Calcium in PDB 6qps: Structural Characterization of A Mannuronic Acid Specific Polysaccharide Family 6 Lyase Enzyme From Human Gut Microbiota

The structure of Structural Characterization of A Mannuronic Acid Specific Polysaccharide Family 6 Lyase Enzyme From Human Gut Microbiota, PDB code: 6qps was solved by F.Fredslund, E.G.P.Stender, B.Svensson, D.H.Welner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.40 / 1.29
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.623, 129.951, 66.995, 90.00, 113.90, 90.00
R / Rfree (%)	15.9 / 17.5

The binding sites of Calcium atom in the Structural Characterization of A Mannuronic Acid Specific Polysaccharide Family 6 Lyase Enzyme From Human Gut Microbiota (pdb code 6qps). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structural Characterization of A Mannuronic Acid Specific Polysaccharide Family 6 Lyase Enzyme From Human Gut Microbiota, PDB code: 6qps:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structural Characterization of A Mannuronic Acid Specific Polysaccharide Family 6 Lyase Enzyme From Human Gut Microbiota


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Characterization of A Mannuronic Acid Specific Polysaccharide Family 6 Lyase Enzyme From Human Gut Microbiota within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:12.2 occ:1.00 OE1 A:GLU244 2.3 12.7 1.0 OD1 A:ASN210 2.3 15.4 1.0 OE2 A:GLU213 2.4 13.1 1.0 OE1 A:GLU242 2.4 11.3 1.0 O A:HOH997 2.4 13.7 1.0 O A:HOH652 2.5 14.5 1.0 OE2 A:GLU242 2.7 12.1 1.0 CD A:GLU242 2.9 12.2 1.0 CD A:GLU213 3.2 12.2 1.0 HG3 A:GLU213 3.4 14.4 1.0 CD A:GLU244 3.4 11.5 1.0 CG A:ASN210 3.4 15.8 1.0 H A:GLY211 3.5 19.4 1.0 HD21 A:ASN210 3.6 25.9 1.0 HB2 A:GLU244 3.6 11.8 1.0 HG3 A:GLU244 3.6 13.8 1.0 CG A:GLU213 3.7 12.0 1.0 HG2 A:GLU213 3.8 14.4 1.0 ND2 A:ASN210 3.9 21.6 1.0 CG A:GLU244 3.9 11.5 1.0 O A:HOH757 4.0 23.1 1.0 O A:HOH829 4.1 9.9 1.0 O A:HOH978 4.1 21.0 1.0 OE1 A:GLU213 4.2 11.8 1.0 CB A:GLU244 4.3 9.9 1.0 HA A:ASN210 4.3 17.2 1.0 O A:HOH1061 4.3 29.9 1.0 N A:GLY211 4.3 16.2 1.0 OD1 A:ASN243 4.3 20.1 1.0 H A:GLU244 4.4 12.4 1.0 CG A:GLU242 4.4 11.3 1.0 OE2 A:GLU244 4.4 12.7 1.0 HB2 A:GLU242 4.6 13.6 1.0 O A:HOH1031 4.6 27.2 1.0 HA2 A:GLY211 4.7 18.7 1.0 H A:ALA212 4.7 14.3 1.0 O A:HOH1074 4.7 50.6 1.0 CB A:ASN210 4.7 15.1 1.0 HG3 A:GLU242 4.7 13.6 1.0 HD22 A:ASN210 4.8 25.9 1.0 HG2 A:GLU242 4.8 13.6 1.0 HG2 A:GLU244 4.9 13.8 1.0 HB2 A:SER247 4.9 10.6 1.0 CA A:ASN210 4.9 14.3 1.0 HB3 A:GLU244 4.9 11.8 1.0

Calcium binding site 2 out of 2 in the Structural Characterization of A Mannuronic Acid Specific Polysaccharide Family 6 Lyase Enzyme From Human Gut Microbiota


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Characterization of A Mannuronic Acid Specific Polysaccharide Family 6 Lyase Enzyme From Human Gut Microbiota within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:10.5 occ:1.00 OD1 B:ASN210 2.3 13.6 1.0 OE1 B:GLU244 2.3 11.2 1.0 OE2 B:GLU213 2.4 12.6 1.0 O B:HOH701 2.4 14.1 1.0 O B:HOH985 2.4 12.5 1.0 OE1 B:GLU242 2.5 10.4 1.0 OE2 B:GLU242 2.6 9.9 1.0 CD B:GLU242 2.9 10.2 1.0 CD B:GLU213 3.2 10.6 1.0 HG3 B:GLU213 3.3 12.4 1.0 CG B:ASN210 3.4 14.6 1.0 CD B:GLU244 3.4 8.8 1.0 HD21 B:ASN210 3.5 21.3 1.0 H B:GLY211 3.5 17.3 1.0 HB2 B:GLU244 3.6 10.0 1.0 HG3 B:GLU244 3.6 11.5 1.0 CG B:GLU213 3.7 10.4 1.0 HG2 B:GLU213 3.8 12.4 1.0 ND2 B:ASN210 3.9 17.8 1.0 O B:HOH801 3.9 24.0 1.0 CG B:GLU244 4.0 9.6 1.0 O B:HOH843 4.1 9.2 1.0 O B:HOH972 4.2 18.1 1.0 OE1 B:GLU213 4.2 11.8 1.0 CB B:GLU244 4.2 8.4 1.0 HA B:ASN210 4.3 17.3 1.0 N B:GLY211 4.3 14.4 1.0 H B:GLU244 4.3 10.8 1.0 O B:HOH1063 4.4 27.8 1.0 OD1 B:ASN243 4.4 20.1 1.0 CG B:GLU242 4.4 9.7 1.0 OE2 B:GLU244 4.5 11.6 1.0 HB2 B:GLU242 4.6 13.1 1.0 H B:ALA212 4.6 13.8 1.0 O B:HOH1037 4.6 21.9 1.0 HA2 B:GLY211 4.7 17.6 1.0 CB B:ASN210 4.7 14.1 1.0 HD22 B:ASN210 4.7 21.3 1.0 HG3 B:GLU242 4.8 11.6 1.0 HB2 B:SER247 4.8 11.4 1.0 HG2 B:GLU242 4.8 11.6 1.0 HH21 B:ARG216 4.9 15.9 1.0 HG2 B:GLU244 4.9 11.5 1.0 HB3 B:GLU244 4.9 10.0 1.0 CA B:ASN210 4.9 14.4 1.0 N B:GLU244 5.0 9.0 1.0

E.G.P.Stender, C.Dybdahl Andersen, F.Fredslund, J.Holck, A.Solberg, D.Teze, G.H.J.Peters, B.E.Christensen, F.L.Aachmann, D.H.Welner, B.Svensson. Structural and Functional Aspects of Mannuronic Acid-Specific PL6 Alginate Lyase From the Human Gut Microbebacteroides Cellulosilyticus. J.Biol.Chem. V. 294 17915 2019.
ISSN: ESSN 1083-351X
PubMed: 31530640
DOI: 10.1074/JBC.RA119.010206