Sodium 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:

Zinc

(Zn)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the The Structure of the Glycopeptidase Catalytic Domain Including the Linker of AMUC_1438, PDB code: 8dek:

Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na502 b:40.3 occ:1.00 O B:VAL411 3.9 32.8 1.0 NE2 B:HIS439 4.5 43.6 1.0 CG1 B:VAL411 4.5 27.7 1.0 CD1 B:TYR412 4.6 33.8 1.0 C B:VAL411 4.8 30.5 1.0 CD2 B:HIS439 4.9 46.0 1.0 CE1 B:TYR412 4.9 38.4 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