
|
1.0
|
C1B
|
H:HEM405
|
3.1
|
18.2
|
1.0
|
C1D
|
H:HEM405
|
3.1
|
17.1
|
1.0
|
C4D
|
H:HEM405
|
3.1
|
16.9
|
1.0
|
CB
|
H:CYS344
|
3.4
|
21.1
|
1.0
|
CHC
|
H:HEM405
|
3.4
|
17.5
|
1.0
|
CHB
|
H:HEM405
|
3.4
|
17.7
|
1.0
|
CHD
|
H:HEM405
|
3.5
|
17.1
|
1.0
|
CHA
|
H:HEM405
|
3.5
|
17.6
|
1.0
|
CA
|
H:CYS344
|
3.9
|
21.1
|
1.0
|
C7
|
G:ZMQ99
|
4.1
|
37.5
|
1.0
|
C8
|
G:ZMQ99
|
4.2
|
37.1
|
1.0
|
C2C
|
H:HEM405
|
4.3
|
16.9
|
1.0
|
C3A
|
H:HEM405
|
4.3
|
17.3
|
1.0
|
C3C
|
H:HEM405
|
4.3
|
17.5
|
1.0
|
C2A
|
H:HEM405
|
4.3
|
16.9
|
1.0
|
C3B
|
H:HEM405
|
4.3
|
18.2
|
1.0
|
C2B
|
H:HEM405
|
4.3
|
18.4
|
1.0
|
C2D
|
H:HEM405
|
4.4
|
16.9
|
1.0
|
C3D
|
H:HEM405
|
4.4
|
17.6
|
1.0
|
N
|
H:LEU345
|
4.4
|
21.1
|
1.0
|
C
|
H:CYS344
|
4.6
|
21.0
|
1.0
|
C6
|
G:ZMQ99
|
4.6
|
37.6
|
1.0
|
N
|
H:GLY346
|
4.7
|
20.9
|
1.0
|
CB
|
H:ALA234
|
5.0
|
29.0
|
1.0
|
|
Reference:
M.J.Cryle,
I.Schlichting.
Structural Insights From A P450 Carrier Protein Complex Reveal How Specificity Is Achieved in the P450(Bioi) Acp Complex. Proc.Natl.Acad.Sci.Usa V. 105 15696 2008.
ISSN: ISSN 0027-8424
PubMed: 18838690
DOI: 10.1073/PNAS.0805983105
Page generated: Sun Aug 4 09:46:09 2024
|