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Zinc in PDB 5na6: Structure of Cys-Null Se-Met Dpp III From Bacteroides Thetaiotaomicron

Enzymatic activity of Structure of Cys-Null Se-Met Dpp III From Bacteroides Thetaiotaomicron

All present enzymatic activity of Structure of Cys-Null Se-Met Dpp III From Bacteroides Thetaiotaomicron:
3.4.14.4;

Protein crystallography data

The structure of Structure of Cys-Null Se-Met Dpp III From Bacteroides Thetaiotaomicron, PDB code: 5na6 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) 48.57 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.442, 103.442, 141.225, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 20

Other elements in 5na6:

The structure of Structure of Cys-Null Se-Met Dpp III From Bacteroides Thetaiotaomicron also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Cys-Null Se-Met Dpp III From Bacteroides Thetaiotaomicron (pdb code 5na6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Structure of Cys-Null Se-Met Dpp III From Bacteroides Thetaiotaomicron, PDB code: 5na6:

Zinc binding site 1 out of 1 in 5na6

Go back to Zinc Binding Sites List in 5na6
Zinc binding site 1 out of 1 in the Structure of Cys-Null Se-Met Dpp III From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Cys-Null Se-Met Dpp III From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:28.4
occ:0.78
 NE2 A:HIS453 2.1 31.6 1.0
NE2 A:HIS448 2.1 25.0 1.0
O1 A:TRS707 2.1 36.3 0.5
N A:TRS707 2.1 37.6 0.5
OE1 A:GLU476 2.2 28.7 1.0
N A:TRS707 2.2 37.6 0.5
O2 A:TRS707 2.4 38.5 0.5
C1 A:TRS707 2.6 37.3 0.5
C A:TRS707 2.8 37.9 0.5
C A:TRS707 2.9 37.9 0.5
C1 A:TRS707 3.0 37.3 0.5
CE1 A:HIS448 3.0 24.6 1.0
CE1 A:HIS453 3.0 31.8 1.0
CD A:GLU476 3.1 30.1 1.0
CD2 A:HIS453 3.1 32.5 1.0
CD2 A:HIS448 3.1 26.3 1.0
O2 A:TRS707 3.1 39.1 0.5
C2 A:TRS707 3.2 38.6 0.5
OE2 A:GLU476 3.2 33.0 1.0
C2 A:TRS707 3.6 38.4 0.5
O1 A:TRS707 4.0 36.6 0.5
O A:HOH1004 4.1 45.0 1.0
C3 A:TRS707 4.1 38.2 0.5
ND1 A:HIS453 4.2 32.2 1.0
ND1 A:HIS448 4.2 24.8 1.0
CG A:HIS453 4.2 32.9 1.0
O3 A:TRS707 4.2 37.6 0.5
CG A:HIS448 4.3 25.0 1.0
C3 A:TRS707 4.3 38.1 0.5
CE1 A:HIS533 4.4 30.5 1.0
CG A:GLU476 4.5 28.7 1.0
CB A:ALA479 4.7 24.1 1.0
O3 A:TRS707 4.8 38.3 0.5
CB A:GLU476 5.0 25.4 1.0

Reference:

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
Page generated: Thu Aug 21 05:31:19 2025

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