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Silicon in PDB 7a9m: Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K

Enzymatic activity of Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K

All present enzymatic activity of Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K:
3.4.21.64;

Protein crystallography data

The structure of Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K, PDB code: 7a9m was solved by J.Breibeck, A.Rompel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.95 / 1.62
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.01, 68.01, 102.58, 90, 90, 90
R / Rfree (%) 14.7 / 19

Other elements in 7a9m:

The structure of Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K also contains other interesting chemical elements:

Tungsten (W) 22 atoms
Nickel (Ni) 2 atoms

Silicon Binding Sites:

The binding sites of Silicon atom in the Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K (pdb code 7a9m). This binding sites where shown within 5.0 Angstroms radius around Silicon atom.
In total 2 binding sites of Silicon where determined in the Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K, PDB code: 7a9m:
Jump to Silicon binding site number: 1; 2;

Silicon binding site 1 out of 2 in 7a9m

Go back to Silicon Binding Sites List in 7a9m
Silicon binding site 1 out of 2 in the Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 1 of Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Si302

b:6.3
occ:0.30
SI2 A:R5N302 0.0 6.3 0.3
O59 A:R5N302 1.6 6.0 0.3
O60 A:R5N302 1.6 7.5 0.3
O62 A:R5N302 1.6 8.1 0.3
O61 A:R5N302 1.6 8.6 0.3
O75 A:R5N302 3.3 9.1 0.3
O76 A:R5N302 3.3 8.2 0.3
O68 A:R5N302 3.3 8.8 0.3
O66 A:R5N302 3.3 6.6 0.3
O67 A:R5N302 3.3 6.9 0.3
O53 A:R5N302 3.4 8.2 0.3
O63 A:R5N302 3.4 9.2 0.3
O65 A:R5N302 3.4 7.7 0.3
O57 A:R5N302 3.4 7.5 0.3
O64 A:R5N302 3.4 6.2 0.3
O49 A:R5N302 3.4 7.2 0.3
O41 A:R5N302 3.4 5.8 0.3
W22 A:R5N302 3.5 7.6 0.3
W19 A:R5N302 3.5 7.3 0.3
W21 A:R5N302 3.5 7.6 0.3
W12 A:R5N302 3.5 7.1 0.3
W18 A:R5N302 3.5 6.5 0.3
W17 A:R5N302 3.5 7.5 0.3
W20 A:R5N302 3.6 7.7 0.3
W16 A:R5N302 3.6 8.0 0.3
W14 A:R5N302 3.6 7.6 0.3
W13 A:R5N302 3.6 7.6 0.3
W15 A:R5N302 3.6 7.8 0.3
NI1 A:R5N302 3.6 11.7 0.3
O73 A:R5N302 3.9 9.4 0.3
O55 A:R5N302 3.9 9.5 0.3
O69 A:R5N302 3.9 7.8 0.3
O71 A:R5N302 3.9 7.8 0.3
O51 A:R5N302 3.9 8.8 0.3
O43 A:R5N302 4.0 5.5 0.3
O46 A:R5N302 4.0 7.9 0.3
O78 A:R5N302 4.0 14.8 0.3
O44 A:R5N302 4.0 6.6 0.3
O77 A:R5N302 4.0 9.0 0.3
O47 A:R5N302 4.0 6.5 0.3
O45 A:R5N302 4.0 10.9 0.3

Silicon binding site 2 out of 2 in 7a9m

Go back to Silicon Binding Sites List in 7a9m
Silicon binding site 2 out of 2 in the Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 2 of Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Si303

b:106.6
occ:0.30
SI2 A:R5N303 0.0 106.6 0.3
O59 A:R5N303 1.6 110.2 0.3
O62 A:R5N303 1.6 109.9 0.3
O61 A:R5N303 1.6 97.8 0.3
O60 A:R5N303 1.6 116.7 0.3
O76 A:R5N303 3.2 100.5 0.3
O63 A:R5N303 3.3 130.2 0.3
O75 A:R5N303 3.3 89.5 0.3
O53 A:R5N303 3.3 107.0 0.3
O68 A:R5N303 3.4 96.0 0.3
O49 A:R5N303 3.4 132.2 0.3
O64 A:R5N303 3.4 132.9 0.3
O65 A:R5N303 3.4 114.6 0.3
O66 A:R5N303 3.4 87.6 0.3
O57 A:R5N303 3.5 71.8 0.3
O67 A:R5N303 3.5 68.7 0.3
W19 A:R5N303 3.5 39.8 0.3
W17 A:R5N303 3.5 52.1 0.3
W21 A:R5N303 3.5 59.0 0.3
W14 A:R5N303 3.5 104.8 0.3
W22 A:R5N303 3.5 56.5 0.3
W20 A:R5N303 3.5 95.9 0.3
NI1 A:R5N303 3.5 78.1 0.3
O41 A:R5N303 3.5 125.9 0.3
W12 A:R5N303 3.6 64.6 0.3
W18 A:R5N303 3.6 30.4 0.3
W16 A:R5N303 3.6 83.2 0.3
W15 A:R5N303 3.6 108.4 0.3
W13 A:R5N303 3.7 88.3 0.3
O77 A:R5N303 3.8 72.8 0.3
O78 A:R5N303 3.8 58.3 0.3
O69 A:R5N303 3.9 113.2 0.3
O73 A:R5N303 3.9 85.0 0.3
O46 A:R5N303 3.9 89.8 0.3
O55 A:R5N303 3.9 71.7 0.3
O47 A:R5N303 3.9 118.1 0.3
O71 A:R5N303 3.9 111.3 0.3
O51 A:R5N303 4.0 126.4 0.3
O45 A:R5N303 4.0 121.7 0.3
O44 A:R5N303 4.1 127.0 0.3
O43 A:R5N303 4.1 129.6 0.3
OD1 A:ASP207 4.8 30.4 1.0

Reference:

J.Breibeck, A.Rompel. Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K To Be Published.
Page generated: Fri Nov 5 16:13:50 2021

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