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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:

Chlorine (Cl) 2 atoms

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: Tue Aug 5 01:00:40 2025

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