Iron in PDB 5j92: Crystal Structure of A Putative Alpha-Ketoglutarate Dependent 2,4-D Dioxygenase From Burkholderia Xenovorans

The structure of Crystal Structure of A Putative Alpha-Ketoglutarate Dependent 2,4-D Dioxygenase From Burkholderia Xenovorans, PDB code: 5j92 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.12 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.700, 77.880, 92.140, 90.00, 92.11, 90.00
R / Rfree (%)	17.6 / 21.5

The binding sites of Iron atom in the Crystal Structure of A Putative Alpha-Ketoglutarate Dependent 2,4-D Dioxygenase From Burkholderia Xenovorans (pdb code 5j92). 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 A Putative Alpha-Ketoglutarate Dependent 2,4-D Dioxygenase From Burkholderia Xenovorans, PDB code: 5j92:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of A Putative Alpha-Ketoglutarate Dependent 2,4-D Dioxygenase From Burkholderia Xenovorans


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 A Putative Alpha-Ketoglutarate Dependent 2,4-D Dioxygenase From Burkholderia Xenovorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:46.2 occ:0.74 NE2 A:HIS263 2.4 23.3 1.0 OD1 A:ASP116 2.5 32.4 1.0 NE2 A:HIS114 2.5 21.9 1.0 CE1 A:HIS263 3.0 21.5 1.0 CG A:ASP116 3.4 29.8 1.0 CD2 A:HIS114 3.4 20.2 1.0 CE1 A:HIS114 3.4 17.7 1.0 OD2 A:ASP116 3.6 26.5 1.0 CD2 A:HIS263 3.7 20.7 1.0 ND1 A:HIS263 4.2 20.6 1.0 OG A:SER110 4.3 29.1 0.5 ND1 A:HIS114 4.5 20.2 1.0 CG A:HIS114 4.5 17.4 1.0 CG A:HIS263 4.6 20.4 1.0 O A:HOH658 4.7 33.6 1.0 CB A:ASP116 4.7 22.7 1.0 CZ2 A:TRP256 4.7 21.6 1.0 CA A:ASP116 5.0 16.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of A Putative Alpha-Ketoglutarate Dependent 2,4-D Dioxygenase From Burkholderia Xenovorans


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 A Putative Alpha-Ketoglutarate Dependent 2,4-D Dioxygenase From Burkholderia Xenovorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:60.8 occ:0.67 O B:HOH748 2.4 32.9 1.0 NE2 B:HIS263 2.5 18.4 1.0 NE2 B:HIS114 2.5 20.2 1.0 OD1 B:ASP116 2.5 26.1 1.0 O B:HOH684 2.5 49.2 1.0 NH2 B:ARG279 2.7 42.4 1.0 CE1 B:HIS263 3.3 15.0 1.0 CE1 B:HIS114 3.4 18.3 1.0 CG B:ASP116 3.5 23.2 1.0 CD2 B:HIS114 3.5 18.2 1.0 CD2 B:HIS263 3.6 18.4 1.0 OD2 B:ASP116 3.6 23.0 1.0 CZ B:ARG279 3.8 48.0 1.0 NH1 B:ARG279 4.1 51.3 1.0 O B:HOH802 4.3 48.6 1.0 OG B:SER110 4.3 21.3 0.4 ND1 B:HIS263 4.5 17.6 1.0 ND1 B:HIS114 4.6 17.9 1.0 CZ2 B:TRP256 4.6 14.1 1.0 CG B:HIS263 4.6 17.1 1.0 CG B:HIS114 4.6 18.2 1.0 NE B:ARG279 4.8 49.3 1.0 CB B:ASP116 4.8 18.0 1.0 O B:HOH591 4.9 47.3 1.0 O B:HOH607 4.9 30.4 1.0

Iron binding site 3 out of 4 in the Crystal Structure of A Putative Alpha-Ketoglutarate Dependent 2,4-D Dioxygenase From Burkholderia Xenovorans


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 A Putative Alpha-Ketoglutarate Dependent 2,4-D Dioxygenase From Burkholderia Xenovorans within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:40.7 occ:0.54 OD1 C:ASP116 2.5 27.2 1.0 NE2 C:HIS114 2.5 23.1 1.0 CE1 C:HIS263 2.6 22.9 1.0 O C:HOH562 2.6 39.6 1.0 NH2 C:ARG279 2.6 48.4 1.0 O C:HOH700 2.6 46.3 1.0 NE2 C:HIS263 2.8 21.8 1.0 CG C:ASP116 3.3 25.3 1.0 CE1 C:HIS114 3.4 23.3 1.0 CD2 C:HIS114 3.4 21.4 1.0 OD2 C:ASP116 3.5 27.3 1.0 CZ C:ARG279 3.7 52.0 1.0 ND1 C:HIS263 3.8 23.0 1.0 NH1 C:ARG279 4.1 53.7 1.0 CD2 C:HIS263 4.2 21.7 1.0 ND1 C:HIS114 4.5 22.0 1.0 CG C:HIS114 4.6 22.1 1.0 CZ2 C:TRP256 4.6 24.0 1.0 O C:HOH675 4.6 41.4 1.0 NE C:ARG279 4.6 50.5 1.0 CG C:HIS263 4.7 21.6 1.0 CB C:ASP116 4.7 19.2 1.0 O C:HOH670 4.8 41.1 1.0

Iron binding site 4 out of 4 in the Crystal Structure of A Putative Alpha-Ketoglutarate Dependent 2,4-D Dioxygenase From Burkholderia Xenovorans


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 A Putative Alpha-Ketoglutarate Dependent 2,4-D Dioxygenase From Burkholderia Xenovorans within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:46.2 occ:0.59 OD1 D:ASP116 2.4 26.3 1.0 NE2 D:HIS114 2.5 19.9 1.0 CE1 D:HIS263 2.6 22.7 1.0 NH2 D:ARG279 2.7 46.1 1.0 NE2 D:HIS263 2.9 18.7 1.0 CG D:ASP116 3.3 26.8 1.0 CD2 D:HIS114 3.4 18.1 1.0 CE1 D:HIS114 3.4 19.1 1.0 OD2 D:ASP116 3.5 27.5 1.0 CZ D:ARG279 3.8 51.4 1.0 ND1 D:HIS263 3.9 21.1 1.0 CD2 D:HIS263 4.2 19.0 1.0 NH1 D:ARG279 4.3 55.4 1.0 ND1 D:HIS114 4.5 18.1 1.0 CG D:HIS114 4.6 16.2 1.0 CZ2 D:TRP256 4.6 25.1 1.0 O D:HOH691 4.6 29.6 1.0 NE D:ARG279 4.6 51.4 1.0 CB D:ASP116 4.7 17.8 1.0 CG D:HIS263 4.7 19.8 1.0 O D:HOH679 4.8 40.0 1.0 CA D:ASP116 5.0 14.9 1.0

D.G.Conrady, D.M.Dranow, D.Lorimer, T.E.Edwards. Crystal Structure of A Putative Alpha-Ketoglutarate Dependent 2,4-D Dioxygenase From Burkholderia Xenovorans To Be Published.