Iron in PDB 2yfl: Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran

All present enzymatic activity of Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran:
1.14.12.18;

The structure of Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran, PDB code: 2yfl 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)	137.36 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.556, 275.982, 92.057, 90.00, 117.46, 90.00
R / Rfree (%)	21.493 / 28.023

The structure of Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran (pdb code 2yfl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran, PDB code: 2yfl:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran


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 Variant RR41 with 2-Chloro Dibenzofuran within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe900 b:48.6 occ:1.00 FE1 A:FES900 0.0 48.6 1.0 ND1 A:HIS102 2.0 49.5 1.0 ND1 A:HIS123 2.1 49.2 1.0 S1 A:FES900 2.2 46.3 1.0 S2 A:FES900 2.2 46.0 1.0 CG A:HIS123 2.9 50.3 1.0 CE1 A:HIS102 3.0 50.0 1.0 CG A:HIS102 3.0 50.1 1.0 FE2 A:FES900 3.0 46.3 1.0 CE1 A:HIS123 3.1 49.1 1.0 CB A:HIS123 3.2 50.7 1.0 CB A:HIS102 3.4 49.2 1.0 N A:HIS123 3.8 48.9 1.0 CD2 A:HIS123 4.0 51.0 1.0 NE2 A:HIS102 4.0 51.0 1.0 NE2 A:HIS123 4.1 49.7 1.0 CD2 A:HIS102 4.1 51.2 1.0 CA A:HIS123 4.1 50.3 1.0 CB A:TYR122 4.1 45.6 1.0 N A:ARG103 4.3 48.1 1.0 CG A:TYR122 4.4 45.2 1.0 SG A:CYS100 4.5 46.3 1.0 SG A:CYS120 4.5 45.5 1.0 CB A:ARG103 4.5 48.1 1.0 CD2 A:TYR122 4.6 44.2 1.0 C A:TYR122 4.6 48.1 1.0 CA A:HIS102 4.7 49.0 1.0 C A:HIS102 4.8 48.8 1.0 NE1 A:TRP125 4.8 52.7 1.0 CD1 A:TRP125 4.8 52.4 1.0 C A:HIS123 5.0 51.2 1.0 CA A:TYR122 5.0 46.5 1.0

Iron binding site 2 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran


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 Variant RR41 with 2-Chloro Dibenzofuran within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe900 b:46.3 occ:1.00 FE2 A:FES900 0.0 46.3 1.0 SG A:CYS100 2.1 46.3 1.0 S2 A:FES900 2.2 46.0 1.0 S1 A:FES900 2.2 46.3 1.0 SG A:CYS120 2.3 45.5 1.0 CB A:CYS100 3.0 44.9 1.0 FE1 A:FES900 3.0 48.6 1.0 CB A:CYS120 3.1 46.1 1.0 CB A:HIS102 4.0 49.2 1.0 CA A:CYS100 4.4 44.6 1.0 CB A:TYR122 4.5 45.6 1.0 ND1 A:HIS102 4.5 49.5 1.0 CB A:MET105 4.5 46.0 1.0 CB A:TRP125 4.5 50.4 1.0 CA A:CYS120 4.6 46.0 1.0 CG A:TRP125 4.7 51.4 1.0 N A:HIS123 4.7 48.9 1.0 ND1 A:HIS123 4.7 49.2 1.0 CG A:HIS102 4.7 50.1 1.0 OH A:TYR127 4.7 46.9 1.0 N A:ARG103 4.7 48.1 1.0 C A:CYS100 4.8 45.1 1.0 N A:HIS102 4.9 48.1 1.0 CD2 A:TRP125 5.0 51.4 1.0 N A:MET105 5.0 45.8 1.0 O A:CYS100 5.0 44.8 1.0

Iron binding site 3 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran


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 Variant RR41 with 2-Chloro Dibenzofuran within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe901 b:40.9 occ:1.00 O A:HOH2030 1.7 52.4 1.0 NE2 A:HIS239 2.0 37.6 1.0 OD1 A:ASP388 2.0 46.2 1.0 NE2 A:HIS233 2.1 44.2 1.0 OD2 A:ASP388 2.3 45.5 1.0 CG A:ASP388 2.5 45.5 1.0 CE1 A:HIS239 2.9 37.9 1.0 CD2 A:HIS239 3.1 39.0 1.0 CD2 A:HIS233 3.1 44.3 1.0 CE1 A:HIS233 3.2 44.4 1.0 OE1 A:GLN226 3.4 44.2 1.0 O A:HOH2042 3.5 40.6 1.0 CD A:GLN226 3.9 44.4 1.0 NE2 A:GLN226 4.0 44.4 1.0 CB A:ASP388 4.0 45.0 1.0 CAE A:DC41460 4.0 49.7 0.5 ND1 A:HIS239 4.1 39.3 1.0 CG A:HIS239 4.2 40.1 1.0 CG A:HIS233 4.2 44.7 1.0 ND1 A:HIS233 4.2 44.3 1.0 CAK A:DC41460 4.2 49.8 0.5 OAI A:DC41460 4.3 49.7 0.5 CG2 A:THR238 4.5 41.1 1.0 CAB A:DC41460 4.7 49.6 0.5 CA A:ASP388 4.8 45.3 1.0 CG A:GLN226 4.9 44.1 1.0

Iron binding site 4 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran


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 Variant RR41 with 2-Chloro Dibenzofuran within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe900 b:49.9 occ:1.00 FE1 C:FES900 0.0 49.9 1.0 ND1 C:HIS123 2.0 45.2 1.0 ND1 C:HIS102 2.1 46.9 1.0 S2 C:FES900 2.2 49.1 1.0 S1 C:FES900 2.2 46.2 1.0 CG C:HIS123 2.9 47.2 1.0 CE1 C:HIS123 3.0 44.7 1.0 FE2 C:FES900 3.0 51.0 1.0 CE1 C:HIS102 3.1 47.5 1.0 CG C:HIS102 3.1 46.9 1.0 CB C:HIS123 3.3 48.6 1.0 CB C:HIS102 3.4 46.1 1.0 N C:HIS123 3.9 47.3 1.0 NE2 C:HIS123 4.0 45.9 1.0 CD2 C:HIS123 4.0 47.2 1.0 CB C:TYR122 4.1 44.9 1.0 N C:ARG103 4.1 44.5 1.0 CA C:HIS123 4.2 48.6 1.0 NE2 C:HIS102 4.2 48.4 1.0 CD2 C:HIS102 4.2 48.1 1.0 CB C:ARG103 4.3 44.4 1.0 CD2 C:TYR122 4.3 43.2 1.0 CG C:TYR122 4.3 44.2 1.0 SG C:CYS100 4.5 45.9 1.0 SG C:CYS120 4.6 46.2 1.0 CA C:HIS102 4.7 45.9 1.0 C C:TYR122 4.7 46.8 1.0 C C:HIS102 4.8 45.2 1.0 CA C:ARG103 4.8 44.0 1.0

Iron binding site 5 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran


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 Variant RR41 with 2-Chloro Dibenzofuran within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe900 b:51.0 occ:1.00 FE2 C:FES900 0.0 51.0 1.0 SG C:CYS120 2.1 46.2 1.0 S1 C:FES900 2.2 46.2 1.0 S2 C:FES900 2.2 49.1 1.0 SG C:CYS100 2.5 45.9 1.0 CB C:CYS100 2.9 43.8 1.0 FE1 C:FES900 3.0 49.9 1.0 CB C:CYS120 3.2 47.2 1.0 CB C:MET105 4.0 41.6 1.0 CB C:TYR122 4.2 44.9 1.0 CB C:HIS102 4.3 46.1 1.0 CA C:CYS100 4.4 43.7 1.0 N C:HIS123 4.5 47.3 1.0 ND1 C:HIS123 4.6 45.2 1.0 ND1 C:HIS102 4.6 46.9 1.0 CA C:CYS120 4.6 47.1 1.0 N C:MET105 4.7 41.7 1.0 CB C:TRP125 4.8 50.3 1.0 CA C:MET105 4.8 41.3 1.0 O C:MET105 4.8 41.9 1.0 N C:ARG103 4.9 44.5 1.0 CG C:MET105 4.9 40.9 0.5 CG C:HIS102 4.9 46.9 1.0 C C:CYS100 5.0 43.8 1.0

Iron binding site 6 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran


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 Variant RR41 with 2-Chloro Dibenzofuran within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe901 b:57.5 occ:1.00 O C:HOH2027 1.5 32.4 1.0 NE2 C:HIS233 1.9 49.6 1.0 OD1 C:ASP388 2.0 51.0 1.0 NE2 C:HIS239 2.1 50.7 1.0 CG C:ASP388 2.7 50.6 1.0 OE1 C:GLN226 2.8 50.5 1.0 OD2 C:ASP388 2.8 50.8 1.0 CD2 C:HIS233 2.9 50.3 1.0 CE1 C:HIS233 3.0 50.5 1.0 CE1 C:HIS239 3.0 50.1 1.0 CD2 C:HIS239 3.2 51.4 1.0 CAH C:DC41460 3.6 53.6 0.5 CD C:GLN226 3.7 50.1 1.0 CAN C:DC41460 4.0 53.7 0.5 CAJ C:DC41460 4.0 53.6 0.5 ND1 C:HIS233 4.1 51.4 1.0 CG C:HIS233 4.1 51.6 1.0 CB C:ASP388 4.1 49.6 1.0 ND1 C:HIS239 4.2 51.2 1.0 CG C:HIS239 4.3 51.9 1.0 NE2 C:GLN226 4.3 49.9 1.0 CAM C:DC41460 4.4 53.7 0.5 CG2 C:THR238 4.5 51.0 1.0 CL1 C:DC41460 4.6 53.7 0.5 CG C:GLN226 4.6 50.1 1.0 CAF C:DC41460 4.6 53.7 0.5 CAL C:DC41460 4.7 53.7 0.5 CAD C:DC41460 4.7 53.6 0.5 CA C:ASP388 4.9 49.6 1.0 CAG C:DC41460 5.0 53.6 0.5

Iron binding site 7 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran


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 Variant RR41 with 2-Chloro Dibenzofuran within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe900 b:41.4 occ:1.00 FE1 E:FES900 0.0 41.4 1.0 ND1 E:HIS123 2.1 40.5 1.0 S2 E:FES900 2.2 40.5 1.0 S1 E:FES900 2.2 40.6 1.0 ND1 E:HIS102 2.2 42.1 1.0 FE2 E:FES900 3.0 41.4 1.0 CG E:HIS123 3.0 41.3 1.0 CE1 E:HIS123 3.0 40.6 1.0 CG E:HIS102 3.1 42.3 1.0 CE1 E:HIS102 3.2 42.5 1.0 CB E:HIS123 3.4 42.1 1.0 CB E:HIS102 3.4 41.3 1.0 N E:HIS123 3.9 41.0 1.0 NE2 E:HIS123 4.1 41.5 1.0 CD2 E:HIS123 4.1 41.8 1.0 CB E:TYR122 4.2 38.9 1.0 N E:ARG103 4.2 40.1 1.0 CA E:HIS123 4.2 41.9 1.0 CD2 E:HIS102 4.3 43.3 1.0 NE2 E:HIS102 4.3 43.0 1.0 CB E:ARG103 4.5 40.2 1.0 CG E:TYR122 4.6 38.9 1.0 SG E:CYS120 4.6 38.5 1.0 SG E:CYS100 4.6 39.1 1.0 CA E:HIS102 4.6 41.2 1.0 CD2 E:TYR122 4.6 37.9 1.0 C E:TYR122 4.7 40.6 1.0 C E:HIS102 4.7 40.7 1.0 CA E:ARG103 4.9 39.8 1.0

Iron binding site 8 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran


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 Variant RR41 with 2-Chloro Dibenzofuran within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe900 b:41.4 occ:1.00 FE2 E:FES900 0.0 41.4 1.0 S1 E:FES900 2.2 40.6 1.0 S2 E:FES900 2.2 40.5 1.0 SG E:CYS120 2.2 38.5 1.0 SG E:CYS100 2.5 39.1 1.0 FE1 E:FES900 3.0 41.4 1.0 CB E:CYS100 3.0 38.4 1.0 CB E:CYS120 3.1 39.1 1.0 CB E:MET105 4.1 37.1 1.0 CB E:HIS102 4.4 41.3 1.0 CB E:TYR122 4.4 38.9 1.0 CA E:CYS100 4.5 38.3 1.0 CA E:CYS120 4.5 39.0 1.0 N E:HIS123 4.6 41.0 1.0 CB E:TRP125 4.6 42.4 1.0 ND1 E:HIS123 4.7 40.5 1.0 N E:MET105 4.8 37.5 1.0 ND1 E:HIS102 4.8 42.1 1.0 CG E:TRP125 4.9 42.8 1.0 O E:MET105 4.9 37.7 1.0 CA E:MET105 4.9 37.3 1.0 N E:ARG103 4.9 40.1 1.0 CG E:MET105 4.9 35.9 0.5 N E:TYR122 5.0 39.2 1.0

Iron binding site 9 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran


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 Variant RR41 with 2-Chloro Dibenzofuran within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe901 b:41.4 occ:1.00 O E:HOH2035 2.0 40.9 1.0 NE2 E:HIS239 2.1 46.4 1.0 NE2 E:HIS233 2.1 49.8 1.0 OD1 E:ASP388 2.3 49.3 1.0 OD2 E:ASP388 2.8 49.1 1.0 CG E:ASP388 2.9 48.6 1.0 CD2 E:HIS239 3.0 48.1 1.0 CD2 E:HIS233 3.0 49.8 1.0 OE1 E:GLN226 3.0 51.4 1.0 CE1 E:HIS239 3.1 46.9 1.0 CE1 E:HIS233 3.1 50.1 1.0 CD E:GLN226 3.7 51.0 1.0 NE2 E:GLN226 4.0 51.3 1.0 ND1 E:HIS239 4.2 47.7 1.0 CG E:HIS239 4.2 48.4 1.0 ND1 E:HIS233 4.2 51.0 1.0 CG E:HIS233 4.2 50.8 1.0 CB E:ASP388 4.4 47.9 1.0 CG2 E:THR238 4.7 47.9 1.0 CG E:GLN226 4.8 50.5 1.0 CD2 E:PHE384 4.9 49.6 1.0 CA E:ASP388 4.9 48.1 1.0

Iron binding site 10 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 with 2-Chloro Dibenzofuran


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 Variant RR41 with 2-Chloro Dibenzofuran within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe900 b:68.5 occ:1.00 FE1 G:FES900 0.0 68.5 1.0 ND1 G:HIS123 1.9 76.6 1.0 S1 G:FES900 2.2 65.7 1.0 S2 G:FES900 2.2 67.1 1.0 ND1 G:HIS102 2.3 72.3 1.0 CG G:HIS123 2.8 78.6 1.0 CE1 G:HIS123 2.9 75.9 1.0 FE2 G:FES900 3.0 68.5 1.0 CE1 G:HIS102 3.1 73.7 1.0 CB G:HIS123 3.1 80.4 1.0 CG G:HIS102 3.2 73.6 1.0 O G:HOH2004 3.3 0.1 1.0 CB G:HIS102 3.5 72.7 1.0 N G:HIS123 3.7 77.2 1.0 CD2 G:HIS123 4.0 78.9 1.0 NE2 G:HIS123 4.0 77.4 1.0 CA G:HIS123 4.0 79.7 1.0 CB G:TYR122 4.1 72.1 1.0 NE2 G:HIS102 4.1 76.0 1.0 CD2 G:HIS102 4.2 76.4 1.0 CB G:ARG103 4.2 68.1 1.0 N G:ARG103 4.3 69.2 1.0 CG G:TYR122 4.4 71.5 1.0 CD2 G:TYR122 4.5 70.4 1.0 C G:TYR122 4.5 75.5 1.0 SG G:CYS100 4.6 67.7 1.0 C G:HIS102 4.7 70.7 1.0 CA G:HIS102 4.7 72.2 1.0 CA G:ARG103 4.8 68.0 1.0 CA G:TYR122 4.9 73.1 1.0 C G:HIS123 4.9 81.7 1.0

P.Kumar, M.Mohammadi, S.Dhindwal, T.T.Pham, J.T.Bolin, M.Sylvestre. Structural Insights Into the Metabolism of 2- Chlorodibenzofuran By An Evolved Biphenyl Dioxygenase. Biochem.Biophys.Res.Commun. V. 421 757 2012.
ISSN: ISSN 0006-291X
PubMed: 22546558
DOI: 10.1016/J.BBRC.2012.04.078