Iron in PDB 5aew: Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl

All present enzymatic activity of Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl:
1.14.12.18;

The structure of Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl, PDB code: 5aew was solved by S.Dhindwal, L.Gomez-Gil, M.Sylvestre, L.D.Eltis, J.T.Bolin, P.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.34 / 1.88
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	132.767, 133.191, 133.965, 102.31, 102.54, 104.54
R / Rfree (%)	22.5 / 26.3

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 II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl (pdb code 5aew). 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 II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl, PDB code: 5aew:
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 II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl


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 II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe460 b:26.4 occ:1.00 FE1 A:FES460 0.0 26.4 1.0 S1 A:FES460 2.2 26.6 1.0 S2 A:FES460 2.2 26.8 1.0 SG A:CYS100 2.3 26.4 1.0 SG A:CYS120 2.3 26.2 1.0 FE2 A:FES460 2.8 26.9 1.0 CB A:CYS100 3.0 26.1 1.0 CB A:CYS120 3.2 26.2 1.0 CB A:HIS102 4.1 27.0 1.0 CB A:MET105 4.3 25.9 1.0 CB A:TYR122 4.5 26.5 1.0 CA A:CYS100 4.5 26.1 1.0 ND1 A:HIS102 4.5 27.3 1.0 N A:HIS123 4.5 26.9 1.0 CB A:TRP125 4.5 26.8 1.0 ND1 A:HIS123 4.6 27.1 1.0 CA A:CYS120 4.7 26.0 1.0 N A:ARG103 4.7 26.8 1.0 CG A:TRP125 4.8 27.0 1.0 CG A:HIS102 4.8 27.3 1.0 N A:MET105 4.8 26.0 1.0 OH A:TYR127 4.9 26.4 1.0 N A:HIS102 4.9 26.8 1.0 C A:CYS100 4.9 26.2 1.0 CA A:HIS102 5.0 27.0 1.0

Iron binding site 2 out of 36 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl


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 II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe460 b:26.9 occ:1.00 FE2 A:FES460 0.0 26.9 1.0 ND1 A:HIS102 2.1 27.3 1.0 ND1 A:HIS123 2.1 27.1 1.0 S2 A:FES460 2.2 26.8 1.0 S1 A:FES460 2.2 26.6 1.0 FE1 A:FES460 2.8 26.4 1.0 CG A:HIS123 3.0 27.3 1.0 CG A:HIS102 3.0 27.3 1.0 CE1 A:HIS123 3.1 27.3 1.0 CE1 A:HIS102 3.1 27.6 1.0 CB A:HIS123 3.3 27.3 1.0 CB A:HIS102 3.3 27.0 1.0 N A:HIS123 3.8 26.9 1.0 CA A:HIS123 4.1 27.1 1.0 CD2 A:HIS123 4.1 27.6 1.0 N A:ARG103 4.1 26.8 1.0 NE2 A:HIS123 4.1 27.5 1.0 CB A:TYR122 4.1 26.5 1.0 CD2 A:HIS102 4.2 27.6 1.0 NE2 A:HIS102 4.2 27.7 1.0 CD2 A:TYR122 4.4 26.7 1.0 SG A:CYS100 4.4 26.4 1.0 SG A:CYS120 4.5 26.2 1.0 CG A:TYR122 4.5 26.7 1.0 CB A:ARG103 4.5 27.0 1.0 CA A:HIS102 4.5 27.0 1.0 C A:HIS102 4.6 27.0 1.0 C A:TYR122 4.6 26.8 1.0 C A:HIS123 4.9 27.1 1.0 CA A:ARG103 4.9 26.8 1.0 CA A:TYR122 5.0 26.6 1.0 CD1 A:TRP125 5.0 27.2 1.0

Iron binding site 3 out of 36 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl


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 II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe461 b:24.0 occ:1.00 OD1 A:ASP388 2.0 23.9 1.0 O A:HOH2236 2.1 31.7 1.0 NE2 A:HIS233 2.1 24.3 1.0 NE2 A:HIS239 2.2 24.0 1.0 O A:HOH2228 2.3 36.1 1.0 O A:HOH2232 2.4 38.3 1.0 CG A:ASP388 2.8 23.8 1.0 OD2 A:ASP388 2.9 23.7 1.0 CD2 A:HIS233 3.1 24.3 1.0 CE1 A:HIS239 3.1 23.8 1.0 CD2 A:HIS239 3.1 24.1 1.0 CE1 A:HIS233 3.2 24.4 1.0 NE2 A:GLN226 3.5 24.1 1.0 CG A:HIS233 4.2 24.5 1.0 ND1 A:HIS239 4.2 23.8 1.0 CB A:ASP388 4.3 23.7 1.0 ND1 A:HIS233 4.3 24.5 1.0 CG A:HIS239 4.3 24.0 1.0 CD A:GLN226 4.6 24.2 1.0 O A:HOH2098 4.7 44.3 1.0 CA A:ASP388 4.9 23.8 1.0 CG2 A:THR238 4.9 24.0 1.0 O A:HOH2226 5.0 29.0 1.0

Iron binding site 4 out of 36 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl


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 II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe460 b:26.2 occ:1.00 FE1 C:FES460 0.0 26.2 1.0 S1 C:FES460 2.2 26.3 1.0 S2 C:FES460 2.2 26.6 1.0 SG C:CYS120 2.2 25.8 1.0 SG C:CYS100 2.4 26.2 1.0 FE2 C:FES460 2.8 26.7 1.0 CB C:CYS120 3.1 25.9 1.0 CB C:CYS100 3.2 25.9 1.0 CB C:HIS102 4.2 27.0 1.0 CB C:MET105 4.3 25.5 1.0 CB C:TYR122 4.4 26.0 1.0 ND1 C:HIS102 4.5 27.1 1.0 N C:HIS123 4.5 26.4 1.0 CA C:CYS120 4.5 25.7 1.0 CB C:TRP125 4.6 26.7 1.0 ND1 C:HIS123 4.6 26.8 1.0 CA C:CYS100 4.6 25.9 1.0 CG C:TRP125 4.8 27.0 1.0 N C:ARG103 4.8 26.7 1.0 CG C:HIS102 4.8 27.2 1.0 N C:MET105 4.9 25.7 1.0 OH C:TYR127 5.0 26.2 1.0

Iron binding site 5 out of 36 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl


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 II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe460 b:26.7 occ:1.00 FE2 C:FES460 0.0 26.7 1.0 ND1 C:HIS102 2.1 27.1 1.0 ND1 C:HIS123 2.1 26.8 1.0 S2 C:FES460 2.2 26.6 1.0 S1 C:FES460 2.2 26.3 1.0 FE1 C:FES460 2.8 26.2 1.0 CG C:HIS123 3.1 27.0 1.0 CE1 C:HIS123 3.1 26.9 1.0 CE1 C:HIS102 3.1 27.4 1.0 CG C:HIS102 3.1 27.2 1.0 CB C:HIS123 3.4 27.0 1.0 CB C:HIS102 3.4 27.0 1.0 N C:HIS123 3.8 26.4 1.0 CB C:TYR122 4.1 26.0 1.0 CA C:HIS123 4.1 26.7 1.0 NE2 C:HIS123 4.2 27.1 1.0 N C:ARG103 4.2 26.7 1.0 CD2 C:HIS123 4.2 27.1 1.0 NE2 C:HIS102 4.2 27.6 1.0 CD2 C:HIS102 4.2 27.5 1.0 CG C:TYR122 4.4 26.1 1.0 CD2 C:TYR122 4.5 26.2 1.0 SG C:CYS120 4.5 25.8 1.0 SG C:CYS100 4.5 26.2 1.0 CB C:ARG103 4.5 26.7 1.0 C C:TYR122 4.6 26.3 1.0 CA C:HIS102 4.6 27.0 1.0 C C:HIS102 4.7 26.9 1.0 C C:HIS123 4.9 26.8 1.0 CA C:TYR122 4.9 26.0 1.0 CA C:ARG103 5.0 26.6 1.0

Iron binding site 6 out of 36 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl


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 II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe461 b:25.9 occ:1.00 OD1 C:ASP388 1.7 24.6 1.0 NE2 C:HIS239 1.9 24.4 1.0 NE2 C:HIS233 2.1 24.6 1.0 O C:HOH2244 2.2 26.1 1.0 CG C:ASP388 2.7 24.9 1.0 CD2 C:HIS239 2.9 24.6 1.0 CE1 C:HIS239 3.0 24.3 1.0 OD2 C:ASP388 3.0 24.9 1.0 CD2 C:HIS233 3.1 24.7 1.0 CE1 C:HIS233 3.1 24.7 1.0 NE2 C:GLN226 3.6 24.4 1.0 CB C:ASP388 4.0 24.9 1.0 CG C:HIS239 4.0 24.6 1.0 ND1 C:HIS239 4.1 24.4 1.0 ND1 C:HIS233 4.2 24.9 1.0 C15 C:BNL462 4.2 33.8 1.0 CG C:HIS233 4.2 24.9 1.0 C14 C:BNL462 4.3 33.5 1.0 CG2 C:THR238 4.5 24.6 1.0 CD C:GLN226 4.5 24.5 1.0 C1 C:BNL462 4.7 35.6 1.0 CA C:ASP388 4.7 25.0 1.0 C16 C:BNL462 4.8 34.3 1.0 CB C:ALA234 5.0 25.1 1.0 C13 C:BNL462 5.0 33.1 1.0

Iron binding site 7 out of 36 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl


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 II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe460 b:24.8 occ:1.00 FE1 E:FES460 0.0 24.8 1.0 S2 E:FES460 2.2 25.2 1.0 S1 E:FES460 2.2 24.6 1.0 SG E:CYS120 2.3 24.4 1.0 SG E:CYS100 2.3 25.1 1.0 FE2 E:FES460 2.8 25.0 1.0 CB E:CYS100 3.1 24.8 1.0 CB E:CYS120 3.2 24.7 1.0 CB E:HIS102 4.1 25.5 1.0 CB E:MET105 4.2 23.9 1.0 CB E:TYR122 4.4 24.1 1.0 ND1 E:HIS102 4.5 25.4 1.0 N E:HIS123 4.5 24.7 1.0 CA E:CYS100 4.5 24.9 1.0 ND1 E:HIS123 4.6 24.9 1.0 CA E:CYS120 4.6 24.6 1.0 CB E:TRP125 4.7 25.9 1.0 N E:ARG103 4.8 24.9 1.0 CG E:TRP125 4.8 26.0 1.0 N E:MET105 4.8 24.0 1.0 CG E:HIS102 4.8 25.5 1.0

Iron binding site 8 out of 36 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl


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 II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe460 b:25.0 occ:1.00 FE2 E:FES460 0.0 25.0 1.0 ND1 E:HIS123 2.1 24.9 1.0 ND1 E:HIS102 2.2 25.4 1.0 S2 E:FES460 2.2 25.2 1.0 S1 E:FES460 2.2 24.6 1.0 FE1 E:FES460 2.8 24.8 1.0 CE1 E:HIS123 3.1 24.7 1.0 CG E:HIS123 3.1 25.0 1.0 CG E:HIS102 3.1 25.5 1.0 CE1 E:HIS102 3.2 25.5 1.0 CB E:HIS102 3.4 25.5 1.0 CB E:HIS123 3.4 25.3 1.0 N E:HIS123 3.8 24.7 1.0 CB E:TYR122 4.1 24.1 1.0 NE2 E:HIS123 4.2 24.8 1.0 CA E:HIS123 4.2 25.1 1.0 CD2 E:HIS123 4.2 25.0 1.0 N E:ARG103 4.2 24.9 1.0 CD2 E:HIS102 4.3 25.8 1.0 NE2 E:HIS102 4.3 25.7 1.0 SG E:CYS100 4.4 25.1 1.0 CG E:TYR122 4.4 24.1 1.0 SG E:CYS120 4.5 24.4 1.0 CD2 E:TYR122 4.5 24.0 1.0 CB E:ARG103 4.5 24.6 1.0 CA E:HIS102 4.6 25.5 1.0 C E:TYR122 4.6 24.5 1.0 C E:HIS102 4.7 25.2 1.0 CA E:TYR122 4.9 24.2 1.0 CD1 E:TRP125 4.9 26.1 1.0 CA E:ARG103 5.0 24.7 1.0 C E:HIS123 5.0 25.3 1.0

Iron binding site 9 out of 36 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl


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 II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe461 b:31.1 occ:1.00 OD1 E:ASP388 1.8 27.9 1.0 NE2 E:HIS239 2.0 26.6 1.0 O E:HOH2167 2.0 34.1 1.0 NE2 E:HIS233 2.1 27.2 1.0 CG E:ASP388 2.6 28.4 1.0 OD2 E:ASP388 2.8 28.5 1.0 CD2 E:HIS239 2.9 26.8 1.0 CE1 E:HIS239 3.0 26.3 1.0 CD2 E:HIS233 3.1 27.3 1.0 CE1 E:HIS233 3.1 27.5 1.0 NE2 E:GLN226 3.7 24.8 1.0 C15 E:BNL462 4.0 51.2 1.0 CG E:HIS239 4.1 26.7 1.0 ND1 E:HIS239 4.1 26.4 1.0 CB E:ASP388 4.1 28.2 1.0 ND1 E:HIS233 4.2 27.7 1.0 CG E:HIS233 4.2 27.6 1.0 C1 E:BNL462 4.3 49.1 1.0 C2 E:BNL462 4.5 50.2 1.0 C6 E:BNL462 4.7 48.7 1.0 CD E:GLN226 4.7 25.0 1.0 CA E:ASP388 4.7 28.6 1.0 C16 E:BNL462 4.8 51.4 1.0 CB E:ALA234 4.8 28.5 1.0 C14 E:BNL462 4.9 51.8 1.0 CG2 E:THR238 4.9 26.4 1.0

Iron binding site 10 out of 36 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl


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 II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with Biphenyl within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe460 b:33.9 occ:1.00 FE1 G:FES460 0.0 33.9 1.0 SG G:CYS120 1.7 42.1 1.0 SG G:CYS100 1.8 42.2 1.0 S1 G:FES460 2.2 34.2 1.0 S2 G:FES460 2.2 35.3 1.0 FE2 G:FES460 2.9 35.7 1.0 CB G:CYS120 3.0 41.3 1.0 CB G:CYS100 3.0 38.8 1.0 CB G:MET105 4.2 32.7 1.0 CB G:HIS102 4.2 37.1 1.0 CA G:CYS120 4.3 40.1 1.0 CB G:TYR122 4.3 36.4 1.0 CA G:CYS100 4.4 37.3 1.0 N G:HIS123 4.5 37.0 1.0 ND1 G:HIS102 4.7 37.0 1.0 ND1 G:HIS123 4.7 37.0 1.0 CB G:TRP125 4.7 38.0 1.0 N G:ARG103 4.8 36.3 1.0 N G:MET105 4.8 33.2 1.0 C G:CYS120 4.9 39.7 1.0 CG G:TRP125 4.9 38.2 1.0 CG G:HIS102 4.9 37.3 1.0

S.Dhindwal, L.Gomez-Gil, D.B.Neau, T.T.M.Pham, M.Sylvestre, L.D.Eltis, J.T.Bolin, P.Kumar. Structural Basis of the Enhanced Pollutant-Degrading Capabilities of An Engineered Biphenyl Dioxygenase. J.Bacteriol. V. 198 1499 2016.
ISSN: ISSN 0021-9193
PubMed: 26953337
DOI: 10.1128/JB.00952-15