Nickel in PDB 8ix6: Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Bradyrhizobium Sp. WSM3983

The structure of Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Bradyrhizobium Sp. WSM3983, PDB code: 8ix6 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)	76.95 / 2.47
Space group	I 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	153.896, 153.896, 153.896, 90, 90, 90
R / Rfree (%)	23 / 25.8

The binding sites of Nickel atom in the Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Bradyrhizobium Sp. WSM3983 (pdb code 8ix6). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Bradyrhizobium Sp. WSM3983, PDB code: 8ix6:

Nickel binding site 1 out of 1 in the Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Bradyrhizobium Sp. WSM3983


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Bradyrhizobium Sp. WSM3983 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:55.5 occ:1.00 NE2 A:HIS121 2.1 55.5 1.0 NE2 A:HIS119 2.1 57.8 1.0 NE2 A:HIS183 2.1 55.5 1.0 O A:HOH405 2.3 55.5 1.0 O A:HOH408 2.6 54.2 1.0 CE1 A:HIS119 2.7 56.9 1.0 CE1 A:HIS121 2.9 53.6 1.0 CE1 A:HIS183 2.9 51.9 1.0 CD2 A:HIS183 3.2 51.9 1.0 CD2 A:HIS121 3.2 54.9 1.0 CD2 A:HIS119 3.4 56.9 1.0 O A:HOH421 3.8 60.5 1.0 ND1 A:HIS119 3.9 54.4 1.0 ND1 A:HIS183 4.0 55.1 1.0 ND1 A:HIS121 4.1 54.5 1.0 CG A:HIS183 4.2 55.9 1.0 CG A:HIS121 4.3 53.2 1.0 CG A:HIS119 4.3 51.7 1.0 NE2 A:GLN53 4.8 66.2 1.0 O A:ALA51 4.8 66.9 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.