Nickel in PDB 5ihy: The Crystal Structure of Bacillus Subtilis Semet-Ypgq

The structure of The Crystal Structure of Bacillus Subtilis Semet-Ypgq, PDB code: 5ihy was solved by Y.J.Jeon, W.S.Song, S.I.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.487, 53.087, 83.388, 90.00, 93.70, 90.00
R / Rfree (%)	21.5 / 26.1

The binding sites of Nickel atom in the The Crystal Structure of Bacillus Subtilis Semet-Ypgq (pdb code 5ihy). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the The Crystal Structure of Bacillus Subtilis Semet-Ypgq, PDB code: 5ihy:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the The Crystal Structure of Bacillus Subtilis Semet-Ypgq


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of Bacillus Subtilis Semet-Ypgq within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:98.0 occ:1.00 NE2 A:HIS29 2.8 33.2 1.0 OD1 A:ASP124 3.0 31.9 1.0 OD1 A:ASP59 3.2 36.9 1.0 OD2 A:ASP124 3.2 35.0 1.0 CG A:ASP124 3.3 31.5 1.0 OD2 A:ASP59 3.4 36.1 1.0 CE1 A:HIS29 3.6 33.6 1.0 NE2 A:HIS58 3.6 33.2 1.0 CG A:ASP59 3.6 34.8 1.0 CD2 A:HIS29 3.8 33.3 1.0 CE1 A:HIS58 4.2 31.9 1.0 CB A:ASP124 4.6 30.5 1.0 CD2 A:HIS58 4.6 32.5 1.0 ND1 A:HIS29 4.8 34.1 1.0 CG A:HIS29 4.9 33.1 1.0

Nickel binding site 2 out of 2 in the The Crystal Structure of Bacillus Subtilis Semet-Ypgq


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of Bacillus Subtilis Semet-Ypgq within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:0.9 occ:1.00 NE2 B:HIS29 2.8 37.5 1.0 OD2 B:ASP124 3.0 36.6 1.0 OD1 B:ASP124 3.1 35.4 1.0 CG B:ASP124 3.4 33.6 1.0 OD1 B:ASP59 3.4 41.0 1.0 OD2 B:ASP59 3.5 42.2 1.0 CE1 B:HIS29 3.7 37.0 1.0 NE2 B:HIS58 3.7 37.6 1.0 CD2 B:HIS29 3.8 38.0 1.0 CG B:ASP59 3.9 40.3 1.0 CE1 B:HIS58 4.4 37.3 1.0 CD2 B:HIS58 4.7 37.7 1.0 ND1 B:HIS29 4.9 37.5 1.0 CB B:ASP124 4.9 32.2 1.0 CG B:HIS29 5.0 37.8 1.0

Y.J.Jeon, S.C.Park, W.S.Song, O.H.Kim, B.C.Oh, S.I.Yoon. Structural and Biochemical Characterization of Bacterial Ypgq Protein Reveals A Metal-Dependent Nucleotide Pyrophosphohydrolase J.Struct.Biol. V. 195 113 2016.
ISSN: ESSN 1095-8657
PubMed: 27062940
DOI: 10.1016/J.JSB.2016.04.002