Calcium in PDB 8xrx: The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose

The structure of The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose, PDB code: 8xrx was solved by J.Y.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	163.095, 183.009, 269.154, 90, 100.59, 90
R / Rfree (%)	19.7 / 23

The binding sites of Calcium atom in the The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose (pdb code 8xrx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose, PDB code: 8xrx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:54.0 occ:1.00 O A:VAL692 2.3 28.4 1.0 OD1 A:ASP690 2.3 30.7 1.0 CG A:ASP690 3.2 28.9 1.0 OD2 A:ASP690 3.4 28.2 1.0 C A:VAL692 3.5 24.0 1.0 O A:PRO740 3.8 30.0 1.0 O A:GLU739 4.0 32.5 1.0 N A:VAL692 4.1 26.4 1.0 O A:GLU742 4.2 32.7 1.0 CA A:GLY741 4.2 25.7 1.0 CA A:VAL692 4.3 22.6 1.0 C A:PRO740 4.4 28.0 1.0 N A:THR693 4.5 22.0 1.0 N A:GLU742 4.5 28.5 1.0 CB A:GLU739 4.5 23.5 1.0 C A:GLY741 4.6 27.6 1.0 CA A:THR693 4.6 23.3 1.0 OE1 A:GLU739 4.6 26.0 1.0 CB A:ASP690 4.6 22.9 1.0 N A:GLY741 4.6 25.9 1.0 CZ A:PHE743 4.6 27.0 1.0 N A:THR691 4.7 25.6 1.0 C A:GLU739 4.7 26.6 1.0 O A:HOH906 4.8 26.6 1.0 CB A:VAL692 4.8 19.7 1.0 CE1 A:PHE743 4.8 25.5 1.0 CG2 A:THR693 4.9 24.4 1.0 C A:ASP690 4.9 26.9 1.0

Calcium binding site 2 out of 6 in the The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:44.7 occ:1.00 O B:VAL692 2.1 30.2 1.0 O B:HOH1000 2.2 27.7 1.0 O B:HOH929 2.3 26.8 1.0 OD1 B:ASP690 2.3 24.3 1.0 CG B:ASP690 3.3 23.4 1.0 C B:VAL692 3.3 26.5 1.0 OD2 B:ASP690 3.4 24.9 1.0 O B:PRO740 3.9 28.8 1.0 OE1 B:GLU739 3.9 26.9 1.0 N B:VAL692 4.1 20.7 1.0 N B:THR693 4.2 24.0 1.0 O B:GLU739 4.2 26.9 1.0 CA B:THR693 4.2 24.4 1.0 CA B:VAL692 4.2 21.4 1.0 CB B:GLU739 4.4 22.2 1.0 O B:HOH1028 4.4 19.9 1.0 CA B:GLY741 4.5 17.7 1.0 O B:GLU742 4.5 25.8 1.0 C B:PRO740 4.6 22.4 1.0 CB B:VAL692 4.7 21.7 1.0 CB B:ASP690 4.7 21.2 1.0 CG2 B:THR693 4.7 20.9 1.0 C B:GLU739 4.8 26.2 1.0 N B:GLU742 4.8 22.9 1.0 N B:GLY741 4.8 20.2 1.0 N B:THR691 5.0 21.0 1.0 CZ B:PHE743 5.0 23.2 1.0 C B:GLY741 5.0 22.9 1.0 CD B:GLU739 5.0 27.1 1.0

Calcium binding site 3 out of 6 in the The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca802 b:62.2 occ:1.00 OD1 C:ASP690 2.1 53.5 1.0 O C:VAL692 2.2 50.9 1.0 CG C:ASP690 3.1 49.0 1.0 C C:VAL692 3.4 45.0 1.0 OD2 C:ASP690 3.4 49.3 1.0 O C:PRO740 3.6 54.9 1.0 O C:GLU742 3.8 59.6 1.0 O C:GLU739 3.9 55.2 1.0 N C:VAL692 3.9 54.4 1.0 OE1 C:GLU739 4.1 54.8 1.0 CA C:VAL692 4.1 45.6 1.0 CA C:GLY741 4.2 54.7 1.0 C C:PRO740 4.3 51.6 1.0 N C:GLU742 4.4 57.2 1.0 N C:THR693 4.4 46.9 1.0 CB C:VAL692 4.4 45.7 1.0 CB C:ASP690 4.5 49.6 1.0 C C:GLY741 4.5 55.8 1.0 N C:GLY741 4.6 50.0 1.0 CA C:THR693 4.6 48.8 1.0 CZ C:PHE743 4.7 49.0 1.0 CE1 C:PHE743 4.7 51.6 1.0 CG1 C:VAL692 4.8 44.0 1.0 N C:THR691 4.8 30.0 1.0 CG C:GLU739 4.8 60.5 1.0 C C:GLU739 4.8 54.1 1.0 C C:ASP690 4.8 49.2 1.0 CA C:ASP690 4.8 49.4 1.0 CD C:GLU739 4.8 54.8 1.0 CG2 C:THR693 4.8 38.5 1.0 C C:GLU742 4.9 56.6 1.0 CB C:GLU739 5.0 54.3 1.0

Calcium binding site 4 out of 6 in the The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca801 b:58.3 occ:1.00 O D:VAL692 2.2 40.4 1.0 OD1 D:ASP690 2.3 46.2 1.0 O D:HOH906 2.4 37.8 1.0 CG D:ASP690 3.3 45.7 1.0 C D:VAL692 3.4 43.7 1.0 OD2 D:ASP690 3.5 47.7 1.0 O D:PRO740 3.9 49.1 1.0 CA D:GLY741 4.0 50.1 1.0 O D:GLU742 4.0 58.5 1.0 N D:VAL692 4.0 44.4 1.0 CA D:VAL692 4.2 46.2 1.0 O D:GLU739 4.2 54.6 1.0 C D:PRO740 4.3 48.2 1.0 N D:GLY741 4.4 47.5 1.0 C D:GLY741 4.4 51.8 1.0 N D:GLU742 4.4 58.5 1.0 N D:THR693 4.5 38.5 1.0 OE2 D:GLU742 4.5 84.5 1.0 CB D:VAL692 4.6 46.3 1.0 CA D:THR693 4.6 39.1 1.0 CB D:ASP690 4.6 39.7 1.0 CZ D:PHE743 4.7 43.9 1.0 CE1 D:PHE743 4.8 46.6 1.0 N D:THR691 4.8 42.9 1.0 C D:ASP690 4.8 45.6 1.0 CG2 D:THR693 4.9 42.4 1.0 C D:GLU742 4.9 52.1 1.0 C D:GLU739 4.9 48.5 1.0 CA D:ASP690 5.0 43.9 1.0 CB D:GLU739 5.0 40.4 1.0

Calcium binding site 5 out of 6 in the The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca801 b:64.2 occ:1.00 O E:VAL692 2.3 50.3 1.0 OD1 E:ASP690 2.3 61.6 1.0 CG E:ASP690 3.1 51.4 1.0 OD2 E:ASP690 3.2 56.5 1.0 C E:VAL692 3.5 48.8 1.0 O E:PRO740 3.7 54.8 1.0 O E:GLU739 3.7 58.4 1.0 CG2 E:VAL692 3.8 59.8 1.0 N E:VAL692 4.2 51.4 1.0 O E:GLU742 4.2 61.4 1.0 CA E:GLY741 4.2 56.4 1.0 C E:PRO740 4.3 53.2 1.0 CA E:VAL692 4.3 49.8 1.0 CB E:GLU739 4.4 51.7 1.0 OE1 E:GLU739 4.4 53.9 1.0 N E:THR693 4.4 48.0 1.0 C E:GLU739 4.5 53.8 1.0 N E:GLY741 4.5 56.7 1.0 CB E:ASP690 4.6 54.0 1.0 CA E:THR693 4.6 49.0 1.0 C E:GLY741 4.6 57.5 1.0 CZ E:PHE743 4.7 54.0 1.0 CB E:VAL692 4.7 51.8 1.0 CE1 E:PHE743 4.7 57.5 1.0 N E:GLU742 4.7 58.4 1.0 CG2 E:THR693 4.8 48.6 1.0 N E:THR691 4.9 49.7 1.0 C E:ASP690 5.0 48.2 1.0

Calcium binding site 6 out of 6 in the The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose and Gentiobiose within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca801 b:75.4 occ:1.00 OD1 F:ASP690 2.2 61.1 1.0 O F:VAL692 2.2 55.6 1.0 OD2 F:ASP690 2.9 49.0 1.0 CG F:ASP690 2.9 53.9 1.0 C F:VAL692 3.5 52.6 1.0 O F:GLU739 4.0 60.0 1.0 O F:PRO740 4.0 58.0 1.0 O F:GLU742 4.2 57.7 1.0 N F:VAL692 4.3 54.5 1.0 N F:THR693 4.4 54.6 1.0 CA F:GLY741 4.4 49.4 1.0 OE1 F:GLU739 4.4 58.8 1.0 CB F:ASP690 4.4 49.0 1.0 CA F:THR693 4.4 56.6 1.0 CB F:GLU739 4.4 53.6 1.0 CA F:VAL692 4.4 53.3 1.0 C F:PRO740 4.5 56.1 1.0 CE1 F:PHE743 4.6 55.4 1.0 CZ F:PHE743 4.6 48.3 1.0 N F:GLU742 4.6 61.8 1.0 N F:GLY741 4.6 51.1 1.0 C F:GLU739 4.6 57.7 1.0 C F:GLY741 4.7 56.8 1.0 CG2 F:THR693 4.8 48.2 1.0 CB F:VAL692 4.9 62.0 1.0 CA F:ASP690 5.0 50.7 1.0

C.Hu, Y.Wang, W.Wang, W.Cui, X.Jia, K.H.Mayo, Y.Zhou, J.Su, Y.Yuan. A Trapped Covalent Intermediate As A Key Catalytic Element in the Hydrolysis of A GH3 Beta-Glucosidase: An X-Ray Crystallographic and Biochemical Study. Int.J.Biol.Macromol. V. 265 31131 2024.
ISSN: ISSN 0141-8130
PubMed: 38527679
DOI: 10.1016/J.IJBIOMAC.2024.131131