Zinc in PDB 8dek: The Structure of the Glycopeptidase Catalytic Domain Including the Linker of AMUC_1438

The structure of The Structure of the Glycopeptidase Catalytic Domain Including the Linker of AMUC_1438, PDB code: 8dek was solved by B.J.Medley, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.92 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.233, 91.471, 161.674, 90, 90, 90
R / Rfree (%)	23.2 / 28.3

The structure of The Structure of the Glycopeptidase Catalytic Domain Including the Linker of AMUC_1438 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the The Structure of the Glycopeptidase Catalytic Domain Including the Linker of AMUC_1438 (pdb code 8dek). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Structure of the Glycopeptidase Catalytic Domain Including the Linker of AMUC_1438, PDB code: 8dek:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the The Structure of the Glycopeptidase Catalytic Domain Including the Linker of AMUC_1438


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of the Glycopeptidase Catalytic Domain Including the Linker of AMUC_1438 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:40.8 occ:1.00 NE2 B:HIS233 2.3 33.2 1.0 NE2 B:HIS223 2.3 31.2 1.0 NE2 B:HIS227 2.3 30.4 1.0 O B:HOH621 2.6 23.4 1.0 O B:HOH607 2.7 16.9 1.0 CE1 B:HIS233 3.0 34.7 1.0 CD2 B:HIS223 3.0 32.3 1.0 CD2 B:HIS227 3.0 29.4 1.0 CE1 B:HIS227 3.4 28.4 1.0 CD2 B:HIS233 3.4 36.2 1.0 CE1 B:HIS223 3.5 32.4 1.0 OH B:TYR346 3.6 60.4 1.0 O A:HOH634 4.0 26.5 1.0 ND1 B:HIS233 4.2 33.1 1.0 CG B:HIS227 4.2 29.0 1.0 CG B:HIS223 4.3 25.6 1.0 O B:HOH622 4.3 20.9 1.0 ND1 B:HIS227 4.4 25.4 1.0 CG B:HIS233 4.4 39.7 1.0 ND1 B:HIS223 4.4 27.5 1.0 CZ B:TYR346 4.5 56.7 1.0 NZ A:LYS207 4.5 38.0 1.0 CE A:LYS207 4.5 33.2 1.0 OE1 B:GLU224 4.7 37.3 1.0 CE1 B:TYR346 4.9 50.8 1.0 CD A:LYS207 4.9 35.9 1.0

Zinc binding site 2 out of 2 in the The Structure of the Glycopeptidase Catalytic Domain Including the Linker of AMUC_1438


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of the Glycopeptidase Catalytic Domain Including the Linker of AMUC_1438 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:41.6 occ:1.00 NE2 A:HIS233 2.3 31.8 1.0 NE2 A:HIS223 2.3 31.7 1.0 NE2 A:HIS227 2.3 26.2 1.0 O A:HOH627 2.6 12.1 1.0 O A:HOH637 2.8 17.9 1.0 CE1 A:HIS233 2.9 38.5 1.0 CD2 A:HIS227 3.0 24.1 1.0 CD2 A:HIS223 3.1 25.8 1.0 CE1 A:HIS223 3.4 28.1 1.0 CE1 A:HIS227 3.4 26.1 1.0 CD2 A:HIS233 3.5 37.2 1.0 OH A:TYR346 3.9 46.8 1.0 O B:HOH619 4.0 23.9 1.0 ND1 A:HIS233 4.2 29.2 1.0 CG A:HIS227 4.2 29.7 1.0 O A:HOH638 4.3 20.9 1.0 CG A:HIS223 4.4 24.5 1.0 ND1 A:HIS227 4.4 27.5 1.0 CE B:LYS207 4.4 24.9 1.0 CG A:HIS233 4.4 38.3 1.0 ND1 A:HIS223 4.4 26.3 1.0 NZ B:LYS207 4.7 26.8 1.0 OE1 A:GLU224 4.8 34.3 1.0 CG B:LYS207 4.8 36.8 1.0 CD B:LYS207 4.8 33.9 1.0 CZ A:TYR346 4.8 52.4 1.0

B.J.Medley, L.Leclaire, N.Thompson, K.E.Mahoney, B.Pluvinage, M.A.H.Parson, J.E.Burke, S.Malaker, W.Wakarchuk, A.B.Boraston. A Previously Uncharacterized O-Glycopeptidase From Akkermansia Muciniphila Requires the Tn-Antigen For Cleavage of the Peptide Bond. J.Biol.Chem. V. 298 02439 2022.
ISSN: ESSN 1083-351X
PubMed: 36049519
DOI: 10.1016/J.JBC.2022.102439