Atomistry » Cobalt » PDB 4rut-4xc6 » 4x8i
Atomistry »
  Cobalt »
    PDB 4rut-4xc6 »
      4x8i »

Cobalt in PDB 4x8i: De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase

Enzymatic activity of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase

All present enzymatic activity of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase:
3.4.11.15;

Protein crystallography data

The structure of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase, PDB code: 4x8i was solved by M.Colombo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.06 / 2.50
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 203.908, 203.908, 112.443, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.8

Other elements in 4x8i:

The structure of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase also contains other interesting chemical elements:

Zinc (Zn) 3 atoms
Gadolinium (Gd) 11 atoms
Chlorine (Cl) 3 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase (pdb code 4x8i). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase, PDB code: 4x8i:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 4x8i

Go back to Cobalt Binding Sites List in 4x8i
Cobalt binding site 1 out of 3 in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:28.0
occ:1.00
OE2 A:GLU208 2.1 35.9 1.0
OD2 A:ASP177 2.2 38.8 1.0
OE1 A:GLU208 2.2 42.9 1.0
NE2 A:HIS314 2.3 48.5 1.0
CD A:GLU208 2.4 37.7 1.0
CE1 A:HIS314 3.1 48.9 1.0
CG A:ASP177 3.2 38.7 1.0
ZN A:ZN401 3.3 31.2 1.0
CL A:CL403 3.3 57.3 1.0
O A:HOH577 3.3 41.0 1.0
CD2 A:HIS314 3.4 46.7 1.0
OD1 A:ASP177 3.5 42.5 1.0
CG A:GLU208 3.9 34.9 1.0
ND1 A:HIS314 4.3 48.3 1.0
OE2 A:GLU207 4.3 46.2 1.0
CG A:HIS314 4.5 47.3 1.0
CB A:ASP177 4.5 39.2 1.0
SD A:MET313 4.5 52.8 1.0
NE2 A:HIS63 4.6 37.0 1.0
O A:HOH569 4.8 43.8 1.0
CE1 A:HIS63 4.8 37.4 1.0
O A:HOH566 4.9 35.7 1.0
CB A:GLU208 4.9 35.8 1.0
OD1 A:ASP230 5.0 53.7 1.0

Cobalt binding site 2 out of 3 in 4x8i

Go back to Cobalt Binding Sites List in 4x8i
Cobalt binding site 2 out of 3 in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co402

b:35.4
occ:1.00
OE1 B:GLU208 2.1 36.5 1.0
OD2 B:ASP177 2.1 43.8 1.0
NE2 B:HIS314 2.2 38.2 1.0
OE2 B:GLU208 2.3 37.8 1.0
O B:HOH558 2.4 46.7 1.0
CD B:GLU208 2.4 37.0 1.0
O B:HOH555 2.7 55.1 1.0
CE1 B:HIS314 3.1 39.4 1.0
CG B:ASP177 3.2 42.5 1.0
CD2 B:HIS314 3.3 40.0 1.0
ZN B:ZN401 3.3 42.8 1.0
OD1 B:ASP177 3.6 44.4 1.0
CL B:CL403 3.7 44.8 1.0
CG B:GLU208 3.9 38.9 1.0
ND1 B:HIS314 4.3 40.4 1.0
OE1 B:GLU207 4.3 46.5 1.0
CG B:HIS314 4.4 39.7 1.0
CB B:ASP177 4.4 42.4 1.0
O B:HOH553 4.5 32.6 1.0
NE2 B:HIS63 4.6 39.7 1.0
O B:HOH538 4.6 41.9 1.0
CE1 B:HIS63 4.6 40.8 1.0
SD B:MET313 4.9 48.3 1.0
CB B:GLU208 4.9 37.1 1.0
CG2 B:ILE67 4.9 31.3 1.0

Cobalt binding site 3 out of 3 in 4x8i

Go back to Cobalt Binding Sites List in 4x8i
Cobalt binding site 3 out of 3 in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co402

b:33.2
occ:1.00
OD2 C:ASP177 2.1 46.3 1.0
O C:HOH556 2.1 68.8 1.0
OE1 C:GLU208 2.2 44.0 1.0
OE2 C:GLU208 2.2 44.3 1.0
O C:HOH554 2.2 67.5 1.0
NE2 C:HIS314 2.3 40.5 1.0
CD C:GLU208 2.5 41.9 1.0
CG C:ASP177 3.2 41.2 1.0
CE1 C:HIS314 3.2 42.0 1.0
ZN C:ZN401 3.3 40.7 1.0
CD2 C:HIS314 3.4 41.1 1.0
CL C:CL403 3.5 49.3 1.0
OD1 C:ASP177 3.6 41.4 1.0
CG C:GLU208 4.0 38.5 1.0
OE2 C:GLU207 4.3 50.3 1.0
ND1 C:HIS314 4.4 41.3 1.0
CB C:ASP177 4.4 38.5 1.0
CG C:HIS314 4.5 39.4 1.0
NE2 C:HIS63 4.6 37.0 1.0
SD C:MET313 4.6 49.1 1.0
CE1 C:HIS63 4.7 32.6 1.0
O C:HOH537 4.7 30.5 1.0
O C:HOH522 4.8 36.4 1.0
OD1 C:ASP230 4.9 57.4 1.0
CB C:GLU208 4.9 36.9 1.0
OD2 C:ASP230 5.0 62.8 1.0

Reference:

M.Colombo, E.Girard, B.Franzetti. Tuned By Metals: the Tet Peptidase Activity Is Controlled By 3 Metal Binding Sites. Sci Rep V. 6 20876 2016.
ISSN: ESSN 2045-2322
PubMed: 26853450
DOI: 10.1038/SREP20876
Page generated: Tue Jul 30 17:36:17 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy