Iron in PDB 3o72: Crystal Structure of Efeb in Complex with Heme

The structure of Crystal Structure of Efeb in Complex with Heme, PDB code: 3o72 was solved by X.Liu, Q.Du, Z.Wang, D.Zhu, Y.Huang, N.Li, S.Xu, L.Gu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.640, 155.568, 97.374, 90.00, 94.70, 90.00
R / Rfree (%)	17 / 20.6

The binding sites of Iron atom in the Crystal Structure of Efeb in Complex with Heme (pdb code 3o72). 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 Efeb in Complex with Heme, PDB code: 3o72:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Efeb in Complex with Heme


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 Efeb in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:13.0 occ:1.00 FE A:HEM500 0.0 13.0 1.0 NC A:HEM500 2.0 10.0 1.0 NB A:HEM500 2.0 13.4 1.0 NA A:HEM500 2.1 11.2 1.0 ND A:HEM500 2.1 13.9 1.0 NE2 A:HIS329 2.1 10.3 1.0 O2 A:OXY600 2.3 18.4 1.0 C4B A:HEM500 3.0 11.3 1.0 C4C A:HEM500 3.0 11.0 1.0 C1C A:HEM500 3.0 13.0 1.0 C1A A:HEM500 3.1 13.2 1.0 C1D A:HEM500 3.1 12.8 1.0 C4D A:HEM500 3.1 13.2 1.0 C1B A:HEM500 3.1 12.7 1.0 C4A A:HEM500 3.1 14.3 1.0 CE1 A:HIS329 3.1 12.5 1.0 CD2 A:HIS329 3.1 12.1 1.0 CHC A:HEM500 3.4 11.1 1.0 CHD A:HEM500 3.4 11.1 1.0 CHA A:HEM500 3.4 13.8 1.0 O1 A:OXY600 3.5 24.4 1.0 CHB A:HEM500 3.5 14.0 1.0 ND1 A:HIS329 4.2 9.8 1.0 C3B A:HEM500 4.2 11.7 1.0 CG A:HIS329 4.2 13.4 1.0 C3C A:HEM500 4.2 11.2 1.0 C2C A:HEM500 4.3 12.2 1.0 NH1 A:ARG347 4.3 16.6 1.0 C2B A:HEM500 4.3 13.8 1.0 C2A A:HEM500 4.3 14.2 1.0 C3A A:HEM500 4.3 13.2 1.0 C3D A:HEM500 4.3 13.4 1.0 C2D A:HEM500 4.3 13.2 1.0 CD A:ARG347 4.7 16.1 1.0 CZ A:ARG347 5.0 15.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Efeb in Complex with Heme


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 Efeb in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:14.2 occ:1.00 FE B:HEM500 0.0 14.2 1.0 NC B:HEM500 2.0 14.1 1.0 NA B:HEM500 2.0 13.6 1.0 NB B:HEM500 2.1 13.4 1.0 ND B:HEM500 2.1 13.3 1.0 NE2 B:HIS329 2.1 15.1 1.0 O1 B:OXY600 2.4 19.7 1.0 C1C B:HEM500 3.1 14.5 1.0 C4A B:HEM500 3.1 13.6 1.0 C1A B:HEM500 3.1 14.8 1.0 C4B B:HEM500 3.1 13.2 1.0 C4C B:HEM500 3.1 14.1 1.0 C1B B:HEM500 3.1 13.8 1.0 CE1 B:HIS329 3.1 14.5 1.0 C4D B:HEM500 3.1 13.5 1.0 CD2 B:HIS329 3.1 12.1 1.0 C1D B:HEM500 3.1 14.5 1.0 CHC B:HEM500 3.4 13.0 1.0 CHB B:HEM500 3.5 13.0 1.0 CHA B:HEM500 3.5 13.0 1.0 CHD B:HEM500 3.5 13.8 1.0 O2 B:OXY600 3.7 22.5 1.0 ND1 B:HIS329 4.2 12.9 1.0 CG B:HIS329 4.3 14.9 1.0 C3A B:HEM500 4.3 15.1 1.0 C2A B:HEM500 4.3 13.4 1.0 C2C B:HEM500 4.3 15.2 1.0 C3C B:HEM500 4.3 15.0 1.0 NH1 B:ARG347 4.3 15.6 1.0 C3B B:HEM500 4.3 15.1 1.0 C2B B:HEM500 4.3 13.7 1.0 C3D B:HEM500 4.4 13.8 1.0 C2D B:HEM500 4.4 14.0 1.0 CD B:ARG347 4.8 18.0 1.0 CZ B:ARG347 5.0 15.9 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Efeb in Complex with Heme


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 Efeb in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe500 b:19.7 occ:1.00 FE C:HEM500 0.0 19.7 1.0 NA C:HEM500 2.0 17.5 1.0 NB C:HEM500 2.0 18.2 1.0 NC C:HEM500 2.1 18.7 1.0 ND C:HEM500 2.1 18.7 1.0 NE2 C:HIS329 2.2 18.6 1.0 O2 C:OXY600 2.6 26.3 1.0 C4A C:HEM500 3.0 21.4 1.0 C1A C:HEM500 3.0 18.6 1.0 C1B C:HEM500 3.0 19.7 1.0 C4B C:HEM500 3.1 18.8 1.0 C4C C:HEM500 3.1 16.9 1.0 C4D C:HEM500 3.1 19.5 1.0 C1C C:HEM500 3.1 17.3 1.0 C1D C:HEM500 3.1 17.1 1.0 CD2 C:HIS329 3.1 20.1 1.0 CE1 C:HIS329 3.2 20.1 1.0 CHA C:HEM500 3.4 19.2 1.0 CHB C:HEM500 3.4 21.5 1.0 CHD C:HEM500 3.4 18.6 1.0 CHC C:HEM500 3.5 18.5 1.0 O1 C:OXY600 3.8 29.9 1.0 NH1 C:ARG347 4.2 20.2 1.0 C3A C:HEM500 4.2 19.9 1.0 C2B C:HEM500 4.3 20.7 1.0 C2A C:HEM500 4.3 21.1 1.0 C3B C:HEM500 4.3 18.5 1.0 ND1 C:HIS329 4.3 20.1 1.0 CG C:HIS329 4.3 20.8 1.0 C3C C:HEM500 4.3 18.5 1.0 C2C C:HEM500 4.3 18.4 1.0 C3D C:HEM500 4.3 19.0 1.0 C2D C:HEM500 4.3 21.1 1.0 CD C:ARG347 4.7 20.5 1.0 OD1 C:ASP235 4.8 32.5 1.0 CZ C:ARG347 4.8 19.8 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Efeb in Complex with Heme


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 Efeb in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe500 b:18.2 occ:1.00 FE D:HEM500 0.0 18.2 1.0 NC D:HEM500 2.1 18.8 1.0 ND D:HEM500 2.1 17.1 1.0 NA D:HEM500 2.1 20.1 1.0 NB D:HEM500 2.1 21.4 1.0 NE2 D:HIS329 2.1 20.9 1.0 O1 D:OXY600 2.6 24.9 1.0 CE1 D:HIS329 3.0 19.6 1.0 C4D D:HEM500 3.1 19.4 1.0 C4C D:HEM500 3.1 19.7 1.0 C1A D:HEM500 3.1 18.4 1.0 C1C D:HEM500 3.1 21.1 1.0 C1D D:HEM500 3.1 17.9 1.0 C4A D:HEM500 3.1 20.9 1.0 C4B D:HEM500 3.1 19.7 1.0 CD2 D:HIS329 3.1 18.0 1.0 C1B D:HEM500 3.1 20.8 1.0 CHA D:HEM500 3.4 17.8 1.0 CHD D:HEM500 3.4 19.6 1.0 CHC D:HEM500 3.4 21.4 1.0 CHB D:HEM500 3.5 17.9 1.0 O2 D:OXY600 3.9 29.9 1.0 NH1 D:ARG347 4.2 21.1 1.0 ND1 D:HIS329 4.2 20.2 1.0 CG D:HIS329 4.2 20.6 1.0 C2A D:HEM500 4.3 19.4 1.0 C3A D:HEM500 4.3 19.3 1.0 C3C D:HEM500 4.3 20.8 1.0 C3D D:HEM500 4.3 21.9 1.0 C2C D:HEM500 4.3 22.3 1.0 C3B D:HEM500 4.3 18.7 1.0 C2D D:HEM500 4.3 18.8 1.0 C2B D:HEM500 4.3 17.2 1.0 CD D:ARG347 4.7 21.3 1.0 CZ D:ARG347 4.9 23.2 1.0

X.Liu, Q.Du, Z.Wang, D.Zhu, Y.Huang, N.Li, T.Wei, S.Xu, L.Gu. Crystal Structure and Biochemical Features of Efeb/Ycdb From Escherichia Coli O157: ASP235 Plays Divergent Roles in Different Enzyme-Catalyzed Processes J.Biol.Chem. V. 286 14922 2011.
ISSN: ISSN 0021-9258
PubMed: 21324904
DOI: 10.1074/JBC.M110.197780