Iron in PDB 3ejb: Crystal Structure of P450BIOI in Complex with Tetradecanoic Acid Ligated Acyl Carrier Protein
Protein crystallography data
The structure of Crystal Structure of P450BIOI in Complex with Tetradecanoic Acid Ligated Acyl Carrier Protein, PDB code: 3ejb
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 /
2.00
|
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 (%)
|
22.2 /
26.6
|
Other elements in 3ejb:
The structure of Crystal Structure of P450BIOI in Complex with Tetradecanoic 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 Tetradecanoic Acid Ligated Acyl Carrier Protein
(pdb code 3ejb). 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 Tetradecanoic Acid Ligated Acyl Carrier Protein, PDB code: 3ejb:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3ejb
Go back to
Iron Binding Sites List in 3ejb
Iron binding site 1 out
of 4 in the Crystal Structure of P450BIOI in Complex with Tetradecanoic 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 Tetradecanoic Acid Ligated Acyl Carrier Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe405
b:15.2
occ:1.00
|
FE
|
B:HEM405
|
0.0
|
15.2
|
1.0
|
NC
|
B:HEM405
|
2.0
|
15.1
|
1.0
|
NB
|
B:HEM405
|
2.1
|
14.8
|
1.0
|
NA
|
B:HEM405
|
2.1
|
14.6
|
1.0
|
ND
|
B:HEM405
|
2.1
|
14.8
|
1.0
|
SG
|
B:CYS344
|
2.4
|
15.6
|
1.0
|
C4C
|
B:HEM405
|
3.1
|
15.0
|
1.0
|
C1C
|
B:HEM405
|
3.1
|
15.1
|
1.0
|
C4B
|
B:HEM405
|
3.1
|
14.8
|
1.0
|
C1B
|
B:HEM405
|
3.1
|
14.8
|
1.0
|
C1A
|
B:HEM405
|
3.1
|
14.6
|
1.0
|
C1D
|
B:HEM405
|
3.1
|
14.5
|
1.0
|
C4A
|
B:HEM405
|
3.1
|
15.0
|
1.0
|
C4D
|
B:HEM405
|
3.1
|
14.2
|
1.0
|
CB
|
B:CYS344
|
3.4
|
15.2
|
1.0
|
CHC
|
B:HEM405
|
3.4
|
15.1
|
1.0
|
CHD
|
B:HEM405
|
3.4
|
14.7
|
1.0
|
CHA
|
B:HEM405
|
3.5
|
14.1
|
1.0
|
CHB
|
B:HEM405
|
3.5
|
14.7
|
1.0
|
CA
|
B:CYS344
|
4.0
|
15.3
|
1.0
|
C3C
|
B:HEM405
|
4.3
|
15.4
|
1.0
|
C3B
|
B:HEM405
|
4.3
|
15.4
|
1.0
|
C2C
|
B:HEM405
|
4.3
|
15.3
|
1.0
|
C2B
|
B:HEM405
|
4.3
|
15.1
|
1.0
|
C2A
|
B:HEM405
|
4.3
|
14.3
|
1.0
|
C3A
|
B:HEM405
|
4.3
|
14.2
|
1.0
|
C2D
|
B:HEM405
|
4.3
|
14.2
|
1.0
|
C3D
|
B:HEM405
|
4.3
|
14.0
|
1.0
|
C3
|
A:ZMP99
|
4.4
|
33.0
|
1.0
|
C4
|
A:ZMP99
|
4.5
|
32.9
|
1.0
|
N
|
B:LEU345
|
4.6
|
14.9
|
1.0
|
C
|
B:CYS344
|
4.7
|
15.3
|
1.0
|
N
|
B:GLY346
|
4.8
|
14.8
|
1.0
|
CB
|
B:ALA234
|
4.9
|
21.6
|
1.0
|
|
Iron binding site 2 out
of 4 in 3ejb
Go back to
Iron Binding Sites List in 3ejb
Iron binding site 2 out
of 4 in the Crystal Structure of P450BIOI in Complex with Tetradecanoic 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 Tetradecanoic Acid Ligated Acyl Carrier Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe405
b:13.8
occ:1.00
|
FE
|
D:HEM405
|
0.0
|
13.8
|
1.0
|
NB
|
D:HEM405
|
2.1
|
13.5
|
1.0
|
NA
|
D:HEM405
|
2.1
|
12.6
|
1.0
|
ND
|
D:HEM405
|
2.1
|
13.3
|
1.0
|
NC
|
D:HEM405
|
2.1
|
13.3
|
1.0
|
SG
|
D:CYS344
|
2.4
|
15.4
|
1.0
|
C1B
|
D:HEM405
|
3.1
|
13.9
|
1.0
|
C4B
|
D:HEM405
|
3.1
|
14.4
|
1.0
|
C4A
|
D:HEM405
|
3.1
|
13.0
|
1.0
|
C1A
|
D:HEM405
|
3.1
|
12.9
|
1.0
|
C4C
|
D:HEM405
|
3.1
|
13.8
|
1.0
|
C4D
|
D:HEM405
|
3.1
|
13.3
|
1.0
|
C1C
|
D:HEM405
|
3.1
|
14.2
|
1.0
|
C1D
|
D:HEM405
|
3.1
|
14.1
|
1.0
|
CB
|
D:CYS344
|
3.4
|
15.7
|
1.0
|
CHB
|
D:HEM405
|
3.4
|
13.5
|
1.0
|
CHA
|
D:HEM405
|
3.4
|
13.0
|
1.0
|
CHD
|
D:HEM405
|
3.5
|
14.0
|
1.0
|
CHC
|
D:HEM405
|
3.5
|
14.3
|
1.0
|
C4
|
C:ZMP99
|
3.9
|
29.7
|
1.0
|
CA
|
D:CYS344
|
4.0
|
15.8
|
1.0
|
C2B
|
D:HEM405
|
4.3
|
13.9
|
1.0
|
C3B
|
D:HEM405
|
4.3
|
14.4
|
1.0
|
C3C
|
D:HEM405
|
4.3
|
14.2
|
1.0
|
C3A
|
D:HEM405
|
4.3
|
12.2
|
1.0
|
C2C
|
D:HEM405
|
4.3
|
14.3
|
1.0
|
C2A
|
D:HEM405
|
4.3
|
12.7
|
1.0
|
C3D
|
D:HEM405
|
4.3
|
13.5
|
1.0
|
C2D
|
D:HEM405
|
4.3
|
13.7
|
1.0
|
N
|
D:LEU345
|
4.6
|
15.9
|
1.0
|
C5
|
C:ZMP99
|
4.7
|
29.7
|
1.0
|
C
|
D:CYS344
|
4.7
|
15.8
|
1.0
|
N
|
D:GLY346
|
4.8
|
16.0
|
1.0
|
CB
|
D:ALA234
|
4.9
|
21.5
|
1.0
|
|
Iron binding site 3 out
of 4 in 3ejb
Go back to
Iron Binding Sites List in 3ejb
Iron binding site 3 out
of 4 in the Crystal Structure of P450BIOI in Complex with Tetradecanoic 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 Tetradecanoic Acid Ligated Acyl Carrier Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe405
b:16.6
occ:1.00
|
FE
|
F:HEM405
|
0.0
|
16.6
|
1.0
|
NB
|
F:HEM405
|
2.1
|
16.5
|
1.0
|
NC
|
F:HEM405
|
2.1
|
15.7
|
1.0
|
NA
|
F:HEM405
|
2.1
|
15.7
|
1.0
|
ND
|
F:HEM405
|
2.1
|
15.7
|
1.0
|
SG
|
F:CYS344
|
2.5
|
17.2
|
1.0
|
C4B
|
F:HEM405
|
3.1
|
16.9
|
1.0
|
C1C
|
F:HEM405
|
3.1
|
16.4
|
1.0
|
C4C
|
F:HEM405
|
3.1
|
15.9
|
1.0
|
C1B
|
F:HEM405
|
3.1
|
16.7
|
1.0
|
C1A
|
F:HEM405
|
3.1
|
15.7
|
1.0
|
C4A
|
F:HEM405
|
3.1
|
15.6
|
1.0
|
C4D
|
F:HEM405
|
3.1
|
15.7
|
1.0
|
C1D
|
F:HEM405
|
3.1
|
15.8
|
1.0
|
CB
|
F:CYS344
|
3.4
|
17.0
|
1.0
|
CHC
|
F:HEM405
|
3.4
|
16.3
|
1.0
|
CHA
|
F:HEM405
|
3.4
|
15.4
|
1.0
|
CHD
|
F:HEM405
|
3.5
|
15.7
|
1.0
|
CHB
|
F:HEM405
|
3.5
|
16.0
|
1.0
|
CA
|
F:CYS344
|
4.0
|
17.0
|
1.0
|
C4
|
E:ZMP99
|
4.1
|
32.2
|
1.0
|
C3B
|
F:HEM405
|
4.3
|
17.0
|
1.0
|
C2C
|
F:HEM405
|
4.3
|
16.3
|
1.0
|
C2B
|
F:HEM405
|
4.3
|
16.9
|
1.0
|
C3C
|
F:HEM405
|
4.3
|
16.4
|
1.0
|
C3A
|
F:HEM405
|
4.3
|
15.3
|
1.0
|
C2A
|
F:HEM405
|
4.3
|
15.2
|
1.0
|
C3D
|
F:HEM405
|
4.3
|
15.6
|
1.0
|
C2D
|
F:HEM405
|
4.3
|
15.3
|
1.0
|
C3
|
E:ZMP99
|
4.5
|
32.4
|
1.0
|
C5
|
E:ZMP99
|
4.6
|
31.9
|
1.0
|
N
|
F:LEU345
|
4.6
|
17.1
|
1.0
|
C
|
F:CYS344
|
4.7
|
16.9
|
1.0
|
N
|
F:GLY346
|
4.8
|
17.5
|
1.0
|
CB
|
F:ALA234
|
4.9
|
21.2
|
1.0
|
|
Iron binding site 4 out
of 4 in 3ejb
Go back to
Iron Binding Sites List in 3ejb
Iron binding site 4 out
of 4 in the Crystal Structure of P450BIOI in Complex with Tetradecanoic 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 Tetradecanoic Acid Ligated Acyl Carrier Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Fe405
b:16.8
occ:1.00
|
FE
|
H:HEM405
|
0.0
|
16.8
|
1.0
|
NC
|
H:HEM405
|
2.0
|
16.2
|
1.0
|
NA
|
H:HEM405
|
2.1
|
16.0
|
1.0
|
NB
|
H:HEM405
|
2.1
|
15.6
|
1.0
|
ND
|
H:HEM405
|
2.1
|
15.6
|
1.0
|
SG
|
H:CYS344
|
2.5
|
16.8
|
1.0
|
C4C
|
H:HEM405
|
3.0
|
16.8
|
1.0
|
C1C
|
H:HEM405
|
3.1
|
16.7
|
1.0
|
C4B
|
H:HEM405
|
3.1
|
16.2
|
1.0
|
C4A
|
H:HEM405
|
3.1
|
16.5
|
1.0
|
C1A
|
H:HEM405
|
3.1
|
16.2
|
1.0
|
C1D
|
H:HEM405
|
3.1
|
16.1
|
1.0
|
C1B
|
H:HEM405
|
3.1
|
16.5
|
1.0
|
C4D
|
H:HEM405
|
3.1
|
16.1
|
1.0
|
CB
|
H:CYS344
|
3.4
|
17.0
|
1.0
|
CHD
|
H:HEM405
|
3.4
|
16.1
|
1.0
|
CHC
|
H:HEM405
|
3.4
|
16.4
|
1.0
|
CHA
|
H:HEM405
|
3.5
|
16.5
|
1.0
|
CHB
|
H:HEM405
|
3.5
|
16.4
|
1.0
|
CA
|
H:CYS344
|
4.0
|
17.1
|
1.0
|
C3C
|
H:HEM405
|
4.3
|
17.2
|
1.0
|
C2C
|
H:HEM405
|
4.3
|
17.0
|
1.0
|
C3A
|
H:HEM405
|
4.3
|
16.3
|
1.0
|
C2A
|
H:HEM405
|
4.3
|
16.3
|
1.0
|
C3B
|
H:HEM405
|
4.3
|
16.7
|
1.0
|
C2B
|
H:HEM405
|
4.3
|
16.6
|
1.0
|
C2D
|
H:HEM405
|
4.3
|
15.4
|
1.0
|
C3D
|
H:HEM405
|
4.3
|
16.2
|
1.0
|
N
|
H:LEU345
|
4.6
|
17.2
|
1.0
|
C5
|
G:ZMP99
|
4.6
|
33.7
|
1.0
|
C4
|
G:ZMP99
|
4.6
|
33.7
|
1.0
|
C3
|
G:ZMP99
|
4.7
|
33.2
|
1.0
|
C
|
H:CYS344
|
4.7
|
17.1
|
1.0
|
N
|
H:GLY346
|
4.8
|
17.4
|
1.0
|
CB
|
H:ALA234
|
5.0
|
25.6
|
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 09:45:54 2024
|