Calcium in PDB 1y7b: Beta-D-Xylosidase, A Family 43 Glycoside Hydrolase

All present enzymatic activity of Beta-D-Xylosidase, A Family 43 Glycoside Hydrolase:
3.2.1.37;

The structure of Beta-D-Xylosidase, A Family 43 Glycoside Hydrolase, PDB code: 1y7b was solved by A.Teplyakov, E.Fedorov, G.L.Gilliland, S.C.Almo, S.K.Burley, New York Sgxresearch Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.480, 136.150, 183.870, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 20.6

The binding sites of Calcium atom in the Beta-D-Xylosidase, A Family 43 Glycoside Hydrolase (pdb code 1y7b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Beta-D-Xylosidase, A Family 43 Glycoside Hydrolase, PDB code: 1y7b:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Beta-D-Xylosidase, A Family 43 Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Beta-D-Xylosidase, A Family 43 Glycoside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3001 b:27.1 occ:1.00 O A:GLY362 2.3 19.8 1.0 O A:ASP528 2.3 16.7 1.0 O A:ASN333 2.4 17.1 1.0 O A:HOH3234 2.4 24.8 1.0 O A:HOH3212 2.5 23.9 1.0 OD1 A:ASP528 2.5 19.0 1.0 C A:GLY362 3.3 15.9 1.0 C A:ASP528 3.3 20.9 1.0 C A:ASN333 3.4 20.5 1.0 CG A:ASP528 3.4 27.1 1.0 CA A:ASN333 3.8 17.9 1.0 CA A:ASP528 3.8 14.6 1.0 O A:HOH3611 3.9 43.0 1.0 CA A:GLY362 3.9 19.2 1.0 CB A:ASN333 3.9 19.5 1.0 OD2 A:ASP528 3.9 35.9 1.0 ND2 A:ASN363 4.1 34.2 1.0 CB A:ASP528 4.2 16.3 1.0 N A:ASN363 4.4 18.3 1.0 OD1 A:ASP335 4.5 35.4 1.0 N A:PHE334 4.5 19.2 1.0 N A:TYR529 4.5 13.4 1.0 O A:HOH3744 4.5 50.5 1.0 ND2 A:ASN333 4.6 21.6 1.0 CB A:PHE334 4.7 18.7 1.0 CG A:ASN333 4.8 22.3 1.0 CA A:ASN363 4.8 15.2 1.0 O A:HOH3524 4.8 39.3 1.0 O A:HOH3535 4.8 39.7 1.0 CA A:TYR529 4.8 11.7 1.0 CA A:PHE334 4.9 18.5 1.0 C A:PHE334 4.9 22.4 1.0 CB A:TYR529 5.0 16.3 1.0

Calcium binding site 2 out of 4 in the Beta-D-Xylosidase, A Family 43 Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Beta-D-Xylosidase, A Family 43 Glycoside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3002 b:26.2 occ:1.00 O B:ASN333 2.3 20.1 1.0 O B:GLY362 2.3 19.6 1.0 O B:ASP528 2.3 17.8 1.0 O B:HOH3165 2.4 23.0 1.0 O B:HOH3213 2.5 25.6 1.0 OD1 B:ASP528 2.5 31.9 1.0 C B:ASN333 3.3 17.9 1.0 C B:GLY362 3.4 20.0 1.0 C B:ASP528 3.4 21.5 1.0 CG B:ASP528 3.5 42.5 1.0 CA B:ASN333 3.8 18.9 1.0 CA B:GLY362 3.8 20.3 1.0 CB B:ASN333 3.9 20.0 1.0 CA B:ASP528 3.9 22.6 1.0 OD2 B:ASP528 4.1 35.1 1.0 O B:HOH3685 4.2 51.5 1.0 CB B:ASP528 4.3 24.8 1.0 ND2 B:ASN333 4.5 26.2 1.0 N B:PHE334 4.5 18.8 1.0 N B:TYR529 4.5 14.0 1.0 OD1 B:ASP335 4.5 26.6 1.0 N B:ASN363 4.6 22.8 1.0 CB B:PHE334 4.6 21.2 1.0 CG B:ASN333 4.7 30.6 1.0 CA B:TYR529 4.9 17.6 1.0 CA B:PHE334 4.9 19.9 1.0 ND2 B:ASN363 5.0 35.3 1.0 CA B:ASN363 5.0 22.8 1.0 CB B:TYR529 5.0 18.4 1.0 C B:PHE334 5.0 22.1 1.0

Calcium binding site 3 out of 4 in the Beta-D-Xylosidase, A Family 43 Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Beta-D-Xylosidase, A Family 43 Glycoside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca3003 b:27.7 occ:1.00 O C:ASP528 2.3 19.7 1.0 O C:GLY362 2.3 19.9 1.0 O C:HOH3234 2.4 26.2 1.0 O C:ASN333 2.4 19.8 1.0 OD1 C:ASP528 2.5 22.9 1.0 O C:HOH3258 2.5 27.5 1.0 C C:GLY362 3.3 25.8 1.0 C C:ASN333 3.3 21.6 1.0 C C:ASP528 3.4 21.7 1.0 CG C:ASP528 3.4 29.1 1.0 CA C:ASN333 3.8 24.8 1.0 CA C:GLY362 3.9 22.1 1.0 CA C:ASP528 3.9 23.2 1.0 CB C:ASN333 3.9 24.1 1.0 O C:HOH3561 3.9 43.9 1.0 OD2 C:ASP528 4.0 34.9 1.0 CB C:ASP528 4.3 19.5 1.0 OD1 C:ASP335 4.4 37.9 1.0 ND2 C:ASN363 4.5 35.1 1.0 N C:ASN363 4.5 23.4 1.0 N C:PHE334 4.5 23.1 1.0 ND2 C:ASN333 4.5 19.0 1.0 N C:TYR529 4.5 19.3 1.0 CB C:PHE334 4.6 23.5 1.0 O C:HOH3439 4.7 37.7 1.0 CG C:ASN333 4.7 29.7 1.0 CA C:ASN363 4.8 21.3 1.0 CA C:TYR529 4.9 17.0 1.0 C C:PHE334 4.9 19.4 1.0 CA C:PHE334 4.9 16.8 1.0 CB C:TYR529 5.0 18.2 1.0 O C:HOH3521 5.0 41.6 1.0

Calcium binding site 4 out of 4 in the Beta-D-Xylosidase, A Family 43 Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Beta-D-Xylosidase, A Family 43 Glycoside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca3004 b:27.8 occ:1.00 O D:GLY362 2.3 20.3 1.0 O D:ASP528 2.3 19.8 1.0 O D:ASN333 2.4 18.4 1.0 O D:HOH3263 2.4 26.9 1.0 O D:HOH3213 2.5 24.3 1.0 OD1 D:ASP528 2.6 21.9 1.0 C D:ASN333 3.3 19.3 1.0 C D:GLY362 3.3 22.6 1.0 C D:ASP528 3.4 21.3 1.0 O D:HOH3584 3.4 44.9 1.0 CG D:ASP528 3.5 26.8 1.0 CA D:ASN333 3.8 19.6 1.0 CA D:ASP528 3.8 15.8 1.0 CA D:GLY362 3.9 19.9 1.0 CB D:ASN333 4.0 18.1 1.0 O D:HOH3730 4.1 52.6 1.0 OD2 D:ASP528 4.1 33.6 1.0 CB D:ASP528 4.3 18.6 1.0 N D:PHE334 4.4 17.5 1.0 N D:ASN363 4.4 19.0 1.0 OD1 D:ASP335 4.5 50.0 1.0 N D:TYR529 4.5 15.3 1.0 CB D:PHE334 4.6 24.3 1.0 ND2 D:ASN333 4.6 19.2 1.0 CA D:ASN363 4.8 20.8 1.0 CA D:TYR529 4.9 14.0 1.0 CG D:ASN333 4.9 27.7 1.0 CA D:PHE334 4.9 18.6 1.0 C D:PHE334 4.9 30.0 1.0 O D:HOH3674 4.9 48.4 1.0 CB D:TYR529 4.9 19.4 1.0 O D:PHE334 5.0 22.4 1.0

A.Teplyakov, E.Fedorov, G.L.Gilliland, S.C.Almo, New York Structural Genomics Research Consortium (Nysgrc). Crystal Structure of Beta-Xylosidase From Clostridium Acetobutylicum To Be Published.