Nickel in PDB 5auo: Crystal Structure of the Hypab-Ni Complex (Amppcp)

The structure of Crystal Structure of the Hypab-Ni Complex (Amppcp), PDB code: 5auo was solved by S.Watanabe, T.Kawashima, Y.Nishitani, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.95 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.361, 81.887, 61.270, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.3

The structure of Crystal Structure of the Hypab-Ni Complex (Amppcp) also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Nickel atom in the Crystal Structure of the Hypab-Ni Complex (Amppcp) (pdb code 5auo). 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 the Hypab-Ni Complex (Amppcp), PDB code: 5auo:

Nickel binding site 1 out of 1 in the Crystal Structure of the Hypab-Ni Complex (Amppcp)


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 the Hypab-Ni Complex (Amppcp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:25.5 occ:1.00 N A:HIS2 2.0 25.0 1.0 NE2 A:HIS98 2.0 22.8 1.0 N A:MET1 2.0 27.6 0.5 ND1 A:HIS2 2.1 26.9 1.0 N A:MET1 2.1 27.6 0.5 C A:MET1 2.8 32.5 0.5 C A:MET1 2.8 32.5 0.5 CA A:MET1 2.8 30.6 0.5 CA A:MET1 2.9 30.6 0.5 CE1 A:HIS98 2.9 24.3 1.0 CD2 A:HIS98 3.0 23.9 1.0 CA A:HIS2 3.0 26.5 1.0 CE1 A:HIS2 3.0 24.4 1.0 CG A:HIS2 3.1 23.8 1.0 CB A:HIS2 3.4 24.5 1.0 C A:HIS2 3.6 25.1 1.0 CB A:MET1 3.6 32.8 0.5 CB A:MET1 3.6 32.8 0.5 OE1 A:GLU3 3.7 30.2 1.0 N A:GLU3 3.7 23.8 1.0 CE1 A:PHE99 3.9 31.3 1.0 O A:MET1 4.0 29.5 0.5 O A:MET1 4.0 29.4 0.5 CD A:GLU3 4.0 24.0 1.0 OE2 A:GLU3 4.0 28.9 1.0 ND1 A:HIS98 4.1 23.9 1.0 CG A:HIS98 4.1 23.6 1.0 NE2 A:HIS2 4.2 27.1 1.0 CD2 A:HIS2 4.2 30.2 1.0 CZ A:PHE99 4.4 32.5 1.0 CE A:MET1 4.4 38.1 0.5 O A:HIS2 4.4 22.8 1.0 CD1 A:PHE99 4.5 29.4 1.0 SD A:MET1 4.6 46.1 0.5 CG A:MET1 4.7 43.1 0.5 CG A:MET1 4.7 43.1 0.5 CA A:GLU3 4.8 25.0 1.0

S.Watanabe, T.Kawashima, Y.Nishitani, T.Kanai, T.Wada, K.Inaba, H.Atomi, T.Imanaka, K.Miki. Structural Basis of A Ni Acquisition Cycle For [Nife] Hydrogenase By Ni-Metallochaperone Hypa and Its Enhancer Proc.Natl.Acad.Sci.Usa V. 112 7701 2015.
ISSN: ESSN 1091-6490
PubMed: 26056269
DOI: 10.1073/PNAS.1503102112