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

All present enzymatic activity of A Bacterial Protein Structure in Glycoside Hydrolase Family 31:
3.2.1.20;

The structure of A Bacterial Protein Structure in Glycoside Hydrolase Family 31, PDB code: 5aee 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)	53.81 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.960, 107.620, 103.300, 90.00, 107.85, 90.00
R / Rfree (%)	16.3 / 20.1

The structure of A Bacterial Protein Structure in Glycoside Hydrolase Family 31 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the A Bacterial Protein Structure in Glycoside Hydrolase Family 31 (pdb code 5aee). 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: 5aee:
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:Ca1679 b:22.9 occ:1.00 OE1 A:GLN153 2.2 24.0 1.0 O A:ASN472 2.3 20.0 1.0 O A:GLY154 2.3 30.7 1.0 O A:HOH2062 2.4 25.5 1.0 O A:HOH2066 2.4 21.5 1.0 OD1 A:ASP481 2.4 27.6 1.0 OD2 A:ASP481 2.5 26.3 1.0 CG A:ASP481 2.8 26.6 1.0 CD A:GLN153 3.5 30.8 1.0 C A:ASN472 3.5 26.4 1.0 C A:GLY154 3.5 28.4 1.0 NE2 A:GLN153 4.1 31.9 1.0 CD A:ARG157 4.3 26.5 1.0 CA A:VAL155 4.3 28.0 1.0 CA A:GLN473 4.3 24.4 1.0 O A:HOH2063 4.3 24.7 1.0 N A:GLN473 4.3 25.3 1.0 N A:VAL155 4.3 24.8 1.0 CB A:ASP481 4.4 25.6 1.0 CB A:ASN472 4.4 24.2 1.0 CA A:ASN472 4.5 21.9 1.0 N A:ASN474 4.5 21.0 1.0 OD1 A:ASN474 4.6 25.8 1.0 CB A:GLN153 4.6 27.0 1.0 CA A:GLY154 4.6 28.1 1.0 N A:GLY154 4.6 28.8 1.0 CG A:GLN153 4.6 27.3 1.0 O A:HOH2065 4.6 28.2 1.0 C A:GLN473 4.6 21.8 1.0 OG1 A:THR509 4.7 23.3 1.0 C A:GLN153 4.7 25.8 1.0 CG A:ARG157 4.7 22.5 1.0 O A:GLN153 4.8 22.6 1.0 O A:HOH2226 4.9 33.3 1.0 N A:GLY156 4.9 26.3 1.0 O A:HOH2218 4.9 13.1 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 A:Ca1680 b:36.2 occ:1.00 OD1 A:ASN16 2.3 38.9 1.0 O A:HOH2003 2.3 30.9 1.0 O A:GLN15 2.4 38.0 1.0 CG A:ASN16 3.5 33.0 1.0 C A:GLN15 3.6 37.5 1.0 CA A:ASN16 3.9 34.5 1.0 N A:ASN16 4.1 32.4 1.0 CB A:ASN16 4.3 33.2 1.0 ND2 A:ASN16 4.5 31.4 1.0 O A:HOH2006 4.8 35.4 1.0 CA A:GLN15 4.8 38.7 1.0 N A:GLN15 4.9 41.5 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:Ca1678 b:23.8 occ:1.00 OE1 B:GLN153 2.3 23.2 1.0 O B:ASN472 2.4 24.3 1.0 O B:GLY154 2.4 23.1 1.0 OD1 B:ASP481 2.4 23.1 1.0 O B:HOH2202 2.4 18.8 1.0 OD2 B:ASP481 2.5 19.6 1.0 O B:HOH2055 2.6 25.5 1.0 CG B:ASP481 2.8 18.4 1.0 C B:ASN472 3.5 23.2 1.0 CD B:GLN153 3.5 23.8 1.0 C B:GLY154 3.6 24.8 1.0 NE2 B:GLN153 4.1 25.2 1.0 CA B:GLN473 4.2 20.4 1.0 CA B:VAL155 4.3 25.2 1.0 CD B:ARG157 4.3 26.4 1.0 N B:GLN473 4.3 23.7 1.0 CB B:ASP481 4.3 20.9 1.0 N B:VAL155 4.4 22.6 1.0 O B:HOH2056 4.4 23.1 1.0 OD1 B:ASN474 4.4 21.8 1.0 CB B:ASN472 4.4 23.0 1.0 N B:ASN474 4.5 21.8 1.0 CA B:ASN472 4.5 24.5 1.0 C B:GLN473 4.5 20.7 1.0 N B:GLY154 4.6 19.8 1.0 C B:GLN153 4.7 21.6 1.0 CA B:GLY154 4.7 19.0 1.0 CG B:GLN153 4.7 23.2 1.0 O B:HOH2058 4.7 32.8 1.0 CG B:ARG157 4.7 26.0 1.0 OG1 B:THR509 4.8 23.5 1.0 CB B:GLN153 4.8 24.1 1.0 N B:GLY156 4.8 22.2 1.0 O B:HOH2203 4.9 28.0 1.0 O B:GLN153 4.9 20.7 1.0 O B:ASP481 5.0 26.0 1.0 CL B:CL1681 5.0 30.3 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