Nickel in PDB 7uk8: Apo Form of Ygic From Escherichia Coli K-12

The structure of Apo Form of Ygic From Escherichia Coli K-12, PDB code: 7uk8 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)	38.20 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.22, 88.22, 141.598, 90, 90, 120
R / Rfree (%)	18.6 / 21.1

The structure of Apo Form of Ygic From Escherichia Coli K-12 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Nickel atom in the Apo Form of Ygic From Escherichia Coli K-12 (pdb code 7uk8). 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 Apo Form of Ygic From Escherichia Coli K-12, PDB code: 7uk8:

Nickel binding site 1 out of 1 in the Apo Form of Ygic From Escherichia Coli K-12


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Apo Form of Ygic From Escherichia Coli K-12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:41.0 occ:0.98 OE2 A:GLU14 1.8 40.5 1.0 ND1 A:HIS17 2.2 44.4 1.0 CD A:GLU14 2.6 36.9 1.0 OE1 A:GLU14 2.6 42.6 1.0 CE1 A:HIS17 3.0 43.7 1.0 CG A:HIS17 3.2 43.3 1.0 CB A:HIS17 3.6 39.2 1.0 CG A:GLU14 4.0 40.8 1.0 NE2 A:HIS17 4.2 47.1 1.0 N A:GLU18 4.2 37.3 1.0 C A:HIS17 4.3 37.5 1.0 CD2 A:HIS17 4.3 45.2 1.0 O A:HOH616 4.3 52.4 1.0 O A:GLU14 4.5 37.7 1.0 CA A:GLU18 4.6 40.3 1.0 CA A:HIS17 4.6 37.0 1.0 O A:HIS17 4.7 37.0 1.0 CB A:GLU18 5.0 42.1 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