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Iron in PDB 2nnh: CYP2C8DH Complexed with 2 Molecules of 9-Cis Retinoic Acid

Enzymatic activity of CYP2C8DH Complexed with 2 Molecules of 9-Cis Retinoic Acid

All present enzymatic activity of CYP2C8DH Complexed with 2 Molecules of 9-Cis Retinoic Acid:
1.14.14.1;

Protein crystallography data

The structure of CYP2C8DH Complexed with 2 Molecules of 9-Cis Retinoic Acid, PDB code: 2nnh was solved by G.A.Schoch, J.K.Yano, C.D.Stout, E.F.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 139.810, 163.620, 73.555, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 29

Iron Binding Sites:

The binding sites of Iron atom in the CYP2C8DH Complexed with 2 Molecules of 9-Cis Retinoic Acid (pdb code 2nnh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the CYP2C8DH Complexed with 2 Molecules of 9-Cis Retinoic Acid, PDB code: 2nnh:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 2nnh

Go back to Iron Binding Sites List in 2nnh
Iron binding site 1 out of 2 in the CYP2C8DH Complexed with 2 Molecules of 9-Cis Retinoic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of CYP2C8DH Complexed with 2 Molecules of 9-Cis Retinoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:32.8
occ:1.00
FE A:HEM500 0.0 32.8 1.0
NA A:HEM500 2.1 33.5 1.0
ND A:HEM500 2.1 33.6 1.0
NC A:HEM500 2.1 33.1 1.0
NB A:HEM500 2.1 31.8 1.0
SG A:CYS435 2.3 36.4 1.0
C1D A:HEM500 3.0 34.5 1.0
C1C A:HEM500 3.0 32.8 1.0
C4B A:HEM500 3.0 29.8 1.0
C4D A:HEM500 3.0 33.6 1.0
C4A A:HEM500 3.0 33.4 1.0
C1A A:HEM500 3.1 35.3 1.0
C1B A:HEM500 3.1 30.0 1.0
C4C A:HEM500 3.1 33.6 1.0
CHC A:HEM500 3.3 31.2 1.0
CHD A:HEM500 3.3 34.2 1.0
CB A:CYS435 3.3 36.6 1.0
CHB A:HEM500 3.3 30.7 1.0
CHA A:HEM500 3.4 34.1 1.0
O A:ALA297 3.9 38.6 1.0
CA A:CYS435 4.1 35.2 1.0
C2D A:HEM500 4.2 32.8 1.0
C2C A:HEM500 4.2 31.9 1.0
C3D A:HEM500 4.3 32.7 1.0
C2A A:HEM500 4.3 35.1 1.0
C3A A:HEM500 4.3 33.5 1.0
C3B A:HEM500 4.3 27.4 1.0
C3C A:HEM500 4.3 34.9 1.0
C2B A:HEM500 4.3 26.0 1.0
C4 A:9CR501 4.5 50.0 1.0
CB A:ALA297 4.6 36.4 1.0
C A:ALA297 4.8 38.4 1.0
C3 A:9CR501 4.8 51.2 1.0
C A:CYS435 4.8 37.5 1.0
N A:ALA436 4.9 37.1 1.0

Iron binding site 2 out of 2 in 2nnh

Go back to Iron Binding Sites List in 2nnh
Iron binding site 2 out of 2 in the CYP2C8DH Complexed with 2 Molecules of 9-Cis Retinoic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of CYP2C8DH Complexed with 2 Molecules of 9-Cis Retinoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:32.9
occ:1.00
FE B:HEM500 0.0 32.9 1.0
NC B:HEM500 2.0 34.3 1.0
NB B:HEM500 2.1 33.0 1.0
NA B:HEM500 2.1 34.3 1.0
ND B:HEM500 2.1 34.3 1.0
SG B:CYS435 2.3 37.2 1.0
C1C B:HEM500 3.0 35.5 1.0
C4B B:HEM500 3.0 32.4 1.0
C1D B:HEM500 3.0 33.8 1.0
C4A B:HEM500 3.0 33.5 1.0
C1B B:HEM500 3.0 33.1 1.0
C4C B:HEM500 3.0 36.5 1.0
C4D B:HEM500 3.0 33.3 1.0
C1A B:HEM500 3.1 33.8 1.0
CHC B:HEM500 3.3 33.4 1.0
CHB B:HEM500 3.3 33.3 1.0
CHD B:HEM500 3.3 35.6 1.0
CHA B:HEM500 3.4 33.0 1.0
CB B:CYS435 3.5 34.3 1.0
O B:ALA297 3.7 40.8 1.0
CA B:CYS435 4.1 35.4 1.0
C2C B:HEM500 4.2 38.1 1.0
C2D B:HEM500 4.2 32.5 1.0
C3C B:HEM500 4.2 37.6 1.0
C3B B:HEM500 4.3 31.6 1.0
C3A B:HEM500 4.3 32.6 1.0
C3D B:HEM500 4.3 32.8 1.0
C2B B:HEM500 4.3 31.7 1.0
C2A B:HEM500 4.3 33.6 1.0
CB B:ALA297 4.7 39.6 1.0
C B:ALA297 4.7 41.5 1.0
CD1 B:PHE428 4.8 31.7 1.0
N B:ALA436 4.8 39.2 1.0
C B:CYS435 4.8 37.4 1.0
N B:GLY437 4.8 39.0 1.0
C4 B:9CR501 4.8 53.0 1.0
C3 B:9CR501 5.0 54.2 1.0

Reference:

G.A.Schoch, J.K.Yano, S.Sansen, P.M.Dansette, C.D.Stout, E.F.Johnson. Determinants of Cytochrome P450 2C8 Substrate Binding: Structures of Complexes with Montelukast, Troglitazone, Felodipine, and 9-Cis-Retinoic Acid. J.Biol.Chem. V. 283 17227 2008.
ISSN: ISSN 0021-9258
PubMed: 18413310
DOI: 10.1074/JBC.M802180200
Page generated: Sun Dec 13 14:49:43 2020

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