Silicon in PDB 6rvg: Co-Substituted Beta-Keggin Bound to Proteinase K Solved By Mr

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

The structure of Co-Substituted Beta-Keggin Bound to Proteinase K Solved By Mr, PDB code: 6rvg 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)	32.17 / 1.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.820, 67.820, 101.660, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 20

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

Tungsten	(W)	44 atoms
Cobalt	(Co)	4 atoms

The binding sites of Silicon atom in the Co-Substituted Beta-Keggin Bound to Proteinase K Solved By Mr (pdb code 6rvg). This binding sites where shown within 5.0 Angstroms radius around Silicon atom.
In total 4 binding sites of Silicon where determined in the Co-Substituted Beta-Keggin Bound to Proteinase K Solved By Mr, PDB code: 6rvg:
Jump to Silicon binding site number: 1; 2; 3; 4;

Silicon binding site 1 out of 4 in the Co-Substituted Beta-Keggin Bound to Proteinase K Solved By Mr


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 1 of Co-Substituted Beta-Keggin Bound to Proteinase K Solved By Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:Si301 b:35.1 occ:0.36 SI1 A:XCO301 0.0 35.1 0.4 O37 A:XCO301 1.6 39.8 0.4 O39 A:XCO301 1.7 34.4 0.4 O40 A:XCO301 1.7 33.2 0.4 O38 A:XCO301 1.8 39.9 0.4 O25 A:XCO301 3.2 34.3 0.4 O22 A:XCO301 3.3 23.5 0.4 O36 A:XCO301 3.4 26.4 0.4 O18 A:XCO301 3.4 31.4 0.4 CO1 A:XCO301 3.4 25.9 0.4 O27 A:XCO301 3.4 34.6 0.4 O34 A:XCO301 3.5 24.3 0.4 O19 A:XCO301 3.5 32.9 0.4 W2 A:XCO301 3.5 24.7 0.4 W6 A:XCO301 3.5 24.6 0.4 W4 A:XCO301 3.5 26.9 0.4 W8 A:XCO301 3.5 34.0 0.4 O21 A:XCO301 3.5 28.6 0.4 W7 A:XCO301 3.5 27.7 0.4 W5 A:XCO301 3.5 24.6 0.4 W1 A:XCO301 3.5 27.2 0.4 W3 A:XCO301 3.5 26.8 0.4 O15 A:XCO301 3.6 48.6 0.4 O14 A:XCO301 3.6 44.4 0.4 O20 A:XCO301 3.6 35.8 0.4 W10 A:XCO301 3.6 26.9 0.4 W9 A:XCO301 3.6 30.7 0.4 W12 A:XCO301 3.6 27.1 0.4 O35 A:XCO301 3.8 29.5 0.4 O29 A:XCO301 3.9 23.1 0.4 O26 A:XCO301 4.0 34.4 0.4 O30 A:XCO301 4.0 27.9 0.4 O28 A:XCO301 4.0 29.7 0.4 O32 A:XCO301 4.0 30.4 0.4 O17 A:XCO301 4.0 47.3 0.4 O31 A:XCO301 4.0 30.5 0.4 O23 A:XCO301 4.0 45.9 0.4 O16 A:XCO301 4.1 37.7 0.4 O33 A:XCO301 4.1 41.8 0.4 O13 A:XCO301 4.1 41.1 0.4 O24 A:XCO301 4.2 21.0 0.4

Silicon binding site 2 out of 4 in the Co-Substituted Beta-Keggin Bound to Proteinase K Solved By Mr


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 2 of Co-Substituted Beta-Keggin Bound to Proteinase K Solved By Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:Si302 b:7.8 occ:0.20 SI1 A:XCO302 0.0 7.8 0.2 O38 A:XCO303 0.8 9.5 0.2 SI1 A:XCO303 1.1 8.8 0.2 O37 A:XCO302 1.7 6.2 0.2 O39 A:XCO302 1.7 7.7 0.2 O40 A:XCO302 1.8 9.3 0.2 O38 A:XCO302 1.8 10.2 0.2 O37 A:XCO303 2.1 12.9 0.2 O39 A:XCO303 2.4 10.1 0.2 O40 A:XCO303 2.4 9.2 0.2 W4 A:XCO303 2.6 10.3 0.2 W9 A:XCO303 2.7 9.9 0.2 O22 A:XCO303 2.7 10.9 0.2 O14 A:XCO303 2.8 12.6 0.2 O15 A:XCO303 2.9 12.0 0.2 W10 A:XCO303 2.9 9.4 0.2 O23 A:XCO303 3.0 11.6 0.2 O27 A:XCO303 3.1 12.9 0.2 O28 A:XCO303 3.1 16.1 0.2 O33 A:XCO303 3.2 6.9 0.2 O25 A:XCO302 3.2 11.9 0.2 W1 A:XCO303 3.2 10.7 0.2 O22 A:XCO302 3.2 9.2 0.2 O34 A:XCO303 3.3 5.1 0.2 O18 A:XCO302 3.4 11.6 0.2 O27 A:XCO302 3.4 12.8 0.2 O36 A:XCO302 3.4 9.7 0.2 O19 A:XCO302 3.5 9.3 0.2 CO1 A:XCO302 3.5 6.5 0.2 O34 A:XCO302 3.5 9.7 0.2 W4 A:XCO302 3.5 10.7 0.2 O14 A:XCO302 3.5 9.9 0.2 W2 A:XCO302 3.5 9.9 0.2 W5 A:XCO302 3.5 9.3 0.2 O20 A:XCO302 3.5 10.6 0.2 W3 A:XCO302 3.5 10.8 0.2 O21 A:XCO302 3.5 10.9 0.2 W7 A:XCO302 3.5 11.0 0.2 W6 A:XCO302 3.5 9.8 0.2 W10 A:XCO302 3.6 8.4 0.2 W9 A:XCO302 3.6 8.8 0.2 O15 A:XCO302 3.6 8.2 0.2 W8 A:XCO302 3.6 10.0 0.2 O18 A:XCO303 3.6 9.6 0.2 W12 A:XCO302 3.6 9.2 0.2 O35 A:XCO303 3.6 12.5 0.2 W1 A:XCO302 3.6 10.0 0.2 W5 A:XCO303 3.6 7.1 0.2 O35 A:XCO302 3.8 14.1 0.2 W8 A:XCO303 3.8 9.0 0.2 O36 A:XCO303 3.8 8.8 0.2 CO1 A:XCO303 3.8 7.0 0.2 O21 A:XCO303 3.8 11.6 0.2 W12 A:XCO303 3.9 8.9 0.2 O32 A:XCO302 3.9 9.6 0.2 O28 A:XCO302 4.0 8.8 0.2 W2 A:XCO303 4.0 10.1 0.2 O29 A:XCO302 4.0 10.8 0.2 O33 A:XCO302 4.0 6.5 0.2 O17 A:XCO302 4.0 9.2 0.2 O31 A:XCO302 4.1 9.0 0.2 O30 A:XCO302 4.1 10.8 0.2 O23 A:XCO302 4.1 9.3 0.2 O13 A:XCO302 4.1 5.7 0.2 W3 A:XCO303 4.1 10.1 0.2 O16 A:XCO302 4.1 12.6 0.2 O16 A:XCO303 4.1 8.5 0.2 O13 A:XCO303 4.1 14.1 0.2 O32 A:XCO303 4.2 11.8 0.2 O29 A:XCO303 4.2 9.6 0.2 O24 A:XCO302 4.2 10.8 0.2 O26 A:XCO302 4.2 11.2 0.2 O4 A:XCO303 4.2 1.6 0.2 O25 A:XCO303 4.3 10.1 0.2 O19 A:XCO303 4.3 10.3 0.2 W6 A:XCO303 4.5 9.4 0.2 O20 A:XCO303 4.5 9.7 0.2 W7 A:XCO303 4.5 10.4 0.2 O9 A:XCO303 4.5 15.2 0.2 O10 A:XCO303 4.7 8.7 0.2 O17 A:XCO303 4.7 12.1 0.2 O31 A:XCO303 4.7 10.7 0.2 O24 A:XCO303 4.7 10.0 0.2 O30 A:XCO303 4.8 10.7 0.2 O1 A:XCO303 4.8 11.6 0.2 O26 A:XCO303 4.8 15.4 0.2

Silicon binding site 3 out of 4 in the Co-Substituted Beta-Keggin Bound to Proteinase K Solved By Mr


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 3 of Co-Substituted Beta-Keggin Bound to Proteinase K Solved By Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:Si303 b:8.8 occ:0.19 SI1 A:XCO303 0.0 8.8 0.2 SI1 A:XCO302 1.1 7.8 0.2 O40 A:XCO302 1.2 9.3 0.2 O37 A:XCO303 1.6 12.9 0.2 O39 A:XCO303 1.7 10.1 0.2 O40 A:XCO303 1.7 9.2 0.2 O39 A:XCO302 1.8 7.7 0.2 O38 A:XCO303 1.8 9.5 0.2 O37 A:XCO302 2.1 6.2 0.2 O25 A:XCO302 2.3 11.9 0.2 W7 A:XCO302 2.5 11.0 0.2 O20 A:XCO302 2.7 10.6 0.2 O38 A:XCO302 2.8 10.2 0.2 O36 A:XCO302 3.0 9.7 0.2 W6 A:XCO302 3.0 9.8 0.2 W12 A:XCO302 3.1 9.2 0.2 O31 A:XCO302 3.1 9.0 0.2 O19 A:XCO302 3.1 9.3 0.2 O22 A:XCO303 3.2 10.9 0.2 O25 A:XCO303 3.2 10.1 0.2 W8 A:XCO302 3.3 10.0 0.2 W3 A:XCO302 3.3 10.8 0.2 O18 A:XCO303 3.4 9.6 0.2 O36 A:XCO303 3.4 8.8 0.2 O21 A:XCO302 3.4 10.9 0.2 CO1 A:XCO302 3.4 6.5 0.2 O26 A:XCO302 3.4 11.2 0.2 O19 A:XCO303 3.5 10.3 0.2 O27 A:XCO303 3.5 12.9 0.2 O34 A:XCO303 3.5 5.1 0.2 W2 A:XCO303 3.5 10.1 0.2 CO1 A:XCO303 3.5 7.0 0.2 W5 A:XCO303 3.5 7.1 0.2 W7 A:XCO303 3.5 10.4 0.2 W4 A:XCO303 3.5 10.3 0.2 O14 A:XCO303 3.5 12.6 0.2 O21 A:XCO303 3.5 11.6 0.2 W6 A:XCO303 3.5 9.4 0.2 W3 A:XCO303 3.5 10.1 0.2 W12 A:XCO303 3.5 8.9 0.2 O15 A:XCO303 3.6 12.0 0.2 O20 A:XCO303 3.6 9.7 0.2 W1 A:XCO303 3.6 10.7 0.2 W9 A:XCO303 3.6 9.9 0.2 W10 A:XCO303 3.6 9.4 0.2 O32 A:XCO302 3.6 9.6 0.2 W8 A:XCO303 3.6 9.0 0.2 O30 A:XCO302 3.6 10.8 0.2 O27 A:XCO302 3.7 12.8 0.2 W2 A:XCO302 3.7 9.9 0.2 O35 A:XCO303 3.8 12.5 0.2 O35 A:XCO302 3.8 14.1 0.2 O34 A:XCO302 3.9 9.7 0.2 O18 A:XCO302 3.9 11.6 0.2 O17 A:XCO302 3.9 9.2 0.2 O31 A:XCO303 3.9 10.7 0.2 O32 A:XCO303 4.0 11.8 0.2 O33 A:XCO303 4.0 6.9 0.2 W5 A:XCO302 4.0 9.3 0.2 O17 A:XCO303 4.0 12.1 0.2 O7 A:XCO302 4.0 13.4 0.2 O28 A:XCO303 4.0 16.1 0.2 O30 A:XCO303 4.1 10.7 0.2 O13 A:XCO303 4.1 14.1 0.2 O16 A:XCO303 4.1 8.5 0.2 O29 A:XCO303 4.1 9.6 0.2 O23 A:XCO303 4.1 11.6 0.2 O22 A:XCO302 4.1 9.2 0.2 O26 A:XCO303 4.1 15.4 0.2 W10 A:XCO302 4.2 8.4 0.2 O24 A:XCO303 4.2 10.0 0.2 O24 A:XCO302 4.2 10.8 0.2 O15 A:XCO302 4.3 8.2 0.2 O29 A:XCO302 4.3 10.8 0.2 W9 A:XCO302 4.3 8.8 0.2 W1 A:XCO302 4.3 10.0 0.2 O13 A:XCO302 4.4 5.7 0.2 O14 A:XCO302 4.5 9.9 0.2 O6 A:XCO302 4.6 10.3 0.2 W4 A:XCO302 4.6 10.7 0.2 O16 A:XCO302 4.6 12.6 0.2 O12 A:XCO302 4.7 15.5 0.2 O33 A:XCO302 4.7 6.5 0.2 O3 A:XCO302 4.8 9.5 0.2 HB2 A:ARG64 4.8 16.7 1.0 O28 A:XCO302 4.9 8.8 0.2

Silicon binding site 4 out of 4 in the Co-Substituted Beta-Keggin Bound to Proteinase K Solved By Mr


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 4 of Co-Substituted Beta-Keggin Bound to Proteinase K Solved By Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:Si304 b:39.3 occ:0.37 SI1 A:KCO304 0.0 39.3 0.4 O37 A:KCO304 1.6 40.9 0.4 O40 A:KCO304 1.7 36.6 0.4 O39 A:KCO304 1.7 36.2 0.4 O38 A:KCO304 1.8 51.6 0.4 O25 A:KCO304 3.1 32.1 0.4 O22 A:KCO304 3.2 46.4 0.4 O18 A:KCO304 3.4 40.3 0.4 O27 A:KCO304 3.5 46.0 0.4 W7 A:KCO304 3.5 29.9 0.4 O19 A:KCO304 3.5 29.0 0.4 O34 A:KCO304 3.5 40.4 0.4 W2 A:KCO304 3.5 30.2 0.4 W5 A:KCO304 3.5 30.3 0.4 W4 A:KCO304 3.5 28.9 0.4 W6 A:KCO304 3.5 31.4 0.4 W10 A:KCO304 3.5 32.7 0.4 O14 A:KCO304 3.5 57.4 0.4 W1 A:KCO304 3.5 30.2 0.4 O21 A:KCO304 3.6 37.9 0.4 CO1 A:KCO304 3.6 34.9 0.4 W8 A:KCO304 3.6 27.9 0.4 W12 A:KCO304 3.6 33.7 0.4 O15 A:KCO304 3.6 51.9 0.4 W9 A:KCO304 3.6 29.7 0.4 W3 A:KCO304 3.6 23.9 0.4 O20 A:KCO304 3.6 22.1 0.4 O35 A:KCO304 3.8 42.9 0.4 O31 A:KCO304 3.9 17.2 0.4 O28 A:KCO304 4.0 59.2 0.4 OD2 A:ASP207 4.0 16.6 1.0 O16 A:KCO304 4.0 44.7 0.4 O33 A:KCO304 4.0 48.3 0.4 O32 A:KCO304 4.1 41.0 0.4 O23 A:KCO304 4.1 56.0 0.4 O17 A:KCO304 4.1 34.3 0.4 O29 A:KCO304 4.1 35.7 0.4 O13 A:KCO304 4.1 42.7 0.4 O30 A:KCO304 4.1 17.0 0.4 O26 A:KCO304 4.1 34.9 0.4 O24 A:KCO304 4.2 20.6 0.4

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