Nickel in PDB 6ruh: Ni-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr

All present enzymatic activity of Ni-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr:
3.4.21.64;

The structure of Ni-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr, PDB code: 6ruh was solved by J.Breibeck, A.Bijelic, A.Rompel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.39 / 1.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.960, 67.960, 102.670, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 15.8

The structure of Ni-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr also contains other interesting chemical elements:

Tungsten

(W)

22 atoms

The binding sites of Nickel atom in the Ni-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr (pdb code 6ruh). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Ni-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr, PDB code: 6ruh:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Ni-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Ni-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:9.2 occ:0.25 NI1 A:WNI301 0.0 9.2 0.2 OD2 A:ASP207 1.5 14.2 1.0 O76 A:WNI301 2.1 10.5 0.2 O77 A:WNI301 2.1 8.6 0.2 O75 A:WNI301 2.1 10.6 0.2 O78 A:WNI301 2.1 9.1 0.2 O61 A:WNI301 2.4 9.1 0.2 CG A:ASP207 2.8 11.0 1.0 W18 A:WNI301 3.3 8.2 0.2 W17 A:WNI301 3.3 8.9 0.2 P2 A:WNI301 3.4 10.2 0.2 OD1 A:ASP207 3.4 11.8 1.0 O55 A:WNI301 3.5 8.9 0.2 W12 A:WNI301 3.6 11.6 0.2 W13 A:WNI301 3.6 11.7 0.2 O41 A:WNI301 3.6 11.6 0.2 HG21 A:THR206 3.7 8.3 1.0 O59 A:WNI301 3.7 11.2 0.2 O60 A:WNI301 3.7 11.5 0.2 HB2 A:ASP207 3.8 9.4 1.0 O57 A:WNI301 3.8 9.3 0.2 O53 A:WNI301 3.8 9.4 0.2 CB A:ASP207 3.8 7.9 1.0 HE A:ARG185 3.9 12.6 1.0 HH22 A:ARG185 4.0 14.4 1.0 HB3 A:ASP207 4.1 9.4 1.0 O46 A:WNI301 4.3 10.6 0.2 O45 A:WNI301 4.4 11.9 0.2 CG2 A:THR206 4.5 6.9 1.0 HG23 A:THR206 4.5 8.3 1.0 O A:HOH592 4.6 7.2 1.0 O40 A:WNI301 4.6 11.9 0.2 O42 A:WNI301 4.6 11.8 0.2 HG22 A:THR206 4.6 8.3 1.0 O56 A:WNI301 4.7 8.7 0.2 O54 A:WNI301 4.7 8.6 0.2 NE A:ARG185 4.7 10.5 1.0 O62 A:WNI301 4.7 10.9 0.2 O67 A:WNI301 4.8 9.8 0.2 O66 A:WNI301 4.8 8.9 0.2 NH2 A:ARG185 4.8 12.0 1.0 W19 A:WNI301 4.9 10.3 0.2 W16 A:WNI301 4.9 10.7 0.2 O A:HOH664 5.0 28.9 1.0

Nickel binding site 2 out of 2 in the Ni-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Ni-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:5.7 occ:0.62 NI1 A:WNI302 0.0 5.7 0.6 O76 A:WNI302 2.1 6.3 0.6 O77 A:WNI302 2.1 6.2 0.6 O75 A:WNI302 2.1 7.0 0.6 O78 A:WNI302 2.1 6.1 0.6 O A:HOH476 2.1 10.2 1.0 O61 A:WNI302 2.3 5.9 0.6 W18 A:WNI302 3.3 6.3 0.6 W17 A:WNI302 3.3 6.9 0.6 P2 A:WNI302 3.4 5.1 0.6 O55 A:WNI302 3.5 6.7 0.6 W13 A:WNI302 3.6 7.0 0.6 HG3 A:MET55 3.6 9.4 1.0 W12 A:WNI302 3.6 6.5 0.6 HA A:ARG64 3.7 9.5 1.0 O41 A:WNI302 3.7 6.9 0.6 HG2 A:MET55 3.7 9.4 1.0 O60 A:WNI302 3.8 6.6 0.6 O57 A:WNI302 3.8 6.5 0.6 O53 A:WNI302 3.8 6.3 0.6 O59 A:WNI302 3.8 6.7 0.6 O A:HOH640 3.9 9.8 1.0 H A:ALA44 4.1 8.0 1.0 CG A:MET55 4.1 7.8 1.0 O A:ILE42 4.2 6.2 1.0 O A:SER63 4.3 7.5 1.0 HB2 A:SER63 4.3 9.6 1.0 O45 A:WNI302 4.4 6.7 0.6 O46 A:WNI302 4.4 7.1 0.6 CA A:ARG64 4.5 8.0 1.0 HB2 A:ALA44 4.5 7.8 1.0 HA A:GLU43 4.6 7.1 1.0 C A:SER63 4.6 7.6 1.0 HB2 A:MET55 4.6 9.2 1.0 N A:ARG64 4.6 7.5 1.0 O56 A:WNI302 4.7 6.3 0.6 O42 A:WNI302 4.7 7.4 0.6 O40 A:WNI302 4.7 7.2 0.6 HB3 A:SER63 4.7 9.6 1.0 O54 A:WNI302 4.7 8.4 0.6 O66 A:WNI302 4.8 7.1 0.6 HB2 A:ARG64 4.8 10.9 1.0 O67 A:WNI302 4.8 6.4 0.6 O62 A:WNI302 4.8 6.2 0.6 N A:ALA44 4.9 6.7 1.0 HB1 A:ALA44 4.9 7.8 1.0 CB A:SER63 4.9 8.0 1.0 W16 A:WNI302 4.9 7.5 0.6 H A:ASP65 5.0 7.8 1.0 CB A:MET55 5.0 7.7 1.0 W19 A:WNI302 5.0 6.7 0.6

J.Breibeck, A.Bijelic, A.Rompel. Transition Metal-Substituted Keggin Polyoxotungstates Enabling Covalent Attachment to Proteinase K Upon Co-Crystallization. Chem.Commun.(Camb.) V. 55 11519 2019.
ISSN: ESSN 1364-548X
PubMed: 31490500
DOI: 10.1039/C9CC05818D