Nickel in PDB 5wxk: Earp Bound with Domain I of Ef-P

The structure of Earp Bound with Domain I of Ef-P, PDB code: 5wxk was solved by T.Sengoku, S.Yokoyama, T.Yanagisawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.97 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.204, 57.254, 72.831, 90.00, 101.44, 90.00
R / Rfree (%)	15.7 / 20.2

The binding sites of Nickel atom in the Earp Bound with Domain I of Ef-P (pdb code 5wxk). 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 Earp Bound with Domain I of Ef-P, PDB code: 5wxk:

Nickel binding site 1 out of 1 in the Earp Bound with Domain I of Ef-P


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Earp Bound with Domain I of Ef-P within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni410 b:45.8 occ:1.00 NE2 A:HIS346 1.9 42.0 1.0 CE1 A:HIS346 2.7 34.9 1.0 CD2 A:HIS346 3.1 30.3 1.0 O A:HOH846 3.4 31.1 1.0 O A:HOH501 3.6 43.9 1.0 O A:HOH841 3.6 43.8 1.0 ND1 A:HIS346 3.9 34.7 1.0 CG A:HIS346 4.1 26.4 1.0 CG A:GLU313 4.4 53.9 1.0 CB A:GLU313 4.9 43.8 1.0 OE2 A:GLU313 5.0 74.5 1.0

T.Sengoku, T.Suzuki, N.Dohmae, C.Watanabe, T.Honma, Y.Hikida, Y.Yamaguchi, H.Takahashi, S.Yokoyama, T.Yanagisawa. Structural Basis of Protein Arginine Rhamnosylation By Glycosyltransferase Earp Nat. Chem. Biol. V. 14 368 2018.
ISSN: ESSN 1552-4469
PubMed: 29440735
DOI: 10.1038/S41589-018-0002-Y