Zinc in PDB 8df2: The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase

The structure of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase, PDB code: 8df2 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)	24.93 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.581, 146.094, 147.289, 90, 90, 90
R / Rfree (%)	22.2 / 27

The structure of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase also contains other interesting chemical elements:

Sodium	(Na)	12 atoms
Calcium	(Ca)	4 atoms

The binding sites of Zinc atom in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase (pdb code 8df2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase, PDB code: 8df2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


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 'Alt' Construct of the AMUC_1438 Glycopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:35.2 occ:1.00 NE2 A:HIS233 2.3 29.6 1.0 NE2 A:HIS227 2.3 27.4 1.0 NE2 A:HIS223 2.3 29.0 1.0 O A:HOH678 2.3 37.3 1.0 O A:HOH671 2.6 33.7 1.0 O A:HOH635 2.7 32.7 1.0 CD2 A:HIS227 3.1 26.6 1.0 CD2 A:HIS223 3.1 27.6 1.0 CE1 A:HIS233 3.2 30.0 1.0 CD2 A:HIS233 3.2 29.8 1.0 CE1 A:HIS227 3.3 27.9 1.0 CE1 A:HIS223 3.4 28.1 1.0 OH A:TYR346 3.9 39.2 1.0 ND1 A:HIS233 4.3 29.8 1.0 CE1 A:TYR346 4.3 27.2 1.0 CG A:HIS227 4.3 28.8 1.0 CG A:HIS223 4.4 29.7 1.0 CG A:HIS233 4.4 31.1 1.0 ND1 A:HIS227 4.4 26.0 1.0 ND1 A:HIS223 4.4 28.9 1.0 CZ A:TYR346 4.6 34.1 1.0

Zinc binding site 2 out of 4 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


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 'Alt' Construct of the AMUC_1438 Glycopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:34.7 occ:1.00 NE2 B:HIS233 2.3 26.1 1.0 NE2 B:HIS227 2.3 25.1 1.0 NE2 B:HIS223 2.3 27.8 1.0 O B:HOH679 2.5 34.5 1.0 O B:HOH658 2.5 31.3 1.0 O B:HOH602 2.7 29.2 1.0 CD2 B:HIS223 3.0 25.7 1.0 CD2 B:HIS227 3.0 24.3 1.0 CE1 B:HIS233 3.2 29.6 1.0 CD2 B:HIS233 3.2 25.2 1.0 CE1 B:HIS227 3.4 26.8 1.0 CE1 B:HIS223 3.4 28.9 1.0 CG B:HIS223 4.3 27.8 1.0 OH B:TYR346 4.3 31.0 1.0 CG B:HIS227 4.3 29.8 1.0 ND1 B:HIS233 4.3 29.4 1.0 CG B:HIS233 4.4 28.9 1.0 ND1 B:HIS223 4.4 29.3 1.0 ND1 B:HIS227 4.4 28.5 1.0 CE1 B:TYR346 4.5 28.3 1.0 CZ B:TYR346 4.8 30.7 1.0 OE2 B:GLU224 4.9 43.2 1.0

Zinc binding site 3 out of 4 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:39.6 occ:1.00 O C:HOH665 2.1 36.5 1.0 NE2 C:HIS233 2.3 28.7 1.0 NE2 C:HIS227 2.3 31.3 1.0 NE2 C:HIS223 2.3 28.7 1.0 O C:HOH639 2.5 32.5 1.0 O C:HOH660 2.6 33.2 1.0 CD2 C:HIS227 3.0 29.9 1.0 CD2 C:HIS223 3.1 28.1 1.0 CD2 C:HIS233 3.2 31.0 1.0 CE1 C:HIS233 3.3 30.3 1.0 CE1 C:HIS227 3.4 29.7 1.0 CE1 C:HIS223 3.4 31.4 1.0 OH C:TYR346 4.2 33.9 1.0 CG C:HIS227 4.3 31.9 1.0 CG C:HIS223 4.3 31.7 1.0 CG C:HIS233 4.4 29.6 1.0 CE1 C:TYR346 4.4 35.9 1.0 ND1 C:HIS233 4.4 29.4 1.0 ND1 C:HIS227 4.4 32.5 1.0 ND1 C:HIS223 4.4 30.0 1.0 CZ C:TYR346 4.8 36.8 1.0 CE C:MET248 4.9 25.1 1.0

Zinc binding site 4 out of 4 in the The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of the 'Alt' Construct of the AMUC_1438 Glycopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:36.3 occ:1.00 NE2 D:HIS233 2.3 27.8 1.0 NE2 D:HIS227 2.3 27.5 1.0 NE2 D:HIS223 2.3 28.0 1.0 O D:HOH670 2.4 35.8 1.0 O D:HOH644 2.6 31.4 1.0 O D:HOH673 2.6 29.9 1.0 CD2 D:HIS227 3.1 24.8 1.0 CD2 D:HIS223 3.1 28.3 1.0 CE1 D:HIS233 3.2 30.7 1.0 CD2 D:HIS233 3.3 31.3 1.0 CE1 D:HIS223 3.4 30.2 1.0 CE1 D:HIS227 3.4 27.9 1.0 OH D:TYR346 4.0 42.1 1.0 CG D:HIS223 4.3 32.1 1.0 CG D:HIS227 4.3 29.7 1.0 ND1 D:HIS233 4.3 29.7 1.0 CG D:HIS233 4.4 31.1 1.0 ND1 D:HIS223 4.4 33.7 1.0 ND1 D:HIS227 4.4 30.6 1.0 CE1 D:TYR346 4.4 35.0 1.0 CZ D:TYR346 4.7 34.2 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