Iron in PDB 3gzy: Crystal Structure of the Biphenyl Dioxygenase From Comamonas Testosteroni Sp. Strain B-356

All present enzymatic activity of Crystal Structure of the Biphenyl Dioxygenase From Comamonas Testosteroni Sp. Strain B-356:
1.14.12.18;

The structure of Crystal Structure of the Biphenyl Dioxygenase From Comamonas Testosteroni Sp. Strain B-356, PDB code: 3gzy was solved by P.Kumar, C.L.Colbert, J.T.Bolin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.33 / 1.62
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	136.233, 136.233, 106.237, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The binding sites of Iron atom in the Crystal Structure of the Biphenyl Dioxygenase From Comamonas Testosteroni Sp. Strain B-356 (pdb code 3gzy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of the Biphenyl Dioxygenase From Comamonas Testosteroni Sp. Strain B-356, PDB code: 3gzy:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Crystal Structure of the Biphenyl Dioxygenase From Comamonas Testosteroni Sp. Strain B-356


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 the Biphenyl Dioxygenase From Comamonas Testosteroni Sp. Strain B-356 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:17.7 occ:1.00 OD1 A:ASP386 2.0 16.6 1.0 O A:HOH514 2.0 23.0 1.0 NE2 A:HIS239 2.0 10.9 1.0 NE2 A:HIS233 2.3 18.0 1.0 OD2 A:ASP386 2.4 15.7 1.0 CG A:ASP386 2.6 22.6 1.0 CE1 A:HIS239 3.0 9.3 1.0 CD2 A:HIS239 3.1 10.8 1.0 NE2 A:GLN226 3.2 17.1 1.0 CD2 A:HIS233 3.3 24.1 1.0 CE1 A:HIS233 3.3 13.2 1.0 O A:HOH772 3.9 35.6 1.0 CD A:GLN226 4.0 16.5 1.0 CB A:ASP386 4.1 15.9 1.0 ND1 A:HIS239 4.2 14.8 1.0 OE1 A:GLN226 4.2 21.3 1.0 CG A:HIS239 4.2 15.6 1.0 CG A:HIS233 4.4 14.2 1.0 ND1 A:HIS233 4.4 11.2 1.0 CE1 A:PHE376 4.6 14.1 1.0 CA A:ASP386 4.9 10.4 1.0 CZ A:PHE376 5.0 14.5 1.0

Iron binding site 2 out of 3 in the Crystal Structure of the Biphenyl Dioxygenase From Comamonas Testosteroni Sp. Strain B-356


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 the Biphenyl Dioxygenase From Comamonas Testosteroni Sp. Strain B-356 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe700 b:10.1 occ:1.00 FE1 A:FES700 0.0 10.1 1.0 S1 A:FES700 2.2 11.5 1.0 S2 A:FES700 2.3 10.1 1.0 SG A:CYS120 2.3 15.2 1.0 SG A:CYS100 2.4 13.8 1.0 FE2 A:FES700 2.6 9.7 1.0 CB A:CYS100 3.0 11.4 1.0 CB A:CYS120 3.2 9.6 1.0 CB A:HIS102 4.1 11.5 1.0 CB A:MET105 4.3 14.3 0.5 CB A:MET105 4.3 14.3 0.5 CB A:TYR122 4.4 9.4 1.0 N A:HIS123 4.4 10.9 1.0 CA A:CYS100 4.5 8.1 1.0 CA A:CYS120 4.5 12.3 1.0 ND1 A:HIS102 4.6 20.2 1.0 CB A:TRP125 4.6 9.2 1.0 ND1 A:HIS123 4.6 9.6 1.0 N A:ARG103 4.6 11.2 1.0 N A:MET105 4.8 12.8 0.5 N A:MET105 4.8 12.7 0.5 CG A:TRP125 4.8 9.8 1.0 N A:HIS102 4.8 6.2 1.0 CG A:HIS102 4.8 6.9 1.0 C A:CYS120 4.9 18.4 1.0 N A:TYR122 4.9 11.7 1.0 CG A:MET105 5.0 18.1 0.5

Iron binding site 3 out of 3 in the Crystal Structure of the Biphenyl Dioxygenase From Comamonas Testosteroni Sp. Strain B-356


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 the Biphenyl Dioxygenase From Comamonas Testosteroni Sp. Strain B-356 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe700 b:9.7 occ:1.00 FE2 A:FES700 0.0 9.7 1.0 ND1 A:HIS123 2.2 9.6 1.0 S2 A:FES700 2.2 10.1 1.0 S1 A:FES700 2.3 11.5 1.0 ND1 A:HIS102 2.3 20.2 1.0 FE1 A:FES700 2.6 10.1 1.0 CE1 A:HIS123 3.1 20.2 1.0 CG A:HIS123 3.1 14.6 1.0 CG A:HIS102 3.2 6.9 1.0 CB A:HIS102 3.3 11.5 1.0 CE1 A:HIS102 3.4 12.1 1.0 CB A:HIS123 3.4 12.5 1.0 N A:HIS123 3.6 10.9 1.0 CB A:TYR122 4.0 9.4 1.0 CA A:HIS123 4.1 17.9 1.0 NE2 A:HIS123 4.2 10.8 1.0 N A:ARG103 4.2 11.2 1.0 CD2 A:HIS123 4.3 14.1 1.0 SG A:CYS100 4.4 13.8 1.0 CD2 A:HIS102 4.4 8.1 1.0 CG A:TYR122 4.4 12.7 1.0 NE2 A:HIS102 4.4 11.5 1.0 CD1 A:TYR122 4.5 10.8 1.0 SG A:CYS120 4.5 15.2 1.0 C A:TYR122 4.5 12.8 1.0 CA A:HIS102 4.6 9.8 1.0 CB A:ARG103 4.7 10.5 1.0 C A:HIS102 4.8 11.1 1.0 CA A:TYR122 4.8 8.9 1.0 C A:HIS123 4.9 17.7 1.0

C.L.Colbert, N.Y.Agar, P.Kumar, M.N.Chakko, S.C.Sinha, J.B.Powlowski, L.D.Eltis, J.T.Bolin. Structural Characterization of Pandoraea Pnomenusa B-356 Biphenyl Dioxygenase Reveals Features of Potent Polychlorinated Biphenyl-Degrading Enzymes Plos One V. 8 52550 2013.
ISSN: ESSN 1932-6203
PubMed: 23308114
DOI: 10.1371/JOURNAL.PONE.0052550