Atomistry » Silicon » PDB 1fuq-6y7o » 6rve
Atomistry »
  Silicon »
    PDB 1fuq-6y7o »
      6rve »

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

Enzymatic activity of 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;

Protein crystallography data

The structure of Co-Substituted Beta-Keggin Bound to Proteinase K Solved By Mr, PDB code: 6rve 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) 35.83 / 1.15
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.420, 68.420, 106.670, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 21.8

Other elements in 6rve:

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

Tungsten (W) 33 atoms
Cobalt (Co) 3 atoms

Silicon Binding Sites:

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

Silicon binding site 1 out of 3 in 6rve

Go back to Silicon Binding Sites List in 6rve
Silicon binding site 1 out of 3 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:22.8
occ:0.54
SI1 A:XCO301 0.0 22.8 0.5
SI1 A:XCO301 0.8 21.9 0.3
O38 A:XCO301 1.1 21.4 0.3
O37 A:XCO301 1.7 24.6 0.5
O39 A:XCO301 1.7 21.8 0.5
O40 A:XCO301 1.8 24.4 0.5
O38 A:XCO301 1.8 24.1 0.5
O40 A:XCO301 1.9 23.9 0.3
O37 A:XCO301 2.2 22.5 0.3
O39 A:XCO301 2.2 20.5 0.3
W10 A:XCO301 2.8 20.6 0.3
W9 A:XCO301 2.8 22.2 0.3
O22 A:XCO301 2.9 20.4 0.3
O27 A:XCO301 2.9 23.9 0.3
O25 A:XCO301 2.9 22.8 0.5
W4 A:XCO301 3.0 21.8 0.3
O35 A:XCO301 3.1 22.1 0.3
O33 A:XCO301 3.1 21.2 0.3
O34 A:XCO301 3.2 20.1 0.3
O22 A:XCO301 3.2 24.7 0.5
O15 A:XCO301 3.2 22.2 0.3
O19 A:XCO301 3.3 21.5 0.5
O18 A:XCO301 3.3 23.9 0.5
O14 A:XCO301 3.3 21.6 0.3
O36 A:XCO301 3.4 21.3 0.5
W12 A:XCO301 3.4 23.7 0.3
CO1 A:XCO301 3.4 21.2 0.5
O28 A:XCO301 3.4 21.9 0.3
W8 A:XCO301 3.4 25.0 0.3
O23 A:XCO301 3.5 21.6 0.3
O36 A:XCO301 3.5 21.8 0.3
W2 A:XCO301 3.5 24.2 0.5
O14 A:XCO301 3.5 25.8 0.5
O21 A:XCO301 3.5 25.1 0.5
O27 A:XCO301 3.5 25.7 0.5
W12 A:XCO301 3.5 23.5 0.5
W4 A:XCO301 3.5 26.0 0.5
W6 A:XCO301 3.5 22.8 0.5
W5 A:XCO301 3.5 23.7 0.5
O32 A:XCO301 3.5 23.7 0.3
CO1 A:XCO301 3.5 20.4 0.3
W7 A:XCO301 3.5 26.0 0.5
O20 A:XCO301 3.5 25.4 0.5
W10 A:XCO301 3.6 22.7 0.5
O34 A:XCO301 3.6 22.2 0.5
W1 A:XCO301 3.6 26.3 0.5
O21 A:XCO301 3.6 24.1 0.3
O15 A:XCO301 3.6 24.7 0.5
W8 A:XCO301 3.6 25.0 0.5
O35 A:XCO301 3.6 23.3 0.5
W9 A:XCO301 3.6 24.7 0.5
W3 A:XCO301 3.6 26.4 0.5
W1 A:XCO301 3.7 21.7 0.3
W5 A:XCO301 3.8 18.1 0.3
O32 A:XCO301 3.8 23.0 0.5
O25 A:XCO301 3.9 22.1 0.3
W3 A:XCO301 4.0 23.6 0.3
O30 A:XCO301 4.0 21.6 0.5
O31 A:XCO301 4.0 24.8 0.5
O18 A:XCO301 4.0 19.5 0.3
O33 A:XCO301 4.0 23.2 0.5
W7 A:XCO301 4.0 24.2 0.3
O28 A:XCO301 4.0 23.1 0.5
O29 A:XCO301 4.1 21.5 0.5
O16 A:XCO301 4.1 24.4 0.5
O24 A:XCO301 4.1 22.8 0.5
O17 A:XCO301 4.1 25.1 0.5
O23 A:XCO301 4.1 24.8 0.5
O13 A:XCO301 4.1 26.4 0.5
O20 A:XCO301 4.2 23.4 0.3
O29 A:XCO301 4.2 19.0 0.3
O17 A:XCO301 4.2 22.9 0.3
W2 A:XCO301 4.2 21.5 0.3
O26 A:XCO301 4.2 25.1 0.5
O19 A:XCO301 4.2 20.9 0.3
W6 A:XCO301 4.3 20.7 0.3
O31 A:XCO301 4.3 23.8 0.3
O13 A:XCO301 4.3 22.7 0.3
O26 A:XCO301 4.4 24.7 0.3
O30 A:XCO301 4.4 20.1 0.3
O16 A:XCO301 4.5 21.0 0.3
O10 A:XCO301 4.5 20.7 0.3
O4 A:XCO301 4.6 19.0 0.3
O9 A:XCO301 4.7 22.4 0.3
O24 A:XCO301 4.8 19.0 0.3
O12 A:XCO301 4.9 24.1 0.3
O4 A:XCO301 5.0 26.1 0.5

Silicon binding site 2 out of 3 in 6rve

Go back to Silicon Binding Sites List in 6rve
Silicon binding site 2 out of 3 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:Si301

b:21.9
occ:0.29
SI1 A:XCO301 0.0 21.9 0.3
SI1 A:XCO301 0.8 22.8 0.5
O37 A:XCO301 1.5 24.6 0.5
O39 A:XCO301 1.6 21.8 0.5
O37 A:XCO301 1.6 22.5 0.3
O40 A:XCO301 1.7 24.4 0.5
O39 A:XCO301 1.7 20.5 0.3
O40 A:XCO301 1.7 23.9 0.3
O38 A:XCO301 1.8 21.4 0.3
O25 A:XCO301 2.3 22.8 0.5
O19 A:XCO301 2.6 21.5 0.5
O38 A:XCO301 2.7 24.1 0.5
O20 A:XCO301 2.8 25.4 0.5
W6 A:XCO301 2.9 22.8 0.5
W7 A:XCO301 2.9 26.0 0.5
O22 A:XCO301 3.0 20.4 0.3
W2 A:XCO301 3.1 24.2 0.5
W3 A:XCO301 3.2 26.4 0.5
O18 A:XCO301 3.3 23.9 0.5
O25 A:XCO301 3.3 22.1 0.3
O21 A:XCO301 3.4 25.1 0.5
O19 A:XCO301 3.4 20.9 0.3
O17 A:XCO301 3.4 22.9 0.3
O27 A:XCO301 3.4 23.9 0.3
O14 A:XCO301 3.4 21.6 0.3
W4 A:XCO301 3.4 21.8 0.3
O36 A:XCO301 3.4 21.3 0.5
O36 A:XCO301 3.5 21.8 0.3
W3 A:XCO301 3.5 23.6 0.3
W5 A:XCO301 3.5 18.1 0.3
O18 A:XCO301 3.5 19.5 0.3
CO1 A:XCO301 3.5 20.4 0.3
W2 A:XCO301 3.5 21.5 0.3
O21 A:XCO301 3.5 24.1 0.3
O20 A:XCO301 3.5 23.4 0.3
W7 A:XCO301 3.5 24.2 0.3
W9 A:XCO301 3.5 22.2 0.3
O15 A:XCO301 3.5 22.2 0.3
W12 A:XCO301 3.5 23.7 0.3
W10 A:XCO301 3.5 20.6 0.3
CO1 A:XCO301 3.5 21.2 0.5
O34 A:XCO301 3.5 20.1 0.3
W8 A:XCO301 3.6 25.0 0.3
W6 A:XCO301 3.6 20.7 0.3
W1 A:XCO301 3.6 21.7 0.3
W12 A:XCO301 3.6 23.5 0.5
O17 A:XCO301 3.6 25.1 0.5
W5 A:XCO301 3.6 23.7 0.5
W8 A:XCO301 3.7 25.0 0.5
O35 A:XCO301 3.7 22.1 0.3
O31 A:XCO301 3.7 24.8 0.5
O30 A:XCO301 3.7 21.6 0.5
O22 A:XCO301 3.7 24.7 0.5
O24 A:XCO301 3.8 22.8 0.5
O32 A:XCO301 3.8 23.7 0.3
W1 A:XCO301 3.8 26.3 0.5
O26 A:XCO301 3.9 25.1 0.5
O33 A:XCO301 3.9 21.2 0.3
O27 A:XCO301 4.0 25.7 0.5
O14 A:XCO301 4.0 25.8 0.5
O32 A:XCO301 4.0 23.0 0.5
O30 A:XCO301 4.0 20.1 0.3
O16 A:XCO301 4.0 24.4 0.5
O31 A:XCO301 4.0 23.8 0.3
O29 A:XCO301 4.0 19.0 0.3
O28 A:XCO301 4.0 21.9 0.3
O13 A:XCO301 4.1 22.7 0.3
O13 A:XCO301 4.1 26.4 0.5
O23 A:XCO301 4.1 21.6 0.3
O34 A:XCO301 4.1 22.2 0.5
O15 A:XCO301 4.1 24.7 0.5
O16 A:XCO301 4.1 21.0 0.3
O35 A:XCO301 4.1 23.3 0.5
O26 A:XCO301 4.1 24.7 0.3
O24 A:XCO301 4.2 19.0 0.3
W4 A:XCO301 4.2 26.0 0.5
O29 A:XCO301 4.3 21.5 0.5
W10 A:XCO301 4.3 22.7 0.5
W9 A:XCO301 4.3 24.7 0.5
O7 A:XCO301 4.4 26.7 0.5
O6 A:XCO301 4.5 23.3 0.5
O3 A:XCO301 4.7 26.4 0.5
O2 A:XCO301 4.7 23.9 0.5
O2 A:XCO301 4.7 22.4 0.3
O33 A:XCO301 4.8 23.2 0.5
O4 A:XCO301 4.8 19.0 0.3
O28 A:XCO301 4.8 23.1 0.5
O23 A:XCO301 4.9 24.8 0.5

Silicon binding site 3 out of 3 in 6rve

Go back to Silicon Binding Sites List in 6rve
Silicon binding site 3 out of 3 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:Si302

b:23.4
occ:0.19
SI1 A:KCO302 0.0 23.4 0.2
O37 A:KCO302 1.6 22.9 0.2
O39 A:KCO302 1.7 24.9 0.2
O40 A:KCO302 1.7 23.0 0.2
O38 A:KCO302 1.8 23.6 0.2
O25 A:KCO302 3.2 23.5 0.2
O22 A:KCO302 3.2 24.6 0.2
O18 A:KCO302 3.4 24.7 0.2
W7 A:KCO302 3.4 22.1 0.2
W2 A:KCO302 3.5 24.2 0.2
O27 A:KCO302 3.5 23.1 0.2
O14 A:KCO302 3.5 23.4 0.2
O34 A:KCO302 3.5 25.0 0.2
CO1 A:KCO302 3.5 25.4 0.2
W5 A:KCO302 3.5 25.1 0.2
W4 A:KCO302 3.5 23.8 0.2
O15 A:KCO302 3.5 22.9 0.2
O19 A:KCO302 3.5 24.6 0.2
W1 A:KCO302 3.5 22.8 0.2
W10 A:KCO302 3.5 23.9 0.2
W8 A:KCO302 3.5 22.6 0.2
W6 A:KCO302 3.5 24.9 0.2
W9 A:KCO302 3.6 23.1 0.2
O21 A:KCO302 3.6 21.5 0.2
W12 A:KCO302 3.6 23.5 0.2
W3 A:KCO302 3.6 20.7 0.2
O20 A:KCO302 3.6 21.2 0.2
O35 A:KCO302 3.8 23.8 0.2
O31 A:KCO302 3.9 22.6 0.2
O28 A:KCO302 4.0 24.0 0.2
O16 A:KCO302 4.0 23.5 0.2
O32 A:KCO302 4.0 22.9 0.2
O23 A:KCO302 4.0 23.5 0.2
O17 A:KCO302 4.0 22.4 0.2
O29 A:KCO302 4.1 25.6 0.2
O33 A:KCO302 4.1 23.6 0.2
O30 A:KCO302 4.1 25.2 0.2
O26 A:KCO302 4.1 22.4 0.2
O13 A:KCO302 4.1 21.6 0.2
O24 A:KCO302 4.2 25.0 0.2
OD2 A:ASP207 4.2 19.2 1.0
O7 A:KCO302 5.0 22.7 0.2

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 02:09:37 2020

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy