Zinc in PDB 4x8i: 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;

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

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

Cobalt	(Co)	3 atoms
Gadolinium	(Gd)	11 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc where determined in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase, PDB code: 4x8i:
Jump to Zinc binding site number: 1; 2; 3;

Zinc 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 Zinc with other atoms in the Zn 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:Zn401 b:31.2 occ:1.00 O A:HOH577 2.0 41.0 1.0 NE2 A:HIS63 2.1 37.0 1.0 OD1 A:ASP230 2.1 53.7 1.0 OD2 A:ASP230 2.1 51.1 1.0 OD1 A:ASP177 2.1 42.5 1.0 CL A:CL403 2.3 57.3 1.0 CG A:ASP230 2.5 47.0 1.0 CD2 A:HIS63 3.0 38.8 1.0 CE1 A:HIS63 3.1 37.4 1.0 CG A:ASP177 3.1 38.7 1.0 CO A:CO402 3.3 28.0 1.0 OE2 A:GLU207 3.4 46.2 1.0 OD2 A:ASP177 3.5 38.8 1.0 OE1 A:GLU207 3.5 50.5 1.0 CD A:GLU207 3.7 45.0 1.0 OE2 A:GLU208 3.7 35.9 1.0 CB A:ASP230 4.0 43.0 1.0 ND1 A:HIS63 4.2 37.2 1.0 CG A:HIS63 4.2 38.0 1.0 CB A:ASP178 4.2 36.0 1.0 CD A:GLU208 4.3 37.7 1.0 CB A:ASP177 4.5 39.2 1.0 CG A:ASP178 4.6 38.5 1.0 OE1 A:GLU208 4.6 42.9 1.0 N A:VAL231 4.8 43.4 1.0 CG2 A:VAL231 4.8 37.1 1.0 CA A:ASP230 4.8 43.6 1.0 OD2 A:ASP178 5.0 38.8 1.0 CG A:GLU207 5.0 43.2 1.0 CA A:ASP177 5.0 39.5 1.0 CG A:GLU208 5.0 34.9 1.0 OD1 A:ASP178 5.0 39.6 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn401 b:42.8 occ:1.00 OD1 B:ASP230 2.0 45.7 1.0 OD2 B:ASP230 2.0 52.6 1.0 OD1 B:ASP177 2.1 44.4 1.0 NE2 B:HIS63 2.2 39.7 1.0 CG B:ASP230 2.3 48.4 1.0 CL B:CL403 2.4 44.8 1.0 CG B:ASP177 3.1 42.5 1.0 CE1 B:HIS63 3.1 40.8 1.0 CD2 B:HIS63 3.2 39.6 1.0 OD2 B:ASP177 3.3 43.8 1.0 OE1 B:GLU207 3.3 46.5 1.0 CO B:CO402 3.3 35.4 1.0 OE2 B:GLU207 3.6 49.2 1.0 O B:HOH555 3.6 55.1 1.0 CD B:GLU207 3.7 45.2 1.0 CB B:ASP230 3.8 48.3 1.0 OE1 B:GLU208 4.0 36.5 1.0 O B:HOH558 4.1 46.7 1.0 ND1 B:HIS63 4.3 38.4 1.0 CG B:HIS63 4.4 38.9 1.0 CB B:ASP178 4.4 37.4 1.0 CD B:GLU208 4.4 37.0 1.0 CB B:ASP177 4.5 42.4 1.0 OE2 B:GLU208 4.7 37.8 1.0 N B:VAL231 4.7 49.4 1.0 CA B:ASP230 4.7 49.4 1.0 CG B:ASP178 4.7 39.5 1.0 CG2 B:VAL231 4.8 39.2 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn401 b:40.7 occ:1.00 OD2 C:ASP230 2.0 62.8 1.0 OD1 C:ASP230 2.0 57.4 1.0 OD1 C:ASP177 2.1 41.4 1.0 NE2 C:HIS63 2.2 37.0 1.0 CG C:ASP230 2.3 56.9 1.0 CL C:CL403 2.4 49.3 1.0 CG C:ASP177 3.0 41.2 1.0 CE1 C:HIS63 3.2 32.6 1.0 OD2 C:ASP177 3.2 46.3 1.0 CD2 C:HIS63 3.2 37.3 1.0 CO C:CO402 3.3 33.2 1.0 OE2 C:GLU207 3.4 50.3 1.0 OE1 C:GLU207 3.4 53.9 1.0 CD C:GLU207 3.7 49.9 1.0 O C:HOH556 3.8 68.8 1.0 OE1 C:GLU208 3.8 44.0 1.0 CB C:ASP230 3.9 52.3 1.0 O C:HOH554 4.2 67.5 1.0 CD C:GLU208 4.3 41.9 1.0 ND1 C:HIS63 4.3 33.0 1.0 CG C:HIS63 4.4 35.9 1.0 CB C:ASP178 4.4 34.6 1.0 CB C:ASP177 4.5 38.5 1.0 OE2 C:GLU208 4.5 44.3 1.0 N C:VAL231 4.7 46.2 1.0 CG C:ASP178 4.7 35.8 1.0 CA C:ASP230 4.8 51.4 1.0 CG2 C:VAL231 4.8 46.4 1.0

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