Zinc in PDB 5na8: Structure of Dpp III From Bacteroides Thetaiotaomicron in Closed Form

All present enzymatic activity of Structure of Dpp III From Bacteroides Thetaiotaomicron in Closed Form:
3.4.14.4;

The structure of Structure of Dpp III From Bacteroides Thetaiotaomicron in Closed Form, PDB code: 5na8 was solved by I.Sabljic, M.Luic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.49 / 3.29
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	123.632, 176.315, 74.177, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25.1

The binding sites of Zinc atom in the Structure of Dpp III From Bacteroides Thetaiotaomicron in Closed Form (pdb code 5na8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Dpp III From Bacteroides Thetaiotaomicron in Closed Form, PDB code: 5na8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Dpp III From Bacteroides Thetaiotaomicron in Closed Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Dpp III From Bacteroides Thetaiotaomicron in Closed Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:47.9 occ:1.00 OE2 A:GLU476 2.4 50.4 1.0 NE2 A:HIS453 2.4 54.3 1.0 NE2 A:HIS448 2.5 46.1 1.0 OE1 A:GLU449 3.0 51.1 1.0 CD2 A:HIS448 3.2 48.9 1.0 CD2 A:HIS453 3.3 61.4 1.0 CE1 A:HIS453 3.4 57.4 1.0 CD A:GLU476 3.4 62.4 1.0 CE1 A:HIS448 3.7 49.4 1.0 CD A:GLU449 3.7 43.4 1.0 OE1 A:GLU476 3.8 70.2 1.0 OE2 A:GLU449 3.9 46.4 1.0 CG A:HIS448 4.4 43.0 1.0 ND1 A:HIS453 4.5 69.5 1.0 CG A:HIS453 4.5 70.8 1.0 ND1 A:HIS448 4.7 40.9 1.0 CG A:GLU476 4.7 52.0 1.0 CG A:GLU449 4.9 36.1 1.0

Zinc binding site 2 out of 2 in the Structure of Dpp III From Bacteroides Thetaiotaomicron in Closed Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Dpp III From Bacteroides Thetaiotaomicron in Closed Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:42.4 occ:1.00 OE2 B:GLU476 2.2 33.2 1.0 NE2 B:HIS448 2.5 32.0 1.0 NE2 B:HIS453 2.7 32.7 1.0 OE2 B:GLU449 3.0 37.2 1.0 CD B:GLU476 3.1 38.4 1.0 CD2 B:HIS448 3.2 32.0 1.0 OE1 B:GLU476 3.3 37.5 1.0 CE1 B:HIS448 3.5 37.3 1.0 CD2 B:HIS453 3.7 40.7 1.0 CE1 B:HIS453 3.7 36.7 1.0 CD B:GLU449 3.8 32.8 1.0 OE1 B:GLU449 4.1 34.8 1.0 CG B:HIS448 4.4 33.3 1.0 CG B:GLU476 4.4 40.5 1.0 ND1 B:HIS448 4.5 40.2 1.0 ND1 B:HIS453 4.8 52.5 1.0 CG B:HIS453 4.8 51.4 1.0 O B:GLY383 4.8 41.2 1.0 CG B:GLU449 5.0 25.6 1.0

I.Sabljic, N.Mestrovic, B.Vukelic, P.Macheroux, K.Gruber, M.Luic, M.Abramic. Crystal Structure of Dipeptidyl Peptidase III From the Human Gut Symbiont Bacteroides Thetaiotaomicron. Plos One V. 12 87295 2017.
ISSN: ESSN 1932-6203
PubMed: 29095893
DOI: 10.1371/JOURNAL.PONE.0187295