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Iron in PDB 2cd8: Crystal Structure of Yc-17-Bound Cytochrome P450 Pikc (CYP107L1)

Protein crystallography data

The structure of Crystal Structure of Yc-17-Bound Cytochrome P450 Pikc (CYP107L1), PDB code: 2cd8 was solved by L.I.Yermalitskaya, Y.Kim, D.H.Sherman, M.R.Waterman, L.M.Podust, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.84 / 1.7
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.401, 92.102, 67.574, 90.00, 89.99, 90.00
R / Rfree (%) 29 / 33.3

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Yc-17-Bound Cytochrome P450 Pikc (CYP107L1) (pdb code 2cd8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Yc-17-Bound Cytochrome P450 Pikc (CYP107L1), PDB code: 2cd8:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 2cd8

Go back to Iron Binding Sites List in 2cd8
Iron binding site 1 out of 2 in the Crystal Structure of Yc-17-Bound Cytochrome P450 Pikc (CYP107L1)


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 Yc-17-Bound Cytochrome P450 Pikc (CYP107L1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe419

b:15.9
occ:1.00
FE A:HEM419 0.0 15.9 1.0
NA A:HEM419 2.0 13.9 1.0
NC A:HEM419 2.0 14.8 1.0
NB A:HEM419 2.0 13.3 1.0
ND A:HEM419 2.0 14.0 1.0
SG A:CYS354 2.7 18.9 1.0
C4B A:HEM419 3.0 15.3 1.0
C1B A:HEM419 3.0 11.9 1.0
C1C A:HEM419 3.1 15.0 1.0
C4A A:HEM419 3.1 10.4 1.0
C4C A:HEM419 3.1 14.6 1.0
C1D A:HEM419 3.1 15.5 1.0
C4D A:HEM419 3.1 15.7 1.0
C1A A:HEM419 3.1 12.0 1.0
CB A:CYS354 3.4 16.3 1.0
CHC A:HEM419 3.4 16.9 1.0
CHB A:HEM419 3.4 13.7 1.0
CHD A:HEM419 3.5 14.2 1.0
CHA A:HEM419 3.5 14.8 1.0
CA A:CYS354 4.1 17.6 1.0
O A:ALA243 4.2 15.7 1.0
C3B A:HEM419 4.3 14.3 1.0
C2C A:HEM419 4.3 15.9 1.0
C3C A:HEM419 4.3 16.3 1.0
C3D A:HEM419 4.3 11.9 1.0
C2D A:HEM419 4.3 13.3 1.0
C2B A:HEM419 4.3 11.8 1.0
C3A A:HEM419 4.3 12.3 1.0
C2A A:HEM419 4.4 12.4 1.0
C1 A:PXI420 4.6 20.4 1.0
N A:GLY356 4.7 16.9 1.0
C A:CYS354 4.8 16.4 1.0
C A:ALA243 4.8 14.9 1.0
N A:ILE355 4.8 15.9 1.0
CB A:ALA243 4.9 17.3 1.0

Iron binding site 2 out of 2 in 2cd8

Go back to Iron Binding Sites List in 2cd8
Iron binding site 2 out of 2 in the Crystal Structure of Yc-17-Bound Cytochrome P450 Pikc (CYP107L1)


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 Yc-17-Bound Cytochrome P450 Pikc (CYP107L1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe419

b:16.7
occ:1.00
FE B:HEM419 0.0 16.7 1.0
ND B:HEM419 2.0 14.6 1.0
NC B:HEM419 2.0 16.5 1.0
NB B:HEM419 2.0 14.2 1.0
NA B:HEM419 2.0 14.8 1.0
SG B:CYS354 2.9 19.6 1.0
C1D B:HEM419 3.0 16.4 1.0
C1C B:HEM419 3.0 16.3 1.0
C4D B:HEM419 3.0 16.2 1.0
C4C B:HEM419 3.1 15.1 1.0
C4A B:HEM419 3.1 15.0 1.0
C1B B:HEM419 3.1 17.8 1.0
C4B B:HEM419 3.1 18.2 1.0
C1A B:HEM419 3.1 14.4 1.0
CHC B:HEM419 3.4 18.7 1.0
CHD B:HEM419 3.4 15.6 1.0
CHA B:HEM419 3.4 13.1 1.0
CHB B:HEM419 3.5 14.3 1.0
CB B:CYS354 3.6 18.7 1.0
CA B:CYS354 4.1 17.3 1.0
O B:ALA243 4.2 22.9 1.0
C2D B:HEM419 4.2 14.6 1.0
C3D B:HEM419 4.3 14.2 1.0
C2C B:HEM419 4.3 17.2 1.0
C3A B:HEM419 4.3 14.2 1.0
C3C B:HEM419 4.3 16.7 1.0
C2B B:HEM419 4.3 15.1 1.0
C3B B:HEM419 4.3 15.1 1.0
C2A B:HEM419 4.3 13.0 1.0
C1 B:PXI420 4.5 21.4 1.0
C B:ALA243 4.7 22.5 1.0
CB B:ALA243 4.7 21.6 1.0
N B:GLY356 4.7 19.5 1.0
N B:ILE355 4.8 17.5 1.0
C B:CYS354 4.8 17.5 1.0

Reference:

D.H.Sherman, S.Li, L.V.Yermalitskaya, Y.Kim, J.A.Smith, M.R.Waterman, L.M.Podust. The Structural Basis For Substrate Anchoring, Active Site Selectivity, and Product Formation By P450 Pikc From Streptomyces Venezuelae. J.Biol.Chem. V. 281 26289 2006.
ISSN: ISSN 0021-9258
PubMed: 16825192
DOI: 10.1074/JBC.M605478200
Page generated: Thu Jul 17 00:23:39 2025

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