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Iron in PDB 7q9e: CYP106A1

Protein crystallography data

The structure of CYP106A1, PDB code: 7q9e was solved by Y.Carius, M.Hutter, F.Kiss, R.Bernhardt, C.R.D.Lancaster, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.82 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.69, 82.87, 84.86, 95.36, 90, 90
R / Rfree (%) 16.9 / 20.6

Other elements in 7q9e:

The structure of CYP106A1 also contains other interesting chemical elements:

Cobalt (Co) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the CYP106A1 (pdb code 7q9e). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the CYP106A1, PDB code: 7q9e:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7q9e

Go back to Iron Binding Sites List in 7q9e
Iron binding site 1 out of 4 in the CYP106A1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of CYP106A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:11.8
occ:1.00
FE A:HEM501 0.0 11.8 1.0
ND A:HEM501 2.0 12.3 1.0
NA A:HEM501 2.0 11.7 1.0
NB A:HEM501 2.1 10.9 1.0
NC A:HEM501 2.1 12.0 1.0
SG A:CYS356 2.3 12.4 1.0
O A:HOH663 2.4 25.8 1.0
C1D A:HEM501 3.0 13.8 1.0
C4D A:HEM501 3.0 12.5 1.0
C1A A:HEM501 3.0 13.4 1.0
C4B A:HEM501 3.0 10.7 1.0
C1B A:HEM501 3.1 11.8 1.0
C4C A:HEM501 3.1 12.5 1.0
C4A A:HEM501 3.1 11.9 1.0
C1C A:HEM501 3.1 11.0 1.0
CB A:CYS356 3.4 11.3 1.0
CHA A:HEM501 3.4 11.6 1.0
CHD A:HEM501 3.4 12.8 1.0
CHC A:HEM501 3.4 11.3 1.0
CHB A:HEM501 3.5 11.5 1.0
CA A:CYS356 4.0 10.9 1.0
O A:ALA244 4.2 17.8 1.0
C2D A:HEM501 4.3 13.0 1.0
C2A A:HEM501 4.3 13.7 1.0
C2B A:HEM501 4.3 10.4 1.0
C2C A:HEM501 4.3 11.8 1.0
C3A A:HEM501 4.3 12.7 1.0
C3D A:HEM501 4.3 12.5 1.0
C3C A:HEM501 4.3 12.5 1.0
C3B A:HEM501 4.3 11.0 1.0
CB A:ALA244 4.6 16.7 1.0
N A:GLY358 4.6 11.4 1.0
C A:CYS356 4.7 10.7 1.0
N A:LEU357 4.8 10.6 1.0
C A:ALA244 4.9 15.9 1.0
CA A:GLY358 4.9 12.9 1.0

Iron binding site 2 out of 4 in 7q9e

Go back to Iron Binding Sites List in 7q9e
Iron binding site 2 out of 4 in the CYP106A1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of CYP106A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:10.8
occ:1.00
FE B:HEM501 0.0 10.8 1.0
ND B:HEM501 2.0 10.0 1.0
NA B:HEM501 2.0 9.7 1.0
NC B:HEM501 2.0 9.8 1.0
NB B:HEM501 2.0 9.3 1.0
O B:HOH708 2.2 22.7 1.0
SG B:CYS356 2.3 10.9 1.0
C1D B:HEM501 3.0 10.9 1.0
C4D B:HEM501 3.0 10.9 1.0
C4B B:HEM501 3.0 9.4 1.0
C1B B:HEM501 3.0 10.1 1.0
C1A B:HEM501 3.0 11.0 1.0
C4C B:HEM501 3.0 11.3 1.0
C1C B:HEM501 3.1 9.6 1.0
C4A B:HEM501 3.1 10.8 1.0
CHA B:HEM501 3.4 10.9 1.0
CB B:CYS356 3.4 10.0 1.0
CHD B:HEM501 3.4 11.0 1.0
CHC B:HEM501 3.4 10.1 1.0
CHB B:HEM501 3.4 10.6 1.0
CA B:CYS356 4.0 9.8 1.0
O B:ALA244 4.1 17.2 1.0
C2D B:HEM501 4.2 10.9 1.0
C2B B:HEM501 4.2 10.4 1.0
C3D B:HEM501 4.2 10.9 1.0
C3C B:HEM501 4.3 10.5 1.0
C3A B:HEM501 4.3 11.4 1.0
C3B B:HEM501 4.3 10.7 1.0
C2C B:HEM501 4.3 10.6 1.0
C2A B:HEM501 4.3 11.7 1.0
O2 B:PEG506 4.5 56.7 1.0
O4 B:PEG506 4.5 50.6 1.0
CB B:ALA244 4.6 14.0 1.0
N B:GLY358 4.7 12.0 1.0
C B:CYS356 4.7 10.4 1.0
N B:LEU357 4.8 11.9 1.0
C B:ALA244 4.9 14.9 1.0
CA B:GLY358 5.0 12.7 1.0

Iron binding site 3 out of 4 in 7q9e

Go back to Iron Binding Sites List in 7q9e
Iron binding site 3 out of 4 in the CYP106A1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of CYP106A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:14.2
occ:1.00
FE C:HEM501 0.0 14.2 1.0
ND C:HEM501 2.0 15.1 1.0
NA C:HEM501 2.0 14.3 1.0
NB C:HEM501 2.1 14.7 1.0
NC C:HEM501 2.1 13.6 1.0
O C:HOH720 2.2 24.0 1.0
SG C:CYS356 2.3 13.1 1.0
C4D C:HEM501 3.0 16.8 1.0
C1A C:HEM501 3.0 15.9 1.0
C1D C:HEM501 3.0 15.1 1.0
C1B C:HEM501 3.0 14.5 1.0
C4A C:HEM501 3.1 15.0 1.0
C4B C:HEM501 3.1 15.0 1.0
C4C C:HEM501 3.1 14.3 1.0
C1C C:HEM501 3.1 14.3 1.0
CHA C:HEM501 3.4 15.5 1.0
CB C:CYS356 3.4 12.7 1.0
CHD C:HEM501 3.4 14.8 1.0
CHB C:HEM501 3.4 14.1 1.0
CHC C:HEM501 3.5 13.3 1.0
CA C:CYS356 4.0 13.4 1.0
O C:ALA244 4.2 22.6 1.0
C2A C:HEM501 4.2 15.9 1.0
C3D C:HEM501 4.3 16.1 1.0
C2B C:HEM501 4.3 13.9 1.0
C3A C:HEM501 4.3 15.2 1.0
C2D C:HEM501 4.3 16.6 1.0
C3C C:HEM501 4.3 14.9 1.0
C2C C:HEM501 4.3 14.5 1.0
C3B C:HEM501 4.3 14.0 1.0
N C:GLY358 4.6 12.6 1.0
N C:LEU357 4.7 15.1 1.0
C C:CYS356 4.7 13.9 1.0
CB C:ALA244 4.8 18.9 1.0
O1 C:PEG505 5.0 49.9 1.0
C2 C:PEG505 5.0 52.5 1.0
CA C:GLY358 5.0 12.2 1.0
C C:ALA244 5.0 18.5 1.0

Iron binding site 4 out of 4 in 7q9e

Go back to Iron Binding Sites List in 7q9e
Iron binding site 4 out of 4 in the CYP106A1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of CYP106A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:13.0
occ:1.00
FE D:HEM501 0.0 13.0 1.0
ND D:HEM501 1.9 13.2 1.0
NA D:HEM501 2.0 12.4 1.0
NB D:HEM501 2.1 12.9 1.0
NC D:HEM501 2.1 12.6 1.0
O D:HOH708 2.1 23.4 1.0
SG D:CYS356 2.2 12.7 1.0
C4D D:HEM501 2.9 14.5 1.0
C1D D:HEM501 3.0 13.6 1.0
C1A D:HEM501 3.0 15.0 1.0
C1B D:HEM501 3.0 13.6 1.0
C4A D:HEM501 3.0 13.2 1.0
C4C D:HEM501 3.0 13.5 1.0
C4B D:HEM501 3.1 13.6 1.0
C1C D:HEM501 3.1 13.5 1.0
CHA D:HEM501 3.4 13.5 1.0
CB D:CYS356 3.4 12.6 1.0
CHB D:HEM501 3.4 12.9 1.0
CHD D:HEM501 3.4 13.3 1.0
CHC D:HEM501 3.5 13.0 1.0
CA D:CYS356 4.1 12.6 1.0
C3D D:HEM501 4.2 14.9 1.0
C2D D:HEM501 4.2 15.0 1.0
C3A D:HEM501 4.2 13.6 1.0
C3C D:HEM501 4.2 15.1 1.0
C2A D:HEM501 4.2 15.5 1.0
O D:ALA244 4.3 18.8 1.0
C2B D:HEM501 4.3 13.2 1.0
C2C D:HEM501 4.3 13.6 1.0
C3B D:HEM501 4.3 13.5 1.0
N D:GLY358 4.6 13.6 1.0
C D:CYS356 4.7 12.6 1.0
N D:LEU357 4.8 14.4 1.0
CB D:ALA244 4.8 18.8 1.0

Reference:

Y.Carius, M.Hutter, F.Kiss, R.Bernhardt, C.R.D.Lancaster. Structural Comparison of the Cytochrome P450 Enzymes CYP106A1 and CYP106A2 Provides Insight Into Their Differences in Steroid Conversion. Febs Lett. V. 596 3133 2022.
ISSN: ISSN 0014-5793
PubMed: 36151590
DOI: 10.1002/1873-3468.14502
Page generated: Wed Apr 5 04:02:22 2023

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