Nickel in PDB 6r54: Crystal Structure of Ppep-1(E184A)

All present enzymatic activity of Crystal Structure of Ppep-1(E184A):
3.4.24.89;

The structure of Crystal Structure of Ppep-1(E184A), PDB code: 6r54 was solved by C.Pichlo, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.44 / 1.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.210, 71.940, 118.080, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 17.3

The structure of Crystal Structure of Ppep-1(E184A) also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of Ppep-1(E184A) (pdb code 6r54). 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 Ppep-1(E184A), PDB code: 6r54:

Nickel binding site 1 out of 1 in the Crystal Structure of Ppep-1(E184A)


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 Ppep-1(E184A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:15.0 occ:0.50 ND1 A:HIS25 1.9 22.8 1.0 N A:SER24 1.9 27.8 1.0 N A:HIS25 2.0 19.2 1.0 N A:GLY23 2.0 27.9 1.0 C A:SER24 2.8 23.7 1.0 C A:GLY23 2.8 30.2 1.0 CG A:HIS25 2.9 20.7 1.0 CA A:SER24 2.9 26.9 1.0 CE1 A:HIS25 2.9 22.9 1.0 CA A:GLY23 2.9 29.9 1.0 CA A:HIS25 3.0 19.7 1.0 H A:MET26 3.1 22.6 1.0 HE1 A:HIS25 3.1 27.4 1.0 CB A:HIS25 3.2 20.7 1.0 HB3 A:HIS25 3.3 24.8 1.0 OG A:SER24 3.3 28.4 1.0 O A:HOH473 3.5 33.7 1.0 HA2 A:GLY23 3.5 35.9 1.0 HA3 A:GLY23 3.6 35.9 1.0 N A:MET26 3.6 18.8 1.0 HA A:SER24 3.6 32.4 1.0 CB A:SER24 3.7 28.6 1.0 C A:HIS25 3.7 19.6 1.0 HA A:HIS25 3.8 23.7 1.0 NE2 A:HIS25 4.0 21.6 1.0 O A:GLY23 4.0 30.4 1.0 O A:SER24 4.0 24.6 1.0 CD2 A:HIS25 4.0 20.9 1.0 HG A:SER24 4.1 34.1 1.0 HB2 A:HIS25 4.2 24.8 1.0 HG3 A:MET26 4.2 25.8 1.0 HB3 A:SER24 4.2 34.3 1.0 HB2 A:SER24 4.4 34.3 1.0 HB2 A:MET26 4.5 33.9 1.0 HE2 A:HIS25 4.8 25.9 1.0 HD2 A:HIS25 4.8 25.1 1.0 HE2 A:MET26 4.9 54.2 1.0 CA A:MET26 4.9 26.9 1.0 O A:HIS25 4.9 20.7 1.0

C.Pichlo, L.Juetten, F.Wojtalla, M.Schacherl, D.Diaz, U.Baumann. Molecular Determinants of the Mechanism and Substrate Specificity Ofclostridium Difficileproline-Proline Endopeptidase-1. J.Biol.Chem. V. 294 11525 2019.
ISSN: ESSN 1083-351X
PubMed: 31182482
DOI: 10.1074/JBC.RA119.009029