Iron in PDB 2xr8: Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400

All present enzymatic activity of Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400:
1.14.12.18;

The structure of Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400, PDB code: 2xr8 was solved by P.Kumar, J.T.Bolin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	129.10 / 2.49
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	132.585, 132.350, 132.984, 102.60, 102.68, 104.61
R / Rfree (%)	21.633 / 26.714

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 (pdb code 2xr8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 36 binding sites of Iron where determined in the Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400, PDB code: 2xr8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 36 in the Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


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 Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe900 b:43.2 occ:1.00 FE1 A:FES900 0.0 43.2 1.0 ND1 A:HIS102 2.1 22.5 1.0 ND1 A:HIS123 2.1 23.3 1.0 S2 A:FES900 2.2 39.9 1.0 S1 A:FES900 2.2 39.6 1.0 CG A:HIS123 3.0 23.6 1.0 FE2 A:FES900 3.0 37.5 1.0 CG A:HIS102 3.1 22.3 1.0 CE1 A:HIS102 3.1 22.3 1.0 CE1 A:HIS123 3.1 23.3 1.0 CB A:HIS123 3.2 23.7 1.0 CB A:HIS102 3.4 22.3 1.0 N A:HIS123 3.8 23.9 1.0 CD2 A:HIS123 4.1 23.7 1.0 CA A:HIS123 4.1 23.7 1.0 CB A:TYR122 4.2 24.6 1.0 NE2 A:HIS123 4.2 23.6 1.0 NE2 A:HIS102 4.2 22.1 1.0 CD2 A:HIS102 4.2 22.6 1.0 N A:ARG103 4.3 22.4 1.0 CB A:ARG103 4.3 22.3 1.0 CG A:TYR122 4.6 24.6 1.0 SG A:CYS120 4.6 26.4 1.0 SG A:CYS100 4.6 23.5 1.0 CA A:HIS102 4.6 22.5 1.0 CD1 A:TYR122 4.6 25.0 1.0 C A:HIS102 4.7 22.5 1.0 C A:TYR122 4.7 24.2 1.0 CD1 A:TRP125 4.9 21.8 1.0 CA A:ARG103 4.9 22.2 1.0 NE1 A:TRP125 4.9 22.0 1.0 C A:HIS123 5.0 23.6 1.0

Iron binding site 2 out of 36 in the Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


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 Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe900 b:37.5 occ:1.00 FE2 A:FES900 0.0 37.5 1.0 S2 A:FES900 2.2 39.9 1.0 S1 A:FES900 2.2 39.6 1.0 SG A:CYS100 2.3 23.5 1.0 SG A:CYS120 2.4 26.4 1.0 CB A:CYS100 2.9 22.5 1.0 FE1 A:FES900 3.0 43.2 1.0 CB A:CYS120 3.2 25.3 1.0 CB A:HIS102 4.1 22.3 1.0 CA A:CYS100 4.4 22.5 1.0 CB A:TRP125 4.4 22.1 1.0 CB A:MET105 4.4 22.0 1.0 ND1 A:HIS102 4.6 22.5 1.0 CG A:TRP125 4.6 21.8 1.0 CA A:CYS120 4.7 25.4 1.0 CB A:TYR122 4.7 24.6 1.0 N A:ARG103 4.8 22.4 1.0 OH A:TYR127 4.8 22.6 1.0 N A:HIS123 4.8 23.9 1.0 ND1 A:HIS123 4.8 23.3 1.0 CG A:HIS102 4.8 22.3 1.0 N A:MET105 4.9 22.2 1.0 C A:CYS100 4.9 22.5 1.0 N A:HIS102 4.9 22.7 1.0 CD2 A:TRP125 4.9 21.6 1.0 CA A:HIS102 5.0 22.5 1.0

Iron binding site 3 out of 36 in the Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


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 Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe901 b:31.8 occ:1.00 NE2 A:HIS239 2.0 24.9 1.0 OD1 A:ASP388 2.2 30.2 1.0 NE2 A:HIS233 2.2 24.6 1.0 O A:HOH2023 2.4 15.3 1.0 OD2 A:ASP388 2.6 31.9 1.0 CG A:ASP388 2.8 31.1 1.0 CE1 A:HIS239 3.0 24.4 1.0 CD2 A:HIS239 3.0 24.5 1.0 CD2 A:HIS233 3.2 24.3 1.0 CE1 A:HIS233 3.2 24.2 1.0 NE2 A:GLN226 3.5 25.1 1.0 ND1 A:HIS239 4.1 24.5 1.0 CG A:HIS239 4.1 24.7 1.0 CB A:ASP388 4.2 30.9 1.0 ND1 A:HIS233 4.3 24.7 1.0 CD A:GLN226 4.3 24.8 1.0 CG A:HIS233 4.3 24.4 1.0 OE1 A:GLN226 4.7 25.3 1.0

Iron binding site 4 out of 36 in the Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


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 Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe900 b:34.4 occ:1.00 FE1 C:FES900 0.0 34.4 1.0 ND1 C:HIS102 2.1 19.9 1.0 S2 C:FES900 2.2 31.0 1.0 S1 C:FES900 2.2 29.7 1.0 ND1 C:HIS123 2.2 23.1 1.0 CG C:HIS102 3.0 19.8 1.0 FE2 C:FES900 3.0 29.6 1.0 CE1 C:HIS123 3.0 23.2 1.0 CE1 C:HIS102 3.1 19.9 1.0 CB C:HIS102 3.2 19.5 1.0 CG C:HIS123 3.2 23.4 1.0 CB C:HIS123 3.7 23.7 1.0 N C:ARG103 4.0 19.6 1.0 CB C:ARG103 4.1 19.6 1.0 NE2 C:HIS123 4.2 23.5 1.0 CD2 C:HIS102 4.2 20.0 1.0 NE2 C:HIS102 4.2 19.8 1.0 N C:HIS123 4.2 24.1 1.0 CD2 C:HIS123 4.3 23.5 1.0 CB C:TYR122 4.3 24.9 1.0 CA C:HIS102 4.4 19.6 1.0 SG C:CYS100 4.5 20.0 1.0 C C:HIS102 4.5 19.6 1.0 CG C:TYR122 4.5 25.0 1.0 CD1 C:TYR122 4.5 25.3 1.0 CA C:HIS123 4.6 23.8 1.0 CA C:ARG103 4.6 19.5 1.0 SG C:CYS120 4.7 25.7 1.0 C C:TYR122 5.0 24.5 1.0

Iron binding site 5 out of 36 in the Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe900 b:29.6 occ:1.00 FE2 C:FES900 0.0 29.6 1.0 S2 C:FES900 2.2 31.0 1.0 S1 C:FES900 2.2 29.7 1.0 SG C:CYS120 2.3 25.7 1.0 SG C:CYS100 2.3 20.0 1.0 CB C:CYS100 2.9 19.7 1.0 FE1 C:FES900 3.0 34.4 1.0 CB C:CYS120 3.1 25.2 1.0 CB C:HIS102 4.2 19.5 1.0 CB C:MET105 4.3 18.1 1.0 CB C:TRP125 4.3 23.6 1.0 CA C:CYS100 4.4 19.8 1.0 CB C:TYR122 4.5 24.9 1.0 CA C:CYS120 4.6 25.4 1.0 CG C:TRP125 4.6 23.6 1.0 ND1 C:HIS123 4.7 23.1 1.0 N C:HIS123 4.7 24.1 1.0 ND1 C:HIS102 4.7 19.9 1.0 N C:MET105 4.7 18.7 1.0 N C:ARG103 4.8 19.6 1.0 C C:CYS100 4.9 19.7 1.0 OH C:TYR127 4.9 23.7 1.0 O C:MET105 4.9 18.8 1.0 CD2 C:TRP125 4.9 23.8 1.0 CG C:HIS102 5.0 19.8 1.0 CA C:MET105 5.0 18.5 1.0 O C:CYS100 5.0 19.7 1.0

Iron binding site 6 out of 36 in the Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe901 b:33.9 occ:1.00 NE2 C:HIS239 2.0 28.0 1.0 NE2 C:HIS233 2.2 26.3 1.0 OD1 C:ASP388 2.2 31.3 1.0 O C:HOH2017 2.4 20.5 1.0 OD2 C:ASP388 2.7 31.4 1.0 CG C:ASP388 2.8 31.0 1.0 CD2 C:HIS233 3.0 26.2 1.0 CE1 C:HIS239 3.0 28.0 1.0 CD2 C:HIS239 3.0 27.6 1.0 NE2 C:GLN226 3.2 25.4 1.0 CE1 C:HIS233 3.3 25.7 1.0 CD C:GLN226 4.0 25.2 1.0 ND1 C:HIS239 4.1 27.8 1.0 CG C:HIS239 4.2 27.4 1.0 CG C:HIS233 4.2 25.8 1.0 CB C:ASP388 4.3 30.8 1.0 ND1 C:HIS233 4.3 25.5 1.0 OE1 C:GLN226 4.5 25.2 1.0 CG2 C:THR238 4.7 25.8 1.0 CG C:GLN226 4.8 25.1 1.0

Iron binding site 7 out of 36 in the Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe900 b:44.7 occ:1.00 FE1 E:FES900 0.0 44.7 1.0 ND1 E:HIS102 2.1 23.7 1.0 ND1 E:HIS123 2.1 23.4 1.0 S1 E:FES900 2.2 40.1 1.0 S2 E:FES900 2.2 42.1 1.0 CG E:HIS102 3.0 23.8 1.0 FE2 E:FES900 3.0 39.3 1.0 CE1 E:HIS123 3.0 23.6 1.0 CG E:HIS123 3.1 24.2 1.0 CE1 E:HIS102 3.2 24.2 1.0 CB E:HIS102 3.2 23.7 1.0 CB E:HIS123 3.5 24.7 1.0 CB E:ARG103 4.0 23.5 1.0 N E:HIS123 4.1 24.9 1.0 CB E:TYR122 4.1 25.4 1.0 N E:ARG103 4.1 23.5 1.0 NE2 E:HIS123 4.1 23.9 1.0 CD2 E:HIS102 4.2 24.2 1.0 CD2 E:HIS123 4.2 24.1 1.0 NE2 E:HIS102 4.2 24.1 1.0 CA E:HIS123 4.4 24.7 1.0 CG E:TYR122 4.4 25.5 1.0 CA E:HIS102 4.4 23.6 1.0 SG E:CYS100 4.4 23.8 1.0 CD1 E:TYR122 4.5 25.7 1.0 C E:HIS102 4.5 23.6 1.0 CA E:ARG103 4.6 23.5 1.0 SG E:CYS120 4.7 25.9 1.0 C E:TYR122 4.8 25.2 1.0

Iron binding site 8 out of 36 in the Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe900 b:39.3 occ:1.00 FE2 E:FES900 0.0 39.3 1.0 S2 E:FES900 2.2 42.1 1.0 S1 E:FES900 2.2 40.1 1.0 SG E:CYS120 2.3 25.9 1.0 SG E:CYS100 2.3 23.8 1.0 CB E:CYS100 3.0 23.5 1.0 FE1 E:FES900 3.0 44.7 1.0 CB E:CYS120 3.2 25.5 1.0 CB E:HIS102 4.2 23.7 1.0 CB E:TRP125 4.3 24.2 1.0 CB E:MET105 4.4 22.9 1.0 CB E:TYR122 4.4 25.4 1.0 CA E:CYS100 4.4 23.6 1.0 CA E:CYS120 4.6 25.6 1.0 CG E:TRP125 4.6 24.2 1.0 N E:HIS123 4.6 24.9 1.0 ND1 E:HIS102 4.7 23.7 1.0 ND1 E:HIS123 4.7 23.4 1.0 OH E:TYR127 4.9 24.7 1.0 N E:MET105 4.9 23.3 1.0 C E:CYS100 4.9 23.6 1.0 CG E:HIS102 4.9 23.8 1.0 CD2 E:TRP125 4.9 24.1 1.0 N E:ARG103 5.0 23.5 1.0

Iron binding site 9 out of 36 in the Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe901 b:33.7 occ:1.00 O E:HOH2019 1.9 20.9 1.0 NE2 E:HIS239 2.1 26.0 1.0 OD1 E:ASP388 2.1 29.3 1.0 NE2 E:HIS233 2.1 29.1 1.0 CG E:ASP388 2.8 29.4 1.0 OD2 E:ASP388 2.8 30.0 1.0 CE1 E:HIS239 3.0 26.3 1.0 CD2 E:HIS233 3.1 28.7 1.0 CD2 E:HIS239 3.1 25.9 1.0 CE1 E:HIS233 3.1 28.7 1.0 NE2 E:GLN226 3.4 25.8 1.0 OE1 E:GLN226 3.9 26.5 1.0 CD E:GLN226 4.0 25.9 1.0 ND1 E:HIS239 4.1 26.3 1.0 CG E:HIS239 4.2 25.9 1.0 CB E:ASP388 4.2 29.2 1.0 ND1 E:HIS233 4.2 28.6 1.0 CG E:HIS233 4.2 27.9 1.0 CG2 E:THR238 4.8 25.4 1.0 CA E:ASP388 5.0 29.2 1.0

Iron binding site 10 out of 36 in the Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe900 b:40.1 occ:1.00 FE1 G:FES900 0.0 40.1 1.0 ND1 G:HIS123 2.1 21.1 1.0 S2 G:FES900 2.2 37.3 1.0 S1 G:FES900 2.2 36.9 1.0 ND1 G:HIS102 2.2 22.7 1.0 FE2 G:FES900 3.0 35.8 1.0 CG G:HIS123 3.1 21.6 1.0 CE1 G:HIS123 3.1 21.0 1.0 CG G:HIS102 3.1 22.2 1.0 CE1 G:HIS102 3.2 22.4 1.0 CB G:HIS102 3.4 21.8 1.0 CB G:HIS123 3.4 21.7 1.0 N G:ARG103 4.0 21.5 1.0 N G:HIS123 4.0 21.8 1.0 CB G:TYR122 4.1 21.9 1.0 NE2 G:HIS123 4.1 20.9 1.0 CD2 G:HIS123 4.1 21.4 1.0 CB G:ARG103 4.2 21.3 1.0 CA G:HIS123 4.3 21.7 1.0 CD2 G:HIS102 4.3 22.3 1.0 NE2 G:HIS102 4.3 22.5 1.0 CG G:TYR122 4.4 21.9 1.0 CD1 G:TYR122 4.4 21.8 1.0 SG G:CYS100 4.5 23.3 1.0 CA G:HIS102 4.6 21.8 1.0 C G:HIS102 4.6 21.8 1.0 CA G:ARG103 4.6 21.3 1.0 SG G:CYS120 4.7 23.5 1.0 C G:TYR122 4.8 21.9 1.0

P.Kumar, M.Mohammadi, J.F.Viger, D.Barriault, L.Gomez-Gil, L.D.Eltis, J.T.Bolin, M.Sylvestre. Structural Insight Into the Expanded Pcb-Degrading Abilities of A Biphenyl Dioxygenase Obtained By Directed Evolution. J.Mol.Biol. V. 405 531 2011.
ISSN: ISSN 0022-2836
PubMed: 21073881
DOI: 10.1016/J.JMB.2010.11.009