Calcium in PDB 6euh: The GH43, Beta 1,3 Galactosidase, BT3683 with Galactodeoxynojirimycin

The structure of The GH43, Beta 1,3 Galactosidase, BT3683 with Galactodeoxynojirimycin, PDB code: 6euh was solved by A.Cartmell, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.19 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	52.180, 77.200, 78.690, 114.00, 101.78, 100.78
R / Rfree (%)	18.3 / 22.6

The binding sites of Calcium atom in the The GH43, Beta 1,3 Galactosidase, BT3683 with Galactodeoxynojirimycin (pdb code 6euh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The GH43, Beta 1,3 Galactosidase, BT3683 with Galactodeoxynojirimycin, PDB code: 6euh:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the The GH43, Beta 1,3 Galactosidase, BT3683 with Galactodeoxynojirimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The GH43, Beta 1,3 Galactosidase, BT3683 with Galactodeoxynojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:46.4 occ:1.00 O A:ASN239 2.6 14.4 1.0 N A:ASN239 3.1 17.4 1.0 O A:ASN211 3.2 16.5 1.0 N A:THR213 3.3 15.2 1.0 C A:THR213 3.3 16.6 1.0 C A:ASN239 3.4 16.5 1.0 C A:LEU212 3.5 17.2 1.0 N A:LEU214 3.5 16.2 1.0 CA A:THR213 3.5 15.8 1.0 OG A:SER207 3.5 14.5 0.5 CA A:ASN239 3.6 17.0 1.0 O A:THR213 3.7 15.7 1.0 O A:LEU212 3.7 17.3 1.0 OE2 A:GLU240 3.8 22.5 1.0 C A:HIS238 3.8 18.3 1.0 CB A:ASN239 3.8 16.8 1.0 CA A:HIS238 3.9 19.4 1.0 CG A:LEU214 4.0 17.3 1.0 C A:ASN211 4.0 16.5 1.0 N A:HIS238 4.0 19.1 1.0 CB A:SER207 4.2 15.6 0.5 CA A:LEU214 4.2 16.3 1.0 OG A:SER207 4.2 16.9 0.5 CD2 A:LEU214 4.3 16.9 1.0 CB A:SER207 4.3 14.7 0.5 CA A:LEU212 4.4 16.0 1.0 CD A:GLU240 4.4 21.3 1.0 CA A:SER207 4.5 15.6 0.5 CA A:SER207 4.5 15.2 0.5 N A:LEU212 4.5 15.8 1.0 OE1 A:GLU240 4.5 23.5 1.0 CB A:LEU214 4.5 16.5 1.0 N A:GLU240 4.7 16.9 1.0 O A:HIS238 4.8 19.5 1.0 C A:GLY237 4.9 20.2 1.0 CA A:ASN211 5.0 18.6 1.0 CG A:ASN239 5.0 16.9 1.0

Calcium binding site 2 out of 3 in the The GH43, Beta 1,3 Galactosidase, BT3683 with Galactodeoxynojirimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The GH43, Beta 1,3 Galactosidase, BT3683 with Galactodeoxynojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:50.5 occ:1.00 O B:ASN239 2.5 17.7 1.0 O B:ASN211 3.0 16.5 1.0 N B:ASN239 3.1 16.2 1.0 N B:THR213 3.3 15.2 1.0 C B:ASN239 3.4 17.9 1.0 C B:THR213 3.4 16.9 1.0 C B:LEU212 3.4 15.5 1.0 OG B:SER207 3.4 13.0 0.5 O B:LEU212 3.5 14.8 1.0 CA B:ASN239 3.6 16.8 1.0 OE2 B:GLU240 3.6 29.4 1.0 N B:LEU214 3.6 16.1 1.0 CA B:THR213 3.7 16.3 1.0 C B:HIS238 3.7 18.8 1.0 O B:THR213 3.7 17.7 1.0 CA B:HIS238 3.8 19.3 1.0 CB B:ASN239 3.9 16.9 1.0 C B:ASN211 3.9 15.8 1.0 CD2 B:LEU214 4.0 19.7 1.0 N B:HIS238 4.0 18.9 1.0 CG B:LEU214 4.2 19.6 1.0 CA B:LEU212 4.3 15.6 1.0 CB B:SER207 4.3 13.7 0.5 CB B:SER207 4.3 15.3 0.5 CA B:LEU214 4.4 16.5 1.0 N B:LEU212 4.4 15.3 1.0 CD B:GLU240 4.4 23.6 1.0 OG B:SER207 4.5 16.6 0.5 CA B:SER207 4.6 14.2 0.5 CA B:SER207 4.6 13.5 0.5 O B:HIS238 4.6 19.8 1.0 N B:GLU240 4.6 18.1 1.0 CB B:LEU214 4.7 18.0 1.0 OE1 B:GLU240 4.7 22.5 1.0 C B:GLY237 4.9 18.7 1.0 CA B:ASN211 4.9 15.8 1.0 ND2 B:ASN239 5.0 15.7 1.0 CG B:ASN239 5.0 16.9 1.0

Calcium binding site 3 out of 3 in the The GH43, Beta 1,3 Galactosidase, BT3683 with Galactodeoxynojirimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The GH43, Beta 1,3 Galactosidase, BT3683 with Galactodeoxynojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:46.7 occ:1.00 O C:ASN239 2.7 18.5 1.0 O C:HOH540 2.9 15.0 1.0 O C:ASN211 2.9 21.1 1.0 N C:ASN239 3.1 19.3 1.0 OG C:SER207 3.2 18.3 0.5 N C:THR213 3.2 18.5 1.0 C C:THR213 3.3 19.3 1.0 C C:LEU212 3.4 19.4 1.0 C C:ASN239 3.5 18.3 1.0 CA C:THR213 3.5 18.6 1.0 O C:LEU212 3.5 20.0 1.0 N C:LEU214 3.5 18.4 1.0 OE2 C:GLU240 3.6 24.2 1.0 C C:HIS238 3.7 21.4 1.0 CA C:ASN239 3.7 18.3 1.0 O C:THR213 3.7 18.4 1.0 C C:ASN211 3.7 21.2 1.0 CA C:HIS238 3.8 24.4 1.0 OG C:SER207 3.9 22.6 0.5 N C:HIS238 4.0 22.7 1.0 CB C:ASN239 4.0 17.6 1.0 CB C:SER207 4.2 20.6 0.5 CA C:LEU212 4.2 20.5 1.0 CB C:SER207 4.2 18.8 0.5 CG C:LEU214 4.3 21.1 1.0 N C:LEU212 4.3 20.0 1.0 CD C:GLU240 4.3 23.6 1.0 CA C:LEU214 4.3 19.0 1.0 CD2 C:LEU214 4.4 19.3 1.0 CA C:SER207 4.5 18.3 0.5 CA C:SER207 4.5 19.1 0.5 OE1 C:GLU240 4.6 24.8 1.0 O C:HIS238 4.7 22.2 1.0 CB C:LEU214 4.7 19.7 1.0 N C:GLU240 4.7 18.2 1.0 CA C:ASN211 4.8 22.1 1.0 C C:GLY237 5.0 23.2 1.0 O C:SER208 5.0 19.1 1.0

A.Cartmell, J.Munoz-Munoz, J.A.Briggs, D.A.Ndeh, E.C.Lowe, A.Basle, N.Terrapon, K.Stott, T.Heunis, J.Gray, L.Yu, P.Dupree, P.Z.Fernandes, S.Shah, S.J.Williams, A.Labourel, M.Trost, B.Henrissat, H.J.Gilbert. A Surface Endogalactanase in Bacteroides Thetaiotaomicron Confers Keystone Status For Arabinogalactan Degradation. Nat Microbiol V. 3 1314 2018.
ISSN: ESSN 2058-5276
PubMed: 30349080
DOI: 10.1038/S41564-018-0258-8