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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6ruh:

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

Tungsten (W) 22 atoms

Nickel Binding Sites:

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 6ruh

Go back to Nickel Binding Sites List in 6ruh
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 6ruh

Go back to Nickel Binding Sites List in 6ruh
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

Reference:

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
Page generated: Wed Dec 16 01:53:24 2020

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