Calcium in PDB 5olp: Galacturonidase

The structure of Galacturonidase, PDB code: 5olp was solved by A.Basle, A.S.Luis, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.73 / 2.00
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	127.545, 127.545, 263.641, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.5

The binding sites of Calcium atom in the Galacturonidase (pdb code 5olp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Galacturonidase, PDB code: 5olp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Galacturonidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Galacturonidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:25.9 occ:1.00 O A:HOH778 3.2 22.0 1.0 NH1 A:ARG343 3.2 20.5 1.0 NH1 A:ARG342 3.3 21.6 1.0 NH1 A:ARG279 3.4 23.0 1.0 ND2 A:ASN280 3.5 17.9 1.0 CD A:ARG342 3.8 21.5 1.0 CE2 A:TYR177 3.8 24.8 1.0 CD A:ARG279 3.9 22.2 1.0 CB A:TRP374 4.0 25.2 1.0 CG A:ARG279 4.0 21.0 1.0 OH A:TYR177 4.2 25.0 1.0 CZ A:ARG343 4.3 20.9 1.0 CZ A:ARG342 4.3 22.5 1.0 CG A:TRP374 4.3 24.0 1.0 CG A:ASN280 4.4 19.5 1.0 CZ A:TYR177 4.4 26.2 1.0 CZ A:ARG279 4.4 22.9 1.0 NE A:ARG342 4.5 21.3 1.0 NH2 A:ARG343 4.5 21.2 1.0 OD1 A:ASN280 4.5 19.5 1.0 NE A:ARG279 4.6 22.2 1.0 CD1 A:LEU371 4.7 25.2 1.0 CD2 A:TYR177 4.7 24.8 1.0 CD2 A:TRP374 4.8 24.4 1.0 CG A:ARG342 4.9 21.0 1.0 CB A:ARG342 4.9 20.6 1.0 CD1 A:TRP374 5.0 24.5 1.0

Calcium binding site 2 out of 4 in the Galacturonidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Galacturonidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:33.5 occ:1.00 O A:HOH778 2.9 22.0 1.0 O A:HOH700 3.3 30.8 1.0 N A:TYR372 3.3 33.7 1.0 N A:TRP374 3.5 25.2 1.0 N A:GLN373 3.7 31.2 1.0 O A:HOH773 3.7 39.6 1.0 O A:HOH788 3.7 29.4 1.0 CD1 A:TRP374 3.7 24.5 1.0 CA A:LEU371 3.9 26.7 1.0 CB A:TRP374 3.9 25.2 1.0 CD1 A:LEU371 4.0 25.2 1.0 C A:TYR372 4.1 32.6 1.0 C A:LEU371 4.1 29.6 1.0 CG A:TRP374 4.2 24.0 1.0 CA A:TYR372 4.2 37.9 1.0 CA A:TRP374 4.3 25.4 1.0 CA A:GLN373 4.4 32.4 1.0 C A:GLN373 4.5 28.6 1.0 O A:VAL370 4.6 22.2 1.0 CB A:GLN373 4.6 36.5 1.0 CB A:LEU371 4.7 26.5 1.0 N A:LEU371 4.8 24.5 1.0 O A:TYR372 4.8 30.1 1.0 CG A:LEU371 4.8 25.4 1.0 CB A:TYR372 4.9 46.4 1.0 N A:LYS375 4.9 26.4 1.0 NE1 A:TRP374 4.9 24.5 1.0 C A:TRP374 4.9 24.1 1.0 NH1 A:ARG279 4.9 23.0 1.0

Calcium binding site 3 out of 4 in the Galacturonidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Galacturonidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:26.3 occ:1.00 O B:HOH718 3.1 22.8 1.0 NH1 B:ARG343 3.2 21.1 1.0 NH1 B:ARG279 3.4 23.9 1.0 NH1 B:ARG342 3.4 23.8 1.0 ND2 B:ASN280 3.5 23.6 1.0 CD B:ARG342 3.7 23.8 1.0 CE2 B:TYR177 3.8 28.6 1.0 CD B:ARG279 3.9 22.4 1.0 CB B:TRP374 4.0 26.6 1.0 CG B:ARG279 4.1 22.4 1.0 OH B:TYR177 4.2 29.4 1.0 CZ B:ARG343 4.2 22.0 1.0 NH2 B:ARG343 4.3 21.0 1.0 CG B:TRP374 4.4 25.1 1.0 CZ B:ARG342 4.4 24.1 1.0 CZ B:ARG279 4.4 25.1 1.0 CZ B:TYR177 4.4 28.3 1.0 CG B:ASN280 4.5 24.1 1.0 NE B:ARG342 4.5 23.6 1.0 OD1 B:ASN280 4.5 23.1 1.0 NE B:ARG279 4.6 23.0 1.0 CD2 B:TYR177 4.7 28.1 1.0 CD1 B:LEU371 4.7 29.1 1.0 CD2 B:TRP374 4.8 24.6 1.0 CG B:ARG342 4.8 23.7 1.0 CB B:ARG342 4.9 22.6 1.0 ND2 B:ASN340 4.9 20.6 1.0

Calcium binding site 4 out of 4 in the Galacturonidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Galacturonidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:35.1 occ:1.00 O B:HOH718 3.2 22.8 1.0 N B:TYR372 3.3 35.3 1.0 O B:HOH658 3.4 36.5 1.0 N B:TRP374 3.5 31.3 1.0 N B:GLN373 3.6 33.8 1.0 O B:HOH741 3.7 29.6 1.0 CD1 B:TRP374 3.8 23.9 1.0 CA B:LEU371 3.9 28.5 1.0 CD1 B:LEU371 3.9 29.1 1.0 CB B:TRP374 3.9 26.6 1.0 C B:LEU371 4.0 29.9 1.0 C B:TYR372 4.1 34.8 1.0 CA B:TYR372 4.2 39.6 1.0 CG B:TRP374 4.3 25.1 1.0 CA B:TRP374 4.3 28.3 1.0 CA B:GLN373 4.3 35.9 1.0 CB B:GLN373 4.4 41.3 1.0 C B:GLN373 4.4 33.0 1.0 O B:VAL370 4.6 25.2 1.0 N B:LEU371 4.7 28.2 1.0 CB B:TYR372 4.8 47.2 1.0 CB B:LEU371 4.8 28.4 1.0 CG B:LEU371 4.8 28.6 1.0 O B:TYR372 4.9 32.2 1.0 C B:TRP374 5.0 27.7 1.0

A.S.Luis, J.Briggs, X.Zhang, B.Farnell, D.Ndeh, A.Labourel, A.Basle, A.Cartmell, N.Terrapon, K.Stott, E.C.Lowe, R.Mclean, K.Shearer, J.Schuckel, I.Venditto, M.C.Ralet, B.Henrissat, E.C.Martens, S.C.Mosimann, D.W.Abbott, H.J.Gilbert. Dietary Pectic Glycans Are Degraded By Coordinated Enzyme Pathways in Human Colonic Bacteroides. Nat Microbiol V. 3 210 2018.
ISSN: ESSN 2058-5276
PubMed: 29255254
DOI: 10.1038/S41564-017-0079-1