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Copper in PDB 6ruk: Cu-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr

Enzymatic activity of Cu-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr

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

Protein crystallography data

The structure of Cu-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr, PDB code: 6ruk 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) 34.99 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.920, 67.920, 102.180, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 16.7

Other elements in 6ruk:

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

Tungsten (W) 55 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Cu-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr (pdb code 6ruk). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 5 binding sites of Copper where determined in the Cu-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr, PDB code: 6ruk:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in 6ruk

Go back to Copper Binding Sites List in 6ruk
Copper binding site 1 out of 5 in the Cu-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cu-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:17.1
occ:0.36
 CU1 A:XCU301 0.0 17.1 0.4
O64 A:XCU301 1.4 26.3 0.2
O76 A:XCU301 2.1 16.9 0.4
O75 A:XCU301 2.1 20.5 0.4
O77 A:XCU301 2.1 13.7 0.4
O78 A:XCU301 2.2 15.4 0.4
O71 A:XCU301 2.3 18.5 0.2
O51 A:XCU301 2.4 27.9 0.2
W20 A:XCU301 2.5 23.7 0.2
W15 A:XCU301 2.6 27.1 0.2
O61 A:XCU301 2.7 18.0 0.4
O65 A:XCU301 2.9 20.3 0.2
O70 A:XCU301 3.1 22.6 0.2
O50 A:XCU301 3.2 24.9 0.2
W18 A:XCU301 3.5 14.2 0.4
W17 A:XCU301 3.5 15.5 0.4
W13 A:XCU301 3.6 16.8 0.4
O62 A:XCU301 3.6 20.2 0.2
O60 A:XCU301 3.6 26.2 0.2
O47 A:XCU301 3.6 21.6 0.2
W12 A:XCU301 3.6 26.6 0.4
W21 A:XCU301 3.7 9.4 0.2
CG A:MET55 3.7 8.7 1.0
OG A:SER63 3.7 15.8 0.5
W16 A:XCU301 3.7 28.5 0.2
O41 A:XCU301 3.7 21.9 0.4
O55 A:XCU301 3.7 14.8 0.4
P2 A:XCU301 3.7 14.4 0.4
O63 A:XCU301 3.8 25.3 0.2
O49 A:XCU301 3.8 25.0 0.2
O53 A:XCU301 4.0 16.1 0.4
O60 A:XCU301 4.0 17.9 0.4
O57 A:XCU301 4.1 15.2 0.4
O59 A:XCU301 4.1 18.7 0.4
O58 A:XCU301 4.1 21.0 0.2
O46 A:XCU301 4.2 25.5 0.2
O69 A:XCU301 4.2 24.9 0.2
O A:ILE42 4.3 8.4 1.0
O A:SER63 4.3 10.8 1.0
P2 A:XCU301 4.3 20.2 0.2
O48 A:XCU301 4.3 23.9 0.2
O A:HOH615 4.3 15.6 1.0
O44 A:XCU301 4.3 24.7 0.2
O43 A:XCU301 4.4 28.6 0.2
CA A:ARG64 4.4 11.2 1.0
CB A:MET55 4.4 8.6 1.0
O45 A:XCU301 4.4 18.5 0.4
C A:SER63 4.4 10.3 1.0
O72 A:XCU301 4.5 11.1 0.2
N A:ARG64 4.5 9.7 1.0
O46 A:XCU301 4.5 21.8 0.4
O42 A:XCU301 4.5 19.5 0.4
CB A:SER63 4.6 13.3 0.5
W19 A:XCU301 4.6 20.3 0.2
O40 A:XCU301 4.6 23.8 0.4
W14 A:XCU301 4.7 21.9 0.2
O52 A:XCU301 4.7 28.5 0.2
O73 A:XCU301 4.7 17.5 0.2
CB A:SER63 4.7 13.3 0.5
O56 A:XCU301 4.8 10.3 0.4
O54 A:XCU301 4.8 15.7 0.4
O45 A:XCU301 4.9 28.9 0.2
W14 A:XCU301 5.0 25.1 0.2

Copper binding site 2 out of 5 in 6ruk

Go back to Copper Binding Sites List in 6ruk
Copper binding site 2 out of 5 in the Cu-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cu-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:37.5
occ:0.14
 CU1 A:XCU301 0.0 37.5 0.1
CU1 A:XCU301 0.9 30.6 0.1
O78 A:XCU301 1.6 30.8 0.1
O75 A:XCU301 1.8 27.9 0.1
O50 A:XCU301 2.0 20.6 0.4
O61 A:XCU301 2.0 32.4 0.1
O76 A:XCU301 2.1 34.7 0.1
O77 A:XCU301 2.1 37.3 0.1
O75 A:XCU301 2.2 34.2 0.1
O78 A:XCU301 2.2 36.0 0.1
CU1 A:XCU301 2.2 25.1 0.2
O77 A:XCU301 2.3 31.9 0.1
O76 A:XCU301 2.4 31.1 0.1
O61 A:XCU301 2.7 33.6 0.1
W18 A:XCU301 2.7 29.0 0.1
P2 A:XCU301 3.0 32.5 0.1
O77 A:XCU301 3.0 21.8 0.2
O55 A:XCU301 3.2 34.0 0.1
O57 A:XCU301 3.2 33.0 0.1
O59 A:XCU301 3.2 32.2 0.1
W17 A:XCU301 3.3 32.1 0.1
W12 A:XCU301 3.3 25.5 0.1
O78 A:XCU301 3.4 24.4 0.2
W17 A:XCU301 3.5 33.5 0.1
W18 A:XCU301 3.5 31.6 0.1
O60 A:XCU301 3.6 32.0 0.1
W12 A:XCU301 3.6 27.2 0.1
W15 A:XCU301 3.7 17.9 0.4
W13 A:XCU301 3.7 27.0 0.1
P2 A:XCU301 3.7 32.7 0.1
O41 A:XCU301 3.7 25.3 0.1
O41 A:XCU301 3.7 31.3 0.1
O55 A:XCU301 3.8 35.3 0.1
O76 A:XCU301 3.8 28.8 0.2
O46 A:XCU301 3.8 32.5 0.1
W13 A:XCU301 3.9 27.4 0.1
O42 A:XCU301 3.9 28.4 0.2
O53 A:XCU301 3.9 33.9 0.1
O60 A:XCU301 4.0 32.0 0.1
O53 A:XCU301 4.0 34.7 0.1
O59 A:XCU301 4.0 32.7 0.1
O75 A:XCU301 4.1 24.6 0.2
O57 A:XCU301 4.1 34.0 0.1
O76 A:XCU301 4.1 26.2 0.2
O56 A:XCU301 4.2 31.2 0.1
CU1 A:XCU301 4.2 24.1 0.2
O67 A:XCU301 4.2 32.0 0.1
W19 A:XCU301 4.3 32.9 0.1
O62 A:XCU301 4.4 35.7 0.1
O49 A:XCU301 4.4 15.0 0.4
O46 A:XCU301 4.4 30.5 0.1
O40 A:XCU301 4.4 28.7 0.1
O41 A:XCU301 4.5 29.6 0.2
O44 A:XCU301 4.5 19.0 0.4
O40 A:XCU301 4.5 27.1 0.2
O64 A:XCU301 4.5 17.7 0.4
O75 A:XCU301 4.5 25.1 0.2
O45 A:XCU301 4.5 30.7 0.1
O40 A:XCU301 4.5 28.3 0.1
W13 A:XCU301 4.6 24.6 0.2
O66 A:XCU301 4.6 36.2 0.1
O51 A:XCU301 4.6 20.2 0.4
O42 A:XCU301 4.6 27.0 0.1
O45 A:XCU301 4.7 30.5 0.1
O54 A:XCU301 4.8 32.1 0.1
W17 A:XCU301 4.8 18.1 0.2
O56 A:XCU301 4.8 27.4 0.1
O54 A:XCU301 4.8 32.9 0.1
O61 A:XCU301 4.8 18.1 0.2
O55 A:XCU301 4.9 16.8 0.2
W12 A:XCU301 4.9 25.6 0.2
O68 A:XCU301 5.0 34.6 0.1
O43 A:XCU301 5.0 31.3 0.1
W18 A:XCU301 5.0 17.6 0.2

Copper binding site 3 out of 5 in 6ruk

Go back to Copper Binding Sites List in 6ruk
Copper binding site 3 out of 5 in the Cu-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Cu-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:24.1
occ:0.18
 CU1 A:XCU301 0.0 24.1 0.2
O78 A:XCU301 1.2 24.4 0.2
W18 A:XCU301 1.8 17.6 0.2
O57 A:XCU301 2.1 20.6 0.2
O77 A:XCU301 2.1 23.2 0.2
O76 A:XCU301 2.1 26.2 0.2
O75 A:XCU301 2.1 25.1 0.2
O78 A:XCU301 2.2 24.9 0.2
O70 A:XCU301 2.2 13.5 0.4
O56 A:XCU301 2.3 15.7 0.2
O63 A:XCU301 2.3 17.2 0.4
O64 A:XCU301 2.4 17.7 0.4
W20 A:XCU301 2.6 14.9 0.4
O61 A:XCU301 2.7 20.6 0.2
O75 A:XCU301 2.9 24.6 0.2
O49 A:XCU301 3.0 15.0 0.4
CU1 A:XCU301 3.0 25.1 0.2
O77 A:XCU301 3.2 31.9 0.1
O48 A:XCU301 3.2 19.9 0.4
W14 A:XCU301 3.3 14.9 0.4
O61 A:XCU301 3.3 18.1 0.2
O55 A:XCU301 3.4 16.8 0.2
W18 A:XCU301 3.5 19.4 0.2
W17 A:XCU301 3.5 18.7 0.2
O50 A:XCU301 3.5 20.6 0.4
W15 A:XCU301 3.5 17.9 0.4
W12 A:XCU301 3.6 25.6 0.2
P2 A:XCU301 3.6 19.9 0.2
O67 A:XCU301 3.7 23.7 0.2
CU1 A:XCU301 3.7 30.6 0.1
O46 A:XCU301 3.7 22.3 0.2
O55 A:XCU301 3.7 20.4 0.2
W13 A:XCU301 3.7 24.6 0.2
O41 A:XCU301 3.7 29.6 0.2
W19 A:XCU301 3.8 19.2 0.2
O78 A:XCU301 3.9 30.8 0.1
O59 A:XCU301 4.0 24.4 0.2
O60 A:XCU301 4.0 22.6 0.2
O76 A:XCU301 4.0 34.7 0.1
O77 A:XCU301 4.0 21.8 0.2
O53 A:XCU301 4.0 21.8 0.2
O57 A:XCU301 4.0 23.0 0.2
O69 A:XCU301 4.0 19.7 0.4
O59 A:XCU301 4.2 22.4 0.2
CU1 A:XCU301 4.2 37.5 0.1
O71 A:XCU301 4.2 15.6 0.4
O42 A:XCU301 4.3 27.0 0.1
W12 A:XCU301 4.3 23.3 0.2
O55 A:XCU301 4.4 34.0 0.1
P2 A:XCU301 4.4 20.2 0.2
O54 A:XCU301 4.4 32.1 0.1
O77 A:XCU301 4.4 37.3 0.1
O46 A:XCU301 4.4 25.5 0.2
W17 A:XCU301 4.5 32.1 0.1
O58 A:XCU301 4.5 21.6 0.2
O68 A:XCU301 4.5 20.7 0.2
O45 A:XCU301 4.5 25.1 0.2
O40 A:XCU301 4.6 27.1 0.2
O62 A:XCU301 4.6 15.7 0.4
W17 A:XCU301 4.6 18.1 0.2
O47 A:XCU301 4.7 14.2 0.4
O42 A:XCU301 4.7 28.4 0.2
O54 A:XCU301 4.7 11.4 0.2
O56 A:XCU301 4.8 20.7 0.2
O76 A:XCU301 4.8 28.8 0.2
O51 A:XCU301 4.8 20.2 0.4
W13 A:XCU301 4.9 27.0 0.1
O43 A:XCU301 4.9 16.9 0.4
O59 A:XCU301 4.9 18.7 0.4
O60 A:XCU301 5.0 17.9 0.4

Copper binding site 4 out of 5 in 6ruk

Go back to Copper Binding Sites List in 6ruk
Copper binding site 4 out of 5 in the Cu-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Cu-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:25.1
occ:0.17
 CU1 A:XCU301 0.0 25.1 0.2
O50 A:XCU301 0.5 20.6 0.4
CU1 A:XCU301 1.4 30.6 0.1
W15 A:XCU301 1.5 17.9 0.4
O76 A:XCU301 2.1 28.8 0.2
O75 A:XCU301 2.1 24.6 0.2
O77 A:XCU301 2.2 21.8 0.2
O78 A:XCU301 2.2 24.4 0.2
CU1 A:XCU301 2.2 37.5 0.1
O64 A:XCU301 2.4 17.7 0.4
O75 A:XCU301 2.5 25.1 0.2
O49 A:XCU301 2.6 15.0 0.4
O40 A:XCU301 2.7 27.1 0.2
O51 A:XCU301 2.7 20.2 0.4
O77 A:XCU301 2.8 31.9 0.1
O61 A:XCU301 2.8 18.1 0.2
O44 A:XCU301 2.9 19.0 0.4
O78 A:XCU301 2.9 30.8 0.1
O76 A:XCU301 2.9 31.1 0.1
W12 A:XCU301 3.0 25.6 0.2
O75 A:XCU301 3.0 27.9 0.1
CU1 A:XCU301 3.0 24.1 0.2
O41 A:XCU301 3.3 29.6 0.2
O76 A:XCU301 3.5 34.7 0.1
O76 A:XCU301 3.5 26.2 0.2
W18 A:XCU301 3.5 17.6 0.2
O77 A:XCU301 3.5 37.3 0.1
W17 A:XCU301 3.6 18.1 0.2
O75 A:XCU301 3.6 34.2 0.1
W12 A:XCU301 3.7 23.3 0.2
O78 A:XCU301 3.7 36.0 0.1
W13 A:XCU301 3.7 25.4 0.2
O55 A:XCU301 3.7 16.8 0.2
O41 A:XCU301 3.8 26.9 0.2
P2 A:XCU301 3.8 20.2 0.2
O60 A:XCU301 3.9 17.9 0.4
O61 A:XCU301 4.1 32.4 0.1
O59 A:XCU301 4.1 22.4 0.2
O63 A:XCU301 4.1 17.2 0.4
W20 A:XCU301 4.2 14.9 0.4
O60 A:XCU301 4.2 26.2 0.2
O57 A:XCU301 4.2 20.6 0.2
W13 A:XCU301 4.2 24.6 0.2
O53 A:XCU301 4.2 23.7 0.2
W14 A:XCU301 4.3 14.9 0.4
O46 A:XCU301 4.3 25.5 0.2
O42 A:XCU301 4.4 28.4 0.2
O40 A:XCU301 4.4 13.3 0.2
W13 A:XCU301 4.5 27.4 0.1
W17 A:XCU301 4.5 32.1 0.1
O70 A:XCU301 4.5 13.5 0.4
O46 A:XCU301 4.5 22.3 0.2
W12 A:XCU301 4.5 25.5 0.1
O78 A:XCU301 4.5 24.9 0.2
W18 A:XCU301 4.5 29.0 0.1
O42 A:XCU301 4.6 27.8 0.2
W16 A:XCU301 4.6 16.1 0.4
O41 A:XCU301 4.6 25.3 0.1
O55 A:XCU301 4.6 34.0 0.1
O45 A:XCU301 4.6 28.9 0.2
O48 A:XCU301 4.6 19.9 0.4
O45 A:XCU301 4.7 18.5 0.4
O56 A:XCU301 4.8 15.7 0.2
W13 A:XCU301 4.8 16.8 0.4
O54 A:XCU301 4.8 15.1 0.2
O65 A:XCU301 4.8 17.9 0.4
W13 A:XCU301 4.9 27.0 0.1
O43 A:XCU301 4.9 28.6 0.2
O42 A:XCU301 4.9 28.7 0.1
O61 A:XCU301 4.9 33.6 0.1
O40 A:XCU301 5.0 28.7 0.1
O71 A:XCU301 5.0 15.6 0.4
W12 A:XCU301 5.0 27.2 0.1
O41 A:XCU301 5.0 31.3 0.1
P2 A:XCU301 5.0 14.4 0.4
O43 A:XCU301 5.0 16.9 0.4
O59 A:XCU301 5.0 24.4 0.2
O41 A:XCU301 5.0 21.9 0.4

Copper binding site 5 out of 5 in 6ruk

Go back to Copper Binding Sites List in 6ruk
Copper binding site 5 out of 5 in the Cu-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Cu-Substituted Alpha-Keggin Bound to Proteinase K Solved By Mr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:30.6
occ:0.15
 CU1 A:XCU301 0.0 30.6 0.1
CU1 A:XCU301 0.9 37.5 0.1
O50 A:XCU301 1.2 20.6 0.4
CU1 A:XCU301 1.4 25.1 0.2
O76 A:XCU301 2.1 31.1 0.1
O77 A:XCU301 2.1 31.9 0.1
O75 A:XCU301 2.2 27.9 0.1
O78 A:XCU301 2.2 30.8 0.1
O75 A:XCU301 2.4 34.2 0.1
O76 A:XCU301 2.4 34.7 0.1
O61 A:XCU301 2.8 32.4 0.1
O77 A:XCU301 2.8 21.8 0.2
O77 A:XCU301 2.8 37.3 0.1
O78 A:XCU301 2.8 36.0 0.1
W15 A:XCU301 2.9 17.9 0.4
O78 A:XCU301 2.9 24.4 0.2
O76 A:XCU301 3.0 28.8 0.2
O75 A:XCU301 3.2 24.6 0.2
W17 A:XCU301 3.5 32.1 0.1
W18 A:XCU301 3.5 29.0 0.1
O64 A:XCU301 3.6 17.7 0.4
O61 A:XCU301 3.7 33.6 0.1
W12 A:XCU301 3.7 25.5 0.1
O55 A:XCU301 3.7 34.0 0.1
CU1 A:XCU301 3.7 24.1 0.2
W13 A:XCU301 3.7 27.4 0.1
O51 A:XCU301 3.7 20.2 0.4
P2 A:XCU301 3.7 32.5 0.1
O75 A:XCU301 3.8 25.1 0.2
O41 A:XCU301 3.8 25.3 0.1
O49 A:XCU301 3.8 15.0 0.4
O40 A:XCU301 3.8 27.1 0.2
W12 A:XCU301 3.8 27.2 0.1
O44 A:XCU301 3.9 19.0 0.4
O41 A:XCU301 3.9 31.3 0.1
W13 A:XCU301 3.9 27.0 0.1
O76 A:XCU301 3.9 26.2 0.2
O59 A:XCU301 4.0 32.2 0.1
O60 A:XCU301 4.0 32.0 0.1
O53 A:XCU301 4.0 34.7 0.1
O57 A:XCU301 4.1 33.0 0.1
O61 A:XCU301 4.1 18.1 0.2
O41 A:XCU301 4.2 29.6 0.2
O42 A:XCU301 4.3 28.4 0.2
W12 A:XCU301 4.3 25.6 0.2
W18 A:XCU301 4.3 31.6 0.1
W17 A:XCU301 4.3 33.5 0.1
O40 A:XCU301 4.4 28.3 0.1
W17 A:XCU301 4.5 18.1 0.2
O46 A:XCU301 4.5 32.5 0.1
W18 A:XCU301 4.5 17.6 0.2
O42 A:XCU301 4.5 27.0 0.1
O45 A:XCU301 4.5 30.5 0.1
P2 A:XCU301 4.5 32.7 0.1
O40 A:XCU301 4.5 28.7 0.1
W13 A:XCU301 4.6 24.6 0.2
O55 A:XCU301 4.6 16.8 0.2
O55 A:XCU301 4.6 35.3 0.1
W13 A:XCU301 4.6 25.4 0.2
W12 A:XCU301 4.6 23.3 0.2
O42 A:XCU301 4.6 28.7 0.1
O60 A:XCU301 4.6 32.0 0.1
O59 A:XCU301 4.6 32.7 0.1
O53 A:XCU301 4.7 33.9 0.1
O41 A:XCU301 4.7 26.9 0.2
O46 A:XCU301 4.7 30.5 0.1
O57 A:XCU301 4.7 34.0 0.1
O54 A:XCU301 4.8 32.1 0.1
O56 A:XCU301 4.8 31.2 0.1
O45 A:XCU301 4.9 30.7 0.1

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 Jul 31 07:28:23 2024

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