Atomistry » Cobalt » PDB 6oxc-6vv9 » 6rvg
Atomistry »
  Cobalt »
    PDB 6oxc-6vv9 »
      6rvg »

Cobalt in PDB 6rvg: 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: 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

Other elements in 6rvg:

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

Cobalt Binding Sites:

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 6rvg

Go back to Cobalt Binding Sites List in 6rvg
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 6rvg

Go back to Cobalt Binding Sites List in 6rvg
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 6rvg

Go back to Cobalt Binding Sites List in 6rvg
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 6rvg

Go back to Cobalt Binding Sites List in 6rvg
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

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: Sun Dec 13 10:51:39 2020

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy