Cobalt 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
Silicon	(Si)	4 atoms

The binding sites of Cobalt 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 Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Co-Substituted Beta-Keggin Bound to Proteinase K Solved By Mr, PDB code: 6rvg:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt 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 Cobalt with other atoms in the Co 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:Co301 b:25.9 occ:0.36 CO1 A:XCO301 0.0 25.9 0.4 O36 A:XCO301 1.8 26.4 0.4 O34 A:XCO301 1.8 24.3 0.4 O30 A:XCO301 1.9 27.9 0.4 O29 A:XCO301 2.0 23.1 0.4 O39 A:XCO301 2.4 34.4 0.4 W6 A:XCO301 3.3 24.6 0.4 W5 A:XCO301 3.3 24.6 0.4 SI1 A:XCO301 3.4 35.1 0.4 O24 A:XCO301 3.6 21.0 0.4 W12 A:XCO301 3.6 27.1 0.4 W10 A:XCO301 3.6 26.9 0.4 O25 A:XCO301 3.7 34.3 0.4 O35 A:XCO301 3.8 29.5 0.4 O A:HOH408 3.8 29.6 1.0 O22 A:XCO301 3.8 23.5 0.4 O40 A:XCO301 3.9 33.2 0.4 O38 A:XCO301 4.1 39.9 0.4 O31 A:XCO301 4.2 30.5 0.4 O28 A:XCO301 4.3 29.7 0.4 O12 A:XCO301 4.4 20.2 0.4 O10 A:XCO301 4.4 21.8 0.4 O6 A:XCO301 4.6 31.4 0.4 O18 A:XCO301 4.7 31.4 0.4 O19 A:XCO301 4.8 32.9 0.4 O5 A:XCO301 4.8 13.2 0.4 O37 A:XCO301 4.8 39.8 0.4 W7 A:XCO301 4.9 27.7 0.4 W4 A:XCO301 5.0 26.9 0.4

Cobalt 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 Cobalt with other atoms in the Co 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:Co302 b:6.5 occ:0.20 CO1 A:XCO302 0.0 6.5 0.2 O34 A:XCO303 1.0 5.1 0.2 CO1 A:XCO303 1.0 7.0 0.2 O29 A:XCO303 1.7 9.6 0.2 O36 A:XCO302 1.8 9.7 0.2 O34 A:XCO302 1.8 9.7 0.2 O29 A:XCO302 1.9 10.8 0.2 O30 A:XCO302 1.9 10.8 0.2 O36 A:XCO303 2.3 8.8 0.2 O A:HOH452 2.3 16.6 1.0 O39 A:XCO302 2.4 7.7 0.2 O39 A:XCO303 2.6 10.1 0.2 W10 A:XCO303 2.9 9.4 0.2 O30 A:XCO303 2.9 10.7 0.2 O22 A:XCO303 3.0 10.9 0.2 W5 A:XCO303 3.1 7.1 0.2 W6 A:XCO302 3.3 9.8 0.2 W5 A:XCO302 3.3 9.3 0.2 HA A:ARG64 3.4 12.6 1.0 O28 A:XCO303 3.4 16.1 0.2 SI1 A:XCO303 3.4 8.8 0.2 SI1 A:XCO302 3.5 7.8 0.2 HG3 A:MET55 3.5 10.2 1.0 O24 A:XCO302 3.6 10.8 0.2 O38 A:XCO303 3.6 9.5 0.2 W12 A:XCO302 3.6 9.2 0.2 W10 A:XCO302 3.6 8.4 0.2 O35 A:XCO303 3.6 12.5 0.2 O10 A:XCO303 3.7 8.7 0.2 O25 A:XCO302 3.7 11.9 0.2 HG2 A:MET55 3.8 10.2 1.0 O22 A:XCO302 3.8 9.2 0.2 O35 A:XCO302 3.8 14.1 0.2 W12 A:XCO303 3.8 8.9 0.2 O40 A:XCO302 3.9 9.3 0.2 O24 A:XCO303 3.9 10.0 0.2 W6 A:XCO303 4.0 9.4 0.2 OG A:SER63 4.1 14.5 0.5 O A:HOH410 4.1 15.2 1.0 O38 A:XCO302 4.1 10.2 0.2 H A:ALA44 4.1 10.5 1.0 CG A:MET55 4.1 8.5 1.0 O A:ILE42 4.1 7.7 1.0 O40 A:XCO303 4.2 9.2 0.2 W4 A:XCO303 4.2 10.3 0.2 CA A:ARG64 4.3 10.5 1.0 O31 A:XCO302 4.3 9.0 0.2 O A:SER63 4.3 10.3 1.0 HB2 A:ARG64 4.3 16.7 1.0 HG A:SER63 4.3 17.4 0.5 O28 A:XCO302 4.3 8.8 0.2 HA A:GLU43 4.4 9.8 1.0 O12 A:XCO302 4.4 15.5 0.2 HB2 A:SER63 4.4 13.9 0.5 O5 A:XCO303 4.4 8.8 0.2 O10 A:XCO302 4.5 9.1 0.2 O25 A:XCO303 4.5 10.1 0.2 HB2 A:ALA44 4.5 17.0 1.0 C A:SER63 4.5 11.3 1.0 N A:ARG64 4.5 10.7 1.0 HB2 A:MET55 4.6 11.4 1.0 O6 A:XCO302 4.6 10.3 0.2 O18 A:XCO303 4.6 9.6 0.2 O12 A:XCO303 4.7 11.9 0.2 O19 A:XCO302 4.7 9.3 0.2 O33 A:XCO303 4.7 6.9 0.2 HB3 A:SER63 4.7 13.9 0.5 O18 A:XCO302 4.7 11.6 0.2 O5 A:XCO302 4.7 9.4 0.2 H A:ASP65 4.7 11.2 1.0 O31 A:XCO303 4.8 10.7 0.2 CB A:ARG64 4.8 13.9 1.0 O37 A:XCO303 4.8 12.9 0.2 O37 A:XCO302 4.9 6.2 0.2 W7 A:XCO302 4.9 11.0 0.2 N A:ALA44 4.9 8.8 1.0 O A:HOH542 4.9 15.9 1.0 CB A:MET55 5.0 9.5 1.0 CB A:SER63 5.0 11.6 0.5 W4 A:XCO302 5.0 10.7 0.2

Cobalt 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 Cobalt with other atoms in the Co 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:Co303 b:7.0 occ:0.19 CO1 A:XCO303 0.0 7.0 0.2 CO1 A:XCO302 1.0 6.5 0.2 O36 A:XCO302 1.4 9.7 0.2 O30 A:XCO302 1.5 10.8 0.2 O34 A:XCO303 1.8 5.1 0.2 O36 A:XCO303 1.8 8.8 0.2 O29 A:XCO303 1.9 9.6 0.2 O30 A:XCO303 1.9 10.7 0.2 O A:HOH452 2.1 16.6 1.0 O39 A:XCO303 2.4 10.1 0.2 HA A:ARG64 2.5 12.6 1.0 O34 A:XCO302 2.6 9.7 0.2 O39 A:XCO302 2.7 7.7 0.2 O29 A:XCO302 2.8 10.8 0.2 W6 A:XCO302 3.1 9.8 0.2 O25 A:XCO302 3.2 11.9 0.2 W5 A:XCO303 3.2 7.1 0.2 W6 A:XCO303 3.3 9.4 0.2 W12 A:XCO302 3.3 9.2 0.2 O A:HOH410 3.4 15.2 1.0 HB2 A:ARG64 3.4 16.7 1.0 CA A:ARG64 3.4 10.5 1.0 SI1 A:XCO303 3.5 8.8 0.2 O24 A:XCO303 3.5 10.0 0.2 O22 A:XCO303 3.6 10.9 0.2 O31 A:XCO302 3.6 9.0 0.2 W12 A:XCO303 3.6 8.9 0.2 W10 A:XCO303 3.6 9.4 0.2 O25 A:XCO303 3.8 10.1 0.2 O24 A:XCO302 3.8 10.8 0.2 SI1 A:XCO302 3.8 7.8 0.2 O40 A:XCO302 3.9 9.3 0.2 CB A:ARG64 3.9 13.9 1.0 N A:ARG64 3.9 10.7 1.0 HG3 A:MET55 3.9 10.2 1.0 O35 A:XCO303 3.9 12.5 0.2 O12 A:XCO302 4.0 15.5 0.2 O A:SER63 4.0 10.3 1.0 H A:ASP65 4.0 11.2 1.0 O40 A:XCO303 4.0 9.2 0.2 O35 A:XCO302 4.0 14.1 0.2 W5 A:XCO302 4.0 9.3 0.2 O38 A:XCO303 4.1 9.5 0.2 C A:SER63 4.1 11.3 1.0 O6 A:XCO302 4.2 10.3 0.2 HA A:GLU43 4.2 9.8 1.0 O A:ILE42 4.2 7.7 1.0 OG A:SER63 4.2 14.5 0.5 O31 A:XCO303 4.2 10.7 0.2 HG3 A:ARG64 4.2 26.4 1.0 W10 A:XCO302 4.3 8.4 0.2 O28 A:XCO303 4.3 16.1 0.2 HG2 A:MET55 4.4 10.2 1.0 H A:ARG64 4.4 12.9 1.0 HG A:SER63 4.4 17.4 0.5 O12 A:XCO303 4.4 11.9 0.2 O10 A:XCO303 4.4 8.7 0.2 W7 A:XCO302 4.5 11.0 0.2 O6 A:XCO303 4.5 14.2 0.2 HB2 A:SER63 4.5 13.9 0.5 H A:ALA44 4.5 10.5 1.0 C A:ARG64 4.5 10.4 1.0 N A:ASP65 4.6 9.3 1.0 CG A:MET55 4.6 8.5 1.0 O5 A:XCO303 4.6 8.8 0.2 CG A:ARG64 4.6 22.0 1.0 HB3 A:ARG64 4.7 16.7 1.0 O22 A:XCO302 4.7 9.2 0.2 O18 A:XCO303 4.7 9.6 0.2 O19 A:XCO303 4.7 10.3 0.2 O19 A:XCO302 4.7 9.3 0.2 O38 A:XCO302 4.7 10.2 0.2 HB3 A:SER63 4.9 13.9 0.5 O37 A:XCO303 4.9 12.9 0.2 W4 A:XCO303 4.9 10.3 0.2 W7 A:XCO303 5.0 10.4 0.2

Cobalt 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 Cobalt with other atoms in the Co 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:Co304 b:34.9 occ:0.37 CO1 A:KCO304 0.0 34.9 0.4 O34 A:KCO304 1.8 40.4 0.4 O29 A:KCO304 1.9 35.7 0.4 OD2 A:ASP207 2.0 16.6 1.0 O30 A:KCO304 2.0 17.0 0.4 O39 A:KCO304 2.4 36.2 0.4 O A:HOH420 2.4 45.1 1.0 HH22 A:ARG185 2.7 17.6 1.0 CG A:ASP207 2.8 11.4 1.0 HB3 A:ASP207 3.1 11.7 1.0 HB2 A:ASP207 3.2 11.7 1.0 W5 A:KCO304 3.3 30.3 0.4 CB A:ASP207 3.3 9.7 1.0 HE A:ARG185 3.3 16.7 1.0 W6 A:KCO304 3.3 31.4 0.4 NH2 A:ARG185 3.6 14.7 1.0 SI1 A:KCO304 3.6 39.3 0.4 O24 A:KCO304 3.6 20.6 0.4 O22 A:KCO304 3.7 46.4 0.4 OD1 A:ASP207 3.7 15.6 1.0 W10 A:KCO304 3.7 32.7 0.4 O25 A:KCO304 3.8 32.1 0.4 W12 A:KCO304 3.9 33.7 0.4 NE A:ARG185 4.0 13.9 1.0 O35 A:KCO304 4.0 42.9 0.4 HH21 A:ARG185 4.1 17.6 1.0 O40 A:KCO304 4.1 36.6 0.4 O38 A:KCO304 4.2 51.6 0.4 CZ A:ARG185 4.3 11.3 1.0 O28 A:KCO304 4.3 59.2 0.4 O31 A:KCO304 4.5 17.2 0.4 O10 A:KCO304 4.5 47.5 0.4 HG23 A:THR206 4.5 10.0 1.0 O5 A:KCO304 4.6 34.1 0.4 O6 A:KCO304 4.7 22.0 0.4 O18 A:KCO304 4.7 40.3 0.4 O A:HOH565 4.8 9.0 1.0 CA A:ASP207 4.8 7.2 1.0 O19 A:KCO304 4.8 29.0 0.4 W4 A:KCO304 4.9 28.9 0.4 O37 A:KCO304 5.0 40.9 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