Calcium in PDB 5aed: A Bacterial Protein Structure in Glycoside Hydrolase Family 31

The structure of A Bacterial Protein Structure in Glycoside Hydrolase Family 31, PDB code: 5aed was solved by Y.Jin, G.Speciale, G.J.Davies, S.J.Williams, E.D.Goddard-Borger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	105.49 / 1.91
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.710, 113.177, 111.720, 90.00, 109.23, 90.00
R / Rfree (%)	16.8 / 20.1

The binding sites of Calcium atom in the A Bacterial Protein Structure in Glycoside Hydrolase Family 31 (pdb code 5aed). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the A Bacterial Protein Structure in Glycoside Hydrolase Family 31, PDB code: 5aed:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the A Bacterial Protein Structure in Glycoside Hydrolase Family 31


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A Bacterial Protein Structure in Glycoside Hydrolase Family 31 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1683 b:26.4 occ:1.00 OE1 A:GLN153 2.3 27.6 1.0 O A:HOH2078 2.3 21.5 1.0 O A:GLY154 2.4 25.0 1.0 O A:ASP472 2.4 29.5 1.0 OD2 A:ASP481 2.5 28.8 1.0 OD2 A:ASP472 2.5 29.7 1.0 OD1 A:ASP481 2.6 27.0 1.0 CG A:ASP481 2.9 24.3 1.0 CD A:GLN153 3.5 29.7 1.0 CG A:ASP472 3.5 36.5 1.0 C A:ASP472 3.6 31.5 1.0 C A:GLY154 3.6 24.2 1.0 NE2 A:GLN153 4.1 32.2 1.0 CB A:ASP472 4.2 34.0 1.0 O A:HOH2076 4.3 22.4 1.0 CA A:VAL155 4.3 22.8 1.0 CA A:GLN473 4.3 25.4 1.0 N A:VAL155 4.4 22.1 1.0 N A:GLN473 4.4 26.5 1.0 CB A:ASP481 4.4 25.6 1.0 CA A:ASP472 4.5 30.1 1.0 CD A:ARG157 4.5 23.8 1.0 OD1 A:ASP472 4.5 24.0 1.0 OD1 A:ASN474 4.5 27.5 1.0 N A:GLY154 4.6 25.9 1.0 O A:HOH2077 4.6 28.0 1.0 N A:ASN474 4.6 25.3 1.0 CA A:GLY154 4.6 25.5 1.0 C A:GLN473 4.7 26.6 1.0 CG A:GLN153 4.7 30.4 1.0 CB A:GLN153 4.7 28.8 1.0 OG1 A:THR509 4.7 26.1 1.0 C A:GLN153 4.8 26.8 1.0 CG A:ARG157 4.8 21.9 1.0 CG2 A:VAL155 5.0 23.7 1.0

Calcium binding site 2 out of 3 in the A Bacterial Protein Structure in Glycoside Hydrolase Family 31


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A Bacterial Protein Structure in Glycoside Hydrolase Family 31 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1681 b:18.8 occ:1.00 OE1 B:GLN153 2.4 20.3 1.0 O B:ASP472 2.4 19.4 1.0 O B:GLY154 2.4 18.2 1.0 O B:HOH2103 2.4 14.7 1.0 OD2 B:ASP472 2.5 19.5 1.0 OD1 B:ASP481 2.5 19.0 1.0 OD2 B:ASP481 2.6 18.8 1.0 CG B:ASP481 3.0 17.2 1.0 CG B:ASP472 3.5 21.9 1.0 CD B:GLN153 3.5 22.2 1.0 C B:GLY154 3.6 18.8 1.0 C B:ASP472 3.6 19.9 1.0 CB B:ASP472 4.1 20.8 1.0 NE2 B:GLN153 4.2 23.0 1.0 CA B:VAL155 4.3 17.8 1.0 CD B:ARG157 4.3 17.3 1.0 N B:VAL155 4.3 18.5 1.0 CA B:GLN473 4.3 14.3 1.0 O B:HOH2102 4.4 14.8 1.0 N B:GLN473 4.4 16.0 1.0 OD1 B:ASP472 4.4 16.6 1.0 CA B:ASP472 4.4 20.0 1.0 N B:GLY154 4.5 16.6 1.0 CB B:ASP481 4.5 16.5 1.0 OD1 B:ASN474 4.6 18.2 1.0 CA B:GLY154 4.6 17.9 1.0 N B:ASN474 4.6 15.2 1.0 C B:GLN473 4.6 14.8 1.0 O B:HOH2101 4.6 19.5 1.0 CB B:GLN153 4.7 20.6 1.0 C B:GLN153 4.7 16.8 1.0 CG B:GLN153 4.7 21.5 1.0 OG1 B:THR509 4.7 15.7 1.0 CG B:ARG157 4.8 16.6 1.0

Calcium binding site 3 out of 3 in the A Bacterial Protein Structure in Glycoside Hydrolase Family 31


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of A Bacterial Protein Structure in Glycoside Hydrolase Family 31 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1682 b:32.2 occ:1.00 O B:GLU648 2.3 23.7 1.0 O B:HOH2388 2.3 47.6 1.0 O B:HOH2402 2.4 34.8 1.0 O B:HOH2389 2.5 39.1 1.0 O B:HOH2401 2.7 34.1 1.0 C B:GLU648 3.5 25.1 1.0 CA B:VAL649 4.2 23.6 1.0 N B:VAL649 4.3 23.3 1.0 N B:GLU648 4.4 22.9 1.0 CA B:GLU648 4.5 22.8 1.0 O B:HOH2384 4.5 29.3 1.0 O B:HOH2387 4.7 31.1 1.0 CB B:VAL649 4.9 26.4 1.0 C B:GLY647 4.9 24.5 1.0 O B:HOH2386 4.9 37.8 1.0 CB B:GLU648 4.9 26.2 1.0

G.Speciale, Y.Jin, G.J.Davies, S.J.Williams, E.D.Goddard-Borger. Yihq Is A Sulfoquinovosidase That Cleaves Sulfoquinovosyl Diacylglyceride Sulfolipids. Nat.Chem.Biol. V. 12 215 2016.
ISSN: ISSN 1552-4450
PubMed: 26878550
DOI: 10.1038/NCHEMBIO.2023