Nickel in PDB 8iqa: Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis Deleted N-Terminal 18 Residues

The structure of Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis Deleted N-Terminal 18 Residues, PDB code: 8iqa 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)	22.68 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.22, 135.045, 138.04, 90, 90, 90
R / Rfree (%)	19.1 / 21.3

The binding sites of Nickel atom in the Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis Deleted N-Terminal 18 Residues (pdb code 8iqa). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis Deleted N-Terminal 18 Residues, PDB code: 8iqa:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis Deleted N-Terminal 18 Residues


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 Alcaligenes Faecalis Deleted N-Terminal 18 Residues within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni300 b:15.3 occ:1.00 NE2 A:HIS183 2.1 14.6 1.0 NE2 A:HIS121 2.1 17.4 1.0 NE2 A:HIS119 2.1 16.9 1.0 O A:HOH537 2.2 31.4 1.0 O A:HOH541 2.3 33.4 1.0 O A:HOH419 2.3 19.6 1.0 CE1 A:HIS121 3.0 16.9 1.0 CD2 A:HIS183 3.0 14.4 1.0 CE1 A:HIS119 3.0 15.6 1.0 CE1 A:HIS183 3.1 15.5 1.0 CD2 A:HIS121 3.1 17.2 1.0 CD2 A:HIS119 3.1 15.5 1.0 CG A:HIS183 4.2 13.5 1.0 ND1 A:HIS121 4.2 16.8 1.0 ND1 A:HIS183 4.2 14.3 1.0 ND1 A:HIS119 4.2 15.1 1.0 CG A:HIS121 4.2 15.6 1.0 CG A:HIS119 4.2 14.8 1.0 O A:ALA51 4.6 22.2 1.0 NE2 A:GLN53 4.8 18.7 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis Deleted N-Terminal 18 Residues


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis Deleted N-Terminal 18 Residues within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni300 b:16.9 occ:1.00 NE2 B:HIS183 2.0 14.7 1.0 NE2 B:HIS121 2.1 15.3 1.0 O B:HOH450 2.1 19.7 1.0 NE2 B:HIS119 2.1 16.6 1.0 O B:HOH503 2.1 32.1 1.0 O B:HOH511 2.5 32.6 1.0 CE1 B:HIS121 3.0 15.8 1.0 CD2 B:HIS183 3.0 14.0 1.0 CE1 B:HIS119 3.0 16.7 1.0 CE1 B:HIS183 3.1 16.0 1.0 CD2 B:HIS121 3.1 15.2 1.0 CD2 B:HIS119 3.2 16.7 1.0 CG B:HIS183 4.2 13.8 1.0 ND1 B:HIS121 4.2 15.6 1.0 ND1 B:HIS183 4.2 15.0 1.0 ND1 B:HIS119 4.2 15.7 1.0 CG B:HIS121 4.2 14.1 1.0 CG B:HIS119 4.3 15.7 1.0 O B:ALA51 4.5 25.0 1.0 CB B:ALA51 4.9 25.1 1.0 NE2 B:GLN53 4.9 27.6 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis Deleted N-Terminal 18 Residues


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis Deleted N-Terminal 18 Residues within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni300 b:14.7 occ:1.00 NE2 C:HIS121 2.1 13.3 1.0 NE2 C:HIS183 2.1 14.0 1.0 NE2 C:HIS119 2.1 18.4 1.0 O C:HOH565 2.2 28.8 1.0 O C:HOH433 2.3 15.9 1.0 O C:HOH578 2.3 22.2 1.0 CE1 C:HIS121 3.0 13.6 1.0 CE1 C:HIS119 3.0 18.6 1.0 CD2 C:HIS183 3.0 14.1 1.0 CE1 C:HIS183 3.1 16.1 1.0 CD2 C:HIS121 3.1 12.9 1.0 CD2 C:HIS119 3.1 17.6 1.0 O C:HOH597 4.1 34.3 1.0 ND1 C:HIS121 4.2 13.2 1.0 CG C:HIS183 4.2 13.6 1.0 ND1 C:HIS119 4.2 17.4 1.0 CG C:HIS121 4.2 12.4 1.0 ND1 C:HIS183 4.2 15.5 1.0 CG C:HIS119 4.2 15.6 1.0 O C:ALA51 4.6 17.3 1.0 O C:HOH518 4.7 25.6 1.0 NE2 C:GLN53 4.9 18.1 1.0 CB C:ALA51 4.9 17.9 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis Deleted N-Terminal 18 Residues


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Pyruvic Oxime Dioxygenase (Pod) From Alcaligenes Faecalis Deleted N-Terminal 18 Residues within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni300 b:16.1 occ:1.00 NE2 D:HIS183 2.0 16.9 1.0 NE2 D:HIS121 2.1 15.6 1.0 NE2 D:HIS119 2.1 16.5 1.0 O D:HOH533 2.2 26.7 1.0 O D:HOH403 2.3 22.9 1.0 O D:HOH542 2.3 28.0 1.0 CD2 D:HIS183 3.0 16.8 1.0 CE1 D:HIS121 3.0 16.2 1.0 CE1 D:HIS183 3.1 18.6 1.0 CE1 D:HIS119 3.1 15.8 1.0 CD2 D:HIS121 3.1 15.8 1.0 CD2 D:HIS119 3.2 16.0 1.0 CG D:HIS183 4.2 15.8 1.0 ND1 D:HIS121 4.2 14.9 1.0 ND1 D:HIS183 4.2 17.5 1.0 CG D:HIS121 4.2 14.4 1.0 ND1 D:HIS119 4.3 15.5 1.0 CG D:HIS119 4.3 15.4 1.0 O D:ALA51 4.5 22.5 1.0 O D:HOH517 4.7 29.7 1.0 NE2 D:GLN53 4.9 22.4 1.0 CB D:ALA51 5.0 20.7 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.