Iron in PDB 8il8: Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis

The structure of Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis, PDB code: 8il8 was solved by S.Tsujino, Y.Yamada, T.Fujiwara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.44 / 1.77
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.002, 107.552, 87.794, 90, 128.07, 90
R / Rfree (%)	18.2 / 21.2

The binding sites of Iron atom in the Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis (pdb code 8il8). 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 Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis, PDB code: 8il8:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis


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 Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:26.0 occ:1.00 O A:HOH478 2.1 24.7 1.0 O A:HOH505 2.2 16.0 1.0 NE2 A:HIS119 2.2 26.1 1.0 NE2 A:HIS183 2.2 24.4 1.0 NE2 A:HIS121 2.2 24.4 1.0 O A:HOH405 2.4 19.4 1.0 CE1 A:HIS121 3.1 24.2 1.0 CE1 A:HIS119 3.2 25.9 1.0 CD2 A:HIS183 3.2 23.8 1.0 CE1 A:HIS183 3.2 24.8 1.0 CD2 A:HIS119 3.2 24.5 1.0 CD2 A:HIS121 3.3 23.1 1.0 O A:HOH560 4.1 59.5 1.0 ND1 A:HIS121 4.3 24.4 1.0 ND1 A:HIS119 4.3 25.2 1.0 CG A:HIS183 4.3 23.5 1.0 CG A:HIS119 4.3 23.9 1.0 ND1 A:HIS183 4.4 24.5 1.0 CG A:HIS121 4.4 23.5 1.0 O A:ALA51 4.4 29.4 1.0 CB A:ALA51 4.8 29.3 1.0 NE2 A:GLN53 4.8 32.8 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis


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 Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:27.8 occ:1.00 NE2 B:HIS183 2.1 27.1 1.0 NE2 B:HIS121 2.2 25.7 1.0 O B:HOH532 2.2 21.9 1.0 O B:HOH491 2.2 26.1 1.0 NE2 B:HIS119 2.3 25.7 1.0 O B:HOH408 2.4 19.8 1.0 CE1 B:HIS121 3.1 24.9 1.0 CD2 B:HIS183 3.1 26.7 1.0 CE1 B:HIS183 3.1 28.3 1.0 CE1 B:HIS119 3.2 25.1 1.0 CD2 B:HIS121 3.2 23.9 1.0 CD2 B:HIS119 3.3 25.1 1.0 CG B:HIS183 4.2 26.8 1.0 ND1 B:HIS121 4.3 25.0 1.0 ND1 B:HIS183 4.3 28.4 1.0 CG B:HIS121 4.3 23.4 1.0 ND1 B:HIS119 4.4 24.7 1.0 CG B:HIS119 4.4 23.6 1.0 O B:ALA51 4.4 32.8 1.0 CB B:ALA51 4.9 32.0 1.0 NE2 B:GLN53 4.9 28.6 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis


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 Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:25.9 occ:1.00 NE2 C:HIS119 2.2 24.8 1.0 NE2 C:HIS183 2.2 24.9 1.0 NE2 C:HIS121 2.2 26.4 1.0 O C:HOH480 2.2 29.1 1.0 O C:HOH491 2.2 19.0 1.0 O C:HOH405 2.4 25.9 1.0 CE1 C:HIS121 3.1 25.9 1.0 CE1 C:HIS119 3.2 24.8 1.0 CD2 C:HIS119 3.2 24.2 1.0 CE1 C:HIS183 3.2 25.4 1.0 CD2 C:HIS183 3.2 24.0 1.0 CD2 C:HIS121 3.3 25.8 1.0 O C:HOH550 4.1 57.4 1.0 O C:HOH541 4.1 57.3 1.0 O C:HOH401 4.2 37.5 1.0 CG C:HIS119 4.3 23.4 1.0 ND1 C:HIS119 4.3 25.0 1.0 ND1 C:HIS121 4.3 26.2 1.0 CG C:HIS121 4.4 25.3 1.0 CG C:HIS183 4.4 24.0 1.0 ND1 C:HIS183 4.4 25.5 1.0 O C:ALA51 4.4 29.5 1.0 CB C:ALA51 4.8 28.9 1.0 NE2 C:GLN53 4.8 33.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis


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 Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:26.3 occ:1.00 NE2 D:HIS183 2.2 27.1 1.0 NE2 D:HIS119 2.2 27.4 1.0 NE2 D:HIS121 2.2 25.1 1.0 O D:HOH485 2.3 28.2 1.0 O D:HOH511 2.3 28.6 1.0 O D:HOH407 2.4 25.5 1.0 CE1 D:HIS121 3.1 24.7 1.0 CE1 D:HIS183 3.2 28.5 1.0 CE1 D:HIS119 3.2 27.5 1.0 CD2 D:HIS183 3.2 25.6 1.0 CD2 D:HIS119 3.2 26.6 1.0 CD2 D:HIS121 3.3 22.9 1.0 ND1 D:HIS121 4.3 24.7 1.0 CG D:HIS183 4.3 24.9 1.0 ND1 D:HIS183 4.3 27.9 1.0 ND1 D:HIS119 4.3 27.1 1.0 CG D:HIS121 4.3 22.8 1.0 CG D:HIS119 4.3 25.3 1.0 O D:ALA51 4.4 30.8 1.0 NE2 D:GLN53 4.9 29.3 1.0 CB D:ALA51 4.9 29.1 1.0

S.Tsujino, Y.Yamada, M.Senda, T.Senda, T.Fujiwara. Structural and Functional Analysis of Pyruvic Oxime Dioxygenase, A Key Enzyme of Heterotrophic Nitrification To Be Published.