Nickel in PDB 7uka: Ygic From Escherichia Coli K-12 in Complex with Adp

The structure of Ygic From Escherichia Coli K-12 in Complex with Adp, PDB code: 7uka was solved by J.L.Pederick, J.B.Bruning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.80 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.131, 88.131, 139.909, 90, 90, 120
R / Rfree (%)	21.8 / 25.5

The binding sites of Nickel atom in the Ygic From Escherichia Coli K-12 in Complex with Adp (pdb code 7uka). 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 Ygic From Escherichia Coli K-12 in Complex with Adp, PDB code: 7uka:

Nickel binding site 1 out of 1 in the Ygic From Escherichia Coli K-12 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Ygic From Escherichia Coli K-12 in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:54.7 occ:0.73 OE1 A:GLU14 1.9 65.0 1.0 ND1 A:HIS17 2.3 75.3 1.0 OE2 A:GLU14 2.4 58.5 1.0 CD A:GLU14 2.5 60.6 1.0 CE1 A:HIS17 3.1 77.1 1.0 CG A:HIS17 3.3 76.2 1.0 CB A:HIS17 3.7 71.9 1.0 CG A:GLU14 4.0 60.1 1.0 NE2 A:HIS17 4.2 68.3 1.0 N A:GLU18 4.3 68.6 1.0 CD2 A:HIS17 4.3 72.8 1.0 C A:HIS17 4.3 66.3 1.0 O A:GLU14 4.4 66.2 1.0 CA A:GLU18 4.6 68.8 1.0 CA A:HIS17 4.7 68.0 1.0 O A:HIS17 4.7 65.8 1.0 CB A:GLU18 4.9 65.4 1.0 CB A:GLU14 5.0 63.3 1.0

J.L.Pederick, J.Klose, B.Jovcevski, T.L.Pukala, J.B.Bruning. Escherichia Coli Ygic and Yjfc Possess Peptide─Spermidine Ligase Activity. Biochemistry 2023.
ISSN: ISSN 0006-2960
PubMed: 36745518
DOI: 10.1021/ACS.BIOCHEM.2C00592