Calcium in PDB 6n1a: Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii

The structure of Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii, PDB code: 6n1a was solved by L.Sim, P.Rahfeld, S.G.Withers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.20 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.584, 69.186, 104.325, 90.00, 90.00, 90.00
R / Rfree (%)	13.9 / 16.7

The structure of Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii (pdb code 6n1a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii, PDB code: 6n1a:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:50.4 occ:1.00 OD1 A:ASP192 2.4 18.6 1.0 O A:HOH859 2.4 21.7 1.0 OD1 A:ASP195 2.5 19.6 1.0 O A:ASP192 2.6 17.8 1.0 OD2 A:ASP195 2.7 17.8 1.0 CG A:ASP195 3.0 17.4 1.0 CG A:ASP192 3.4 22.2 1.0 C A:ASP192 3.6 16.6 1.0 O A:HOH665 3.9 36.6 1.0 CA A:ASP192 4.0 17.0 1.0 OD2 A:ASP192 4.1 25.9 1.0 CB A:ASP192 4.2 17.9 1.0 CB A:ASP195 4.5 16.3 1.0 O A:PHE193 4.7 16.2 1.0 N A:PHE193 4.7 15.0 1.0 OH A:TYR190 4.9 18.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:16.5 occ:1.00 O A:HOH653 2.3 21.8 1.0 OD1 A:ASP253 2.3 15.9 1.0 O A:HOH645 2.4 17.3 1.0 O A:HOH637 2.4 18.3 1.0 OD1 A:ASP35 2.4 15.7 1.0 OD1 A:ASP101 2.5 17.7 1.0 OD2 A:ASP35 2.6 16.2 1.0 O A:HOH819 2.8 18.7 1.0 CG A:ASP35 2.9 14.8 1.0 CG A:ASP253 3.4 16.6 1.0 CG A:ASP101 3.4 17.3 1.0 OD2 A:ASP101 3.6 18.5 1.0 OD2 A:ASP253 3.7 19.3 1.0 OG1 A:THR187 4.0 16.2 1.0 O A:MET102 4.3 15.0 1.0 NH2 A:ARG315 4.3 15.4 1.0 CB A:ASP35 4.4 13.9 1.0 O A:VAL254 4.4 16.2 1.0 NE2 A:GLN255 4.4 24.4 1.0 OG A:SER317 4.6 15.1 1.0 O A:HOH890 4.6 24.6 1.0 NH1 A:ARG315 4.6 16.4 1.0 CB A:ASP101 4.7 15.5 1.0 CB A:ASP253 4.7 13.3 1.0 N A:MET102 4.7 13.9 1.0 O A:ILE188 4.8 14.9 1.0 CZ A:ARG315 4.9 14.8 1.0 O A:HOH839 5.0 23.1 1.0 CA A:ASP101 5.0 14.1 1.0

P.Rahfeld, L.Sim, H.Moon, I.Constantinescu, C.Morgan-Lang, S.J.Hallam, J.N.Kizhakkedathu, S.G.Withers. An Enzymatic Pathway in the Human Gut Microbiome That Converts A to Universal O Type Blood. Nat Microbiol V. 4 1475 2019.
ISSN: ESSN 2058-5276
PubMed: 31182795
DOI: 10.1038/S41564-019-0469-7