Calcium in PDB 7f7r: Enterococcus Faecalis GH31 Alpha-N-Acetylgalactosaminidase D455N in Complex with Tn Antigen

The structure of Enterococcus Faecalis GH31 Alpha-N-Acetylgalactosaminidase D455N in Complex with Tn Antigen, PDB code: 7f7r was solved by T.Miyazaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.04 / 1.63
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.706, 82.973, 148.58, 90, 90, 90
R / Rfree (%)	17.7 / 20

The binding sites of Calcium atom in the Enterococcus Faecalis GH31 Alpha-N-Acetylgalactosaminidase D455N in Complex with Tn Antigen (pdb code 7f7r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Enterococcus Faecalis GH31 Alpha-N-Acetylgalactosaminidase D455N in Complex with Tn Antigen, PDB code: 7f7r:

Calcium binding site 1 out of 1 in the Enterococcus Faecalis GH31 Alpha-N-Acetylgalactosaminidase D455N in Complex with Tn Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Enterococcus Faecalis GH31 Alpha-N-Acetylgalactosaminidase D455N in Complex with Tn Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1016 b:46.1 occ:1.00 OE1 A:GLU350 2.2 23.1 1.0 O A:HOH1389 2.3 28.8 1.0 O A:HOH1528 2.3 22.7 1.0 O A:ALA309 2.4 18.7 1.0 OE2 A:GLU336 2.5 22.1 1.0 O A:HOH1451 2.7 28.1 1.0 OD2 A:ASP313 2.9 35.9 1.0 CD A:GLU350 3.0 24.4 1.0 OE2 A:GLU350 3.1 28.1 1.0 C A:ALA309 3.5 19.8 1.0 CD A:GLU336 3.7 22.3 1.0 CB A:ASP313 3.7 24.8 1.0 CG A:ASP313 3.7 27.7 1.0 O A:HOH1377 4.3 21.4 1.0 OD1 A:ASN308 4.3 18.3 1.0 N A:TYR310 4.3 18.3 1.0 OE1 A:GLU336 4.4 21.1 1.0 CG A:GLU350 4.4 22.6 1.0 CA A:ALA309 4.4 19.2 1.0 CA A:TYR310 4.4 19.5 1.0 CB A:ALA309 4.5 20.1 1.0 O A:HOH1361 4.5 33.5 1.0 O A:HOH1192 4.5 22.5 1.0 N A:ASP313 4.5 21.5 1.0 CG A:GLU336 4.7 22.4 1.0 CA A:ASP313 4.7 23.5 1.0 N A:ALA309 4.7 18.6 1.0 CG A:ASN308 4.8 17.2 1.0 OD1 A:ASP313 4.9 28.1 1.0 ND2 A:ASN308 4.9 17.2 1.0 CB A:GLU350 4.9 21.6 1.0 NH2 A:ARG312 4.9 38.6 1.0

T.Miyazaki, M.Ikegaya, S.Alonso-Gil. Structural and Mechanistic Insights Into the Substrate Specificity and Hydrolysis of GH31 Alpha-N-Acetylgalactosaminidase. Biochimie 2021.
ISSN: ISSN 0300-9084
PubMed: 34826537
DOI: 10.1016/J.BIOCHI.2021.11.007