Iron in PDB 2yfi: Crystal Structure of Biphenyl Dioxygenase Variant RR41 (Bpdo-RR41)

All present enzymatic activity of Crystal Structure of Biphenyl Dioxygenase Variant RR41 (Bpdo-RR41):
1.14.12.18;

The structure of Crystal Structure of Biphenyl Dioxygenase Variant RR41 (Bpdo-RR41), PDB code: 2yfi 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)	138.68 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.969, 277.808, 92.933, 90.00, 117.61, 90.00
R / Rfree (%)	19.992 / 23.163

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 (Bpdo-RR41) (pdb code 2yfi). 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 (Bpdo-RR41), PDB code: 2yfi:
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 (Bpdo-RR41)


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 (Bpdo-RR41) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe900 b:30.5 occ:1.00 FE1 A:FES900 0.0 30.5 1.0 ND1 A:HIS102 2.1 37.4 1.0 ND1 A:HIS123 2.1 39.4 1.0 S2 A:FES900 2.2 31.9 1.0 S1 A:FES900 2.2 29.6 1.0 FE2 A:FES900 2.9 29.5 1.0 CG A:HIS123 3.0 39.1 1.0 CE1 A:HIS102 3.1 37.9 1.0 CG A:HIS102 3.1 37.9 1.0 CE1 A:HIS123 3.1 39.5 1.0 CB A:HIS123 3.3 39.7 1.0 CB A:HIS102 3.4 37.7 1.0 N A:HIS123 3.8 40.0 1.0 CB A:TYR122 4.1 40.4 1.0 CA A:HIS123 4.2 39.9 1.0 NE2 A:HIS102 4.2 37.9 1.0 CD2 A:HIS123 4.2 39.4 1.0 N A:ARG103 4.2 38.5 1.0 NE2 A:HIS123 4.2 39.0 1.0 CD2 A:HIS102 4.2 38.1 1.0 CG A:TYR122 4.4 40.1 1.0 CB A:ARG103 4.5 39.0 1.0 CD2 A:TYR122 4.5 39.6 1.0 SG A:CYS120 4.5 41.4 1.0 SG A:CYS100 4.6 37.8 1.0 CA A:HIS102 4.6 37.9 1.0 C A:TYR122 4.7 40.3 1.0 C A:HIS102 4.7 38.1 1.0 CA A:ARG103 4.9 38.9 1.0 CA A:TYR122 5.0 40.4 1.0

Iron binding site 2 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 (Bpdo-RR41)


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 (Bpdo-RR41) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe900 b:29.5 occ:1.00 FE2 A:FES900 0.0 29.5 1.0 S1 A:FES900 2.2 29.6 1.0 SG A:CYS120 2.2 41.4 1.0 S2 A:FES900 2.2 31.9 1.0 SG A:CYS100 2.4 37.8 1.0 FE1 A:FES900 2.9 30.5 1.0 CB A:CYS100 3.0 37.3 1.0 CB A:CYS120 3.2 41.6 1.0 CB A:HIS102 4.1 37.7 1.0 CB A:MET105 4.3 38.6 1.0 CB A:TYR122 4.4 40.4 1.0 CA A:CYS100 4.5 37.5 1.0 ND1 A:HIS102 4.5 37.4 1.0 CB A:TRP125 4.5 40.2 1.0 N A:HIS123 4.6 40.0 1.0 CA A:CYS120 4.6 41.6 1.0 ND1 A:HIS123 4.7 39.4 1.0 CG A:HIS102 4.8 37.9 1.0 CG A:TRP125 4.8 40.4 1.0 N A:ARG103 4.8 38.5 1.0 N A:MET105 4.9 39.2 1.0 OH A:TYR127 5.0 39.3 1.0

Iron binding site 3 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 (Bpdo-RR41)


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 (Bpdo-RR41) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe901 b:40.4 occ:1.00 O A:HOH2125 1.8 41.0 1.0 OD1 A:ASP388 2.0 46.0 1.0 NE2 A:HIS239 2.1 40.0 1.0 NE2 A:HIS233 2.2 40.4 1.0 CG A:ASP388 2.7 45.4 1.0 OD2 A:ASP388 2.9 45.3 1.0 CE1 A:HIS239 3.0 40.4 1.0 CD2 A:HIS233 3.1 40.4 1.0 OE1 A:GLN226 3.1 46.0 1.0 CD2 A:HIS239 3.1 40.1 1.0 CE1 A:HIS233 3.3 40.1 1.0 O A:HOH2057 3.8 59.7 1.0 CD A:GLN226 4.0 44.4 1.0 ND1 A:HIS239 4.1 39.8 1.0 CB A:ASP388 4.2 45.4 1.0 CG A:HIS239 4.2 39.8 1.0 CG A:HIS233 4.3 40.3 1.0 ND1 A:HIS233 4.3 40.4 1.0 NE2 A:GLN226 4.6 45.5 1.0 O A:HOH2171 4.7 45.0 1.0 CG2 A:THR238 4.7 40.1 1.0 CA A:ASP388 4.8 45.3 1.0 O A:HOH2123 5.0 50.6 1.0

Iron binding site 4 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 (Bpdo-RR41)


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 (Bpdo-RR41) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe900 b:35.5 occ:1.00 FE1 C:FES900 0.0 35.5 1.0 ND1 C:HIS123 2.0 38.2 1.0 S1 C:FES900 2.2 35.0 1.0 S2 C:FES900 2.2 35.9 1.0 ND1 C:HIS102 2.2 39.6 1.0 FE2 C:FES900 3.0 33.6 1.0 CG C:HIS123 3.0 38.5 1.0 CE1 C:HIS123 3.0 38.2 1.0 CG C:HIS102 3.2 39.5 1.0 CE1 C:HIS102 3.2 39.8 1.0 CB C:HIS123 3.3 38.7 1.0 CB C:HIS102 3.5 39.1 1.0 N C:HIS123 3.8 38.8 1.0 CB C:TYR122 4.0 39.2 1.0 NE2 C:HIS123 4.1 37.9 1.0 CD2 C:HIS123 4.1 38.0 1.0 CA C:HIS123 4.1 38.7 1.0 N C:ARG103 4.3 39.3 1.0 NE2 C:HIS102 4.3 40.0 1.0 CG C:TYR122 4.3 39.0 1.0 CD2 C:HIS102 4.3 39.8 1.0 CD2 C:TYR122 4.4 39.0 1.0 SG C:CYS100 4.5 38.9 1.0 SG C:CYS120 4.6 40.4 1.0 CB C:ARG103 4.6 39.6 1.0 C C:TYR122 4.6 39.1 1.0 CA C:HIS102 4.7 39.1 1.0 C C:HIS102 4.7 39.2 1.0 CA C:TYR122 4.9 39.2 1.0

Iron binding site 5 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 (Bpdo-RR41)


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 (Bpdo-RR41) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe900 b:33.6 occ:1.00 FE2 C:FES900 0.0 33.6 1.0 S2 C:FES900 2.2 35.9 1.0 S1 C:FES900 2.2 35.0 1.0 SG C:CYS100 2.2 38.9 1.0 SG C:CYS120 2.3 40.4 1.0 FE1 C:FES900 3.0 35.5 1.0 CB C:CYS100 3.0 38.6 1.0 CB C:CYS120 3.1 40.1 1.0 CB C:HIS102 4.2 39.1 1.0 CB C:MET105 4.3 38.8 1.0 CB C:TYR122 4.4 39.2 1.0 CA C:CYS100 4.5 38.6 1.0 CB C:TRP125 4.5 38.2 1.0 CA C:CYS120 4.6 40.2 1.0 N C:HIS123 4.6 38.8 1.0 ND1 C:HIS102 4.6 39.6 1.0 ND1 C:HIS123 4.7 38.2 1.0 CG C:TRP125 4.8 37.9 1.0 N C:ARG103 4.9 39.3 1.0 N C:MET105 4.9 39.1 1.0 CG C:HIS102 4.9 39.5 1.0 C C:CYS100 4.9 38.6 1.0 OH C:TYR127 5.0 39.4 1.0

Iron binding site 6 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 (Bpdo-RR41)


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 (Bpdo-RR41) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe901 b:39.2 occ:1.00 OD1 C:ASP388 1.9 47.6 1.0 NE2 C:HIS239 2.0 39.4 1.0 NE2 C:HIS233 2.1 40.7 1.0 O C:HOH2165 2.3 47.8 1.0 CG C:ASP388 2.8 47.7 1.0 OD2 C:ASP388 2.9 49.0 1.0 CE1 C:HIS239 3.0 39.0 1.0 CD2 C:HIS239 3.0 39.4 1.0 CE1 C:HIS233 3.1 40.4 1.0 CD2 C:HIS233 3.1 40.8 1.0 O C:HOH2081 3.2 46.0 1.0 OE1 C:GLN226 3.4 45.7 1.0 ND1 C:HIS239 4.1 39.4 1.0 CD C:GLN226 4.2 43.5 1.0 CG C:HIS239 4.2 39.8 1.0 ND1 C:HIS233 4.2 40.4 1.0 CB C:ASP388 4.2 47.1 1.0 CG C:HIS233 4.2 40.8 1.0 NE2 C:GLN226 4.7 44.0 1.0 O C:HOH2161 4.7 48.4 1.0 CG2 C:THR238 4.8 40.3 1.0 CD2 C:PHE384 4.9 45.4 1.0 CA C:ASP388 4.9 47.2 1.0 O C:HOH2110 5.0 40.5 1.0

Iron binding site 7 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 (Bpdo-RR41)


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 (Bpdo-RR41) within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe900 b:35.6 occ:1.00 FE1 E:FES900 0.0 35.6 1.0 ND1 E:HIS123 2.0 36.8 1.0 ND1 E:HIS102 2.1 38.2 1.0 S2 E:FES900 2.2 35.7 1.0 S1 E:FES900 2.2 35.1 1.0 CG E:HIS123 3.0 37.2 1.0 FE2 E:FES900 3.0 35.3 1.0 CE1 E:HIS123 3.0 36.5 1.0 CE1 E:HIS102 3.1 38.3 1.0 CG E:HIS102 3.1 38.2 1.0 CB E:HIS123 3.3 37.9 1.0 CB E:HIS102 3.4 38.1 1.0 N E:HIS123 3.8 38.1 1.0 CD2 E:HIS123 4.1 36.3 1.0 CB E:TYR122 4.1 38.5 1.0 NE2 E:HIS123 4.1 36.4 1.0 CA E:HIS123 4.1 37.9 1.0 NE2 E:HIS102 4.2 38.4 1.0 CD2 E:HIS102 4.2 38.1 1.0 N E:ARG103 4.2 38.5 1.0 CG E:TYR122 4.4 38.2 1.0 CD2 E:TYR122 4.4 38.3 1.0 SG E:CYS100 4.5 38.0 1.0 SG E:CYS120 4.5 40.1 1.0 CB E:ARG103 4.6 38.8 1.0 C E:TYR122 4.7 38.3 1.0 CA E:HIS102 4.7 38.2 1.0 C E:HIS102 4.7 38.4 1.0 C E:HIS123 5.0 38.0 1.0 CA E:TYR122 5.0 38.5 1.0

Iron binding site 8 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 (Bpdo-RR41)


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 (Bpdo-RR41) within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe900 b:35.3 occ:1.00 FE2 E:FES900 0.0 35.3 1.0 SG E:CYS120 2.2 40.1 1.0 S2 E:FES900 2.2 35.7 1.0 S1 E:FES900 2.2 35.1 1.0 SG E:CYS100 2.3 38.0 1.0 FE1 E:FES900 3.0 35.6 1.0 CB E:CYS100 3.0 37.7 1.0 CB E:CYS120 3.1 40.7 1.0 CB E:HIS102 4.2 38.1 1.0 CB E:MET105 4.2 38.9 1.0 CB E:TYR122 4.4 38.5 1.0 CA E:CYS100 4.5 37.8 1.0 CB E:TRP125 4.5 37.5 1.0 CA E:CYS120 4.6 40.6 1.0 N E:HIS123 4.6 38.1 1.0 ND1 E:HIS102 4.6 38.2 1.0 ND1 E:HIS123 4.7 36.8 1.0 CG E:TRP125 4.8 36.9 1.0 N E:MET105 4.9 39.2 1.0 N E:ARG103 4.9 38.5 1.0 CG E:HIS102 4.9 38.2 1.0 C E:CYS100 5.0 37.9 1.0

Iron binding site 9 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 (Bpdo-RR41)


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 (Bpdo-RR41) within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe901 b:44.3 occ:1.00 OD1 E:ASP388 1.9 47.8 1.0 O E:HOH2091 1.9 46.3 1.0 NE2 E:HIS239 2.1 41.8 1.0 NE2 E:HIS233 2.2 41.3 1.0 CG E:ASP388 2.8 48.5 1.0 OD2 E:ASP388 3.0 48.9 1.0 CE1 E:HIS239 3.0 41.7 1.0 CE1 E:HIS233 3.1 41.3 1.0 CD2 E:HIS233 3.2 41.2 1.0 CD2 E:HIS239 3.2 41.5 1.0 OE1 E:GLN226 3.4 44.7 1.0 O E:HOH2039 3.8 66.2 1.0 CD E:GLN226 4.1 44.0 1.0 ND1 E:HIS239 4.2 41.9 1.0 CB E:ASP388 4.2 48.2 1.0 ND1 E:HIS233 4.3 41.1 1.0 CG E:HIS239 4.3 41.7 1.0 CG E:HIS233 4.3 41.5 1.0 NE2 E:GLN226 4.5 44.1 1.0 CG2 E:THR238 4.9 41.6 1.0 CA E:ASP388 4.9 48.3 1.0 CD2 E:PHE384 4.9 47.1 1.0

Iron binding site 10 out of 18 in the Crystal Structure of Biphenyl Dioxygenase Variant RR41 (Bpdo-RR41)


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 (Bpdo-RR41) within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe900 b:60.8 occ:1.00 FE1 G:FES900 0.0 60.8 1.0 ND1 G:HIS123 2.0 42.3 1.0 S2 G:FES900 2.2 60.7 1.0 S1 G:FES900 2.2 61.3 1.0 ND1 G:HIS102 2.5 44.6 1.0 CG G:HIS123 2.9 42.9 1.0 CE1 G:HIS123 3.0 42.5 1.0 FE2 G:FES900 3.1 60.9 1.0 CB G:HIS123 3.3 43.2 1.0 CG G:HIS102 3.4 44.6 1.0 CE1 G:HIS102 3.4 44.7 1.0 CB G:HIS102 3.6 44.7 1.0 N G:HIS123 3.8 43.5 1.0 CB G:TYR122 3.8 43.6 1.0 NE2 G:HIS123 4.0 42.7 1.0 CD2 G:HIS123 4.1 42.6 1.0 CG G:TYR122 4.1 43.5 1.0 CA G:HIS123 4.1 43.3 1.0 CD2 G:TYR122 4.2 43.6 1.0 N G:ARG103 4.3 44.9 1.0 C G:TYR122 4.5 43.6 1.0 CB G:ARG103 4.5 45.0 1.0 NE2 G:HIS102 4.5 44.7 1.0 CD2 G:HIS102 4.6 44.8 1.0 SG G:CYS120 4.6 44.4 1.0 SG G:CYS100 4.7 43.6 1.0 CA G:TYR122 4.7 43.6 1.0 CA G:HIS102 4.8 44.7 1.0 C G:HIS102 4.8 44.8 1.0 CD1 G:TYR122 5.0 43.2 1.0 CA G:ARG103 5.0 45.0 1.0

M.Mohammadi, J.Viger, P.Kumar, D.Barriault, J.T.Bolin, M.Sylvestre. Retuning Rieske-Type Oxygenases to Expand Substrate Range. J.Biol.Chem. V. 286 27612 2011.
ISSN: ISSN 0021-9258
PubMed: 21653696
DOI: 10.1074/JBC.M111.255174