Iron in PDB 3vb0: Crystal Structure of 2,2',3-Trihydroxybiphenyl 1,2-Dioxygenase From Dibenzofuran-Degrading Sphingomonas Wittichii Strain RW1

The structure of Crystal Structure of 2,2',3-Trihydroxybiphenyl 1,2-Dioxygenase From Dibenzofuran-Degrading Sphingomonas Wittichii Strain RW1, PDB code: 3vb0 was solved by M.Koksal, P.Kumar, J.T.Bolin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.85 / 2.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	131.587, 131.587, 103.146, 90.00, 90.00, 90.00
R / Rfree (%)	25.4 / 28.9

The binding sites of Iron atom in the Crystal Structure of 2,2',3-Trihydroxybiphenyl 1,2-Dioxygenase From Dibenzofuran-Degrading Sphingomonas Wittichii Strain RW1 (pdb code 3vb0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of 2,2',3-Trihydroxybiphenyl 1,2-Dioxygenase From Dibenzofuran-Degrading Sphingomonas Wittichii Strain RW1, PDB code: 3vb0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of 2,2',3-Trihydroxybiphenyl 1,2-Dioxygenase From Dibenzofuran-Degrading Sphingomonas Wittichii Strain RW1


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 2,2',3-Trihydroxybiphenyl 1,2-Dioxygenase From Dibenzofuran-Degrading Sphingomonas Wittichii Strain RW1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:21.0 occ:0.80 OE1 A:GLU260 2.1 20.7 0.8 O A:HOH502 2.1 20.3 0.8 NE2 A:HIS147 2.2 17.4 0.8 NE2 A:HIS209 2.2 20.9 0.8 O A:HOH501 2.3 22.8 0.8 CE1 A:HIS147 3.0 16.3 0.8 CE1 A:HIS209 3.0 21.0 0.8 OH A:TYR250 3.1 23.8 0.8 CD A:GLU260 3.1 21.0 0.8 CD2 A:HIS147 3.2 17.5 0.8 CD2 A:HIS209 3.3 20.9 0.8 OE2 A:GLU260 3.6 20.6 0.8 CB A:MET211 4.0 19.6 0.8 CZ A:TYR250 4.1 23.1 0.8 NE2 A:HIS191 4.2 21.2 0.8 ND1 A:HIS209 4.2 21.3 0.8 ND1 A:HIS147 4.2 16.7 0.8 CG A:MET211 4.3 19.6 0.8 CG A:HIS147 4.3 16.7 0.8 CG A:HIS209 4.3 20.2 0.8 O A:HOH503 4.3 38.5 0.8 CG A:GLU260 4.5 20.4 0.8 CE1 A:TYR250 4.5 23.3 0.8 CB A:GLU260 4.7 19.1 0.8 CE1 A:HIS191 4.7 19.0 0.8 NE2 A:HIS241 4.7 23.6 0.8 CG2 A:VAL149 4.7 20.3 0.8 OD2 A:ASP244 4.8 32.0 0.8 CD2 A:HIS241 4.8 23.1 0.8

Iron binding site 2 out of 4 in the Crystal Structure of 2,2',3-Trihydroxybiphenyl 1,2-Dioxygenase From Dibenzofuran-Degrading Sphingomonas Wittichii Strain RW1


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 2,2',3-Trihydroxybiphenyl 1,2-Dioxygenase From Dibenzofuran-Degrading Sphingomonas Wittichii Strain RW1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:21.0 occ:0.80 OE1 B:GLU260 2.1 18.1 0.8 NE2 B:HIS147 2.1 17.1 0.8 O B:HOH502 2.2 21.6 0.8 NE2 B:HIS209 2.3 19.5 0.8 O B:HOH501 2.3 22.5 0.8 CE1 B:HIS147 3.0 15.5 0.8 OH B:TYR250 3.1 22.5 0.8 CE1 B:HIS209 3.1 20.6 0.8 CD B:GLU260 3.2 19.4 0.8 CD2 B:HIS147 3.2 17.0 0.8 CD2 B:HIS209 3.4 20.3 0.8 OE2 B:GLU260 3.5 18.8 0.8 CB B:MET211 4.1 18.5 0.8 CZ B:TYR250 4.1 22.5 0.8 ND1 B:HIS147 4.1 15.1 0.8 NE2 B:HIS191 4.2 21.4 0.8 ND1 B:HIS209 4.3 20.1 0.8 CG B:MET211 4.3 19.5 0.8 CG B:HIS147 4.3 15.4 0.8 O B:HOH503 4.4 35.7 0.8 CG B:HIS209 4.4 20.1 0.8 CE1 B:TYR250 4.5 21.4 0.8 CG B:GLU260 4.5 18.5 0.8 CE1 B:HIS191 4.6 17.7 0.8 NE2 B:HIS241 4.7 21.8 0.8 CB B:GLU260 4.7 18.3 0.8 OD2 B:ASP244 4.7 31.8 0.8 CG2 B:VAL149 4.7 20.5 0.8 CD2 B:HIS241 4.8 22.7 0.8

Iron binding site 3 out of 4 in the Crystal Structure of 2,2',3-Trihydroxybiphenyl 1,2-Dioxygenase From Dibenzofuran-Degrading Sphingomonas Wittichii Strain RW1


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 2,2',3-Trihydroxybiphenyl 1,2-Dioxygenase From Dibenzofuran-Degrading Sphingomonas Wittichii Strain RW1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe300 b:20.4 occ:0.20 OE1 C:GLU260 2.1 19.5 0.2 NE2 C:HIS147 2.1 16.1 0.2 NE2 C:HIS209 2.3 20.1 0.2 CE1 C:HIS147 2.8 15.7 0.2 CE1 C:HIS209 3.0 20.7 0.2 OH C:TYR250 3.1 22.3 0.2 CD C:GLU260 3.2 19.4 0.2 CD2 C:HIS147 3.3 16.1 0.2 CD2 C:HIS209 3.4 20.5 0.2 OE2 C:GLU260 3.6 19.3 0.2 ND1 C:HIS147 4.0 15.8 0.2 CB C:MET211 4.1 19.0 0.2 CZ C:TYR250 4.1 22.1 0.2 ND1 C:HIS209 4.2 20.9 0.2 NE2 C:HIS191 4.2 19.2 0.2 CG C:HIS147 4.3 16.3 0.2 CE1 C:TYR250 4.4 22.1 0.2 CG C:MET211 4.4 19.3 0.2 CG C:HIS209 4.4 20.9 0.2 CG C:GLU260 4.5 19.6 0.2 NE2 C:HIS241 4.6 23.8 0.2 CE1 C:HIS191 4.6 18.4 0.2 CD2 C:HIS241 4.7 24.1 0.2 CB C:GLU260 4.7 19.3 0.2 CG2 C:VAL149 4.9 20.6 0.2 OD2 C:ASP244 4.9 28.1 0.2

Iron binding site 4 out of 4 in the Crystal Structure of 2,2',3-Trihydroxybiphenyl 1,2-Dioxygenase From Dibenzofuran-Degrading Sphingomonas Wittichii Strain RW1


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 2,2',3-Trihydroxybiphenyl 1,2-Dioxygenase From Dibenzofuran-Degrading Sphingomonas Wittichii Strain RW1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe300 b:20.6 occ:0.20 NE2 D:HIS147 2.1 16.6 0.2 OE1 D:GLU260 2.2 18.5 0.2 NE2 D:HIS209 2.3 20.0 0.2 CE1 D:HIS147 2.9 16.0 0.2 CE1 D:HIS209 3.1 20.2 0.2 OH D:TYR250 3.3 21.7 0.2 CD2 D:HIS209 3.3 20.1 0.2 CD2 D:HIS147 3.3 16.1 0.2 CD D:GLU260 3.3 18.9 0.2 OE2 D:GLU260 3.9 17.8 0.2 CB D:MET211 4.1 18.0 0.2 ND1 D:HIS147 4.1 16.1 0.2 NE2 D:HIS191 4.2 18.8 0.2 CZ D:TYR250 4.2 21.4 0.2 ND1 D:HIS209 4.2 20.4 0.2 CG D:HIS147 4.3 15.9 0.2 CG D:HIS209 4.3 20.5 0.2 CG D:MET211 4.4 18.4 0.2 CE1 D:TYR250 4.4 21.9 0.2 CG D:GLU260 4.5 18.9 0.2 CE1 D:HIS191 4.6 18.3 0.2 CB D:GLU260 4.6 18.6 0.2 CG2 D:VAL149 4.7 20.1 0.2 NE2 D:HIS241 4.8 23.8 0.2 CD2 D:HIS241 4.9 24.2 0.2

M.Koksal, P.Kumar, P.D.Fortin, L.D.Eltis, J.T.Bolin. Crystal Structure of A Dibenzofuran-Degrading Dioxygenase: An Unusual Spatially Heterogeneous Crystal with A Hypersymmetric Intensity Distribution To Be Published.