Calcium in PDB 8xrv: The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose

The structure of The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose, PDB code: 8xrv 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)	19.97 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	163.33, 177.574, 265.787, 90, 100.86, 90
R / Rfree (%)	17.6 / 21.5

The binding sites of Calcium atom in the The Crystal Structure of A GH3 Enzyme CCBGL3B with Glucose (pdb code 8xrv). 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, PDB code: 8xrv:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:60.5 occ:1.00 O A:HOH921 2.1 45.8 1.0 O A:VAL692 2.2 49.3 1.0 O A:HOH938 2.3 42.5 1.0 O A:HOH1006 2.3 52.7 1.0 OD1 A:ASP690 2.4 51.6 1.0 O A:HOH978 2.6 51.3 1.0 C A:VAL692 3.3 46.1 1.0 CG A:ASP690 3.4 46.6 1.0 N A:VAL692 3.7 45.3 1.0 O A:GLU742 3.8 43.6 1.0 OD2 A:ASP690 3.8 45.4 1.0 CA A:VAL692 4.0 44.3 1.0 CA A:GLY741 4.1 40.5 1.0 O A:PRO740 4.2 39.5 1.0 N A:GLU742 4.2 46.3 1.0 O A:GLU739 4.3 47.5 1.0 N A:THR693 4.4 42.4 1.0 C A:GLY741 4.4 44.6 1.0 CB A:VAL692 4.5 46.9 1.0 N A:THR691 4.6 45.9 1.0 N A:GLY741 4.6 41.1 1.0 C A:PRO740 4.6 44.5 1.0 CA A:THR693 4.6 41.0 1.0 CB A:ASP690 4.7 42.5 1.0 C A:ASP690 4.8 43.0 1.0 C A:GLU742 4.8 49.9 1.0 C A:THR691 4.9 45.6 1.0 CZ A:PHE743 4.9 43.5 1.0 CG2 A:THR693 4.9 43.4 1.0 CE1 A:PHE743 5.0 46.2 1.0 CB A:GLU739 5.0 50.4 1.0 CA A:ASP690 5.0 44.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:49.0 occ:1.00 O B:VAL692 2.1 36.3 1.0 OD1 B:ASP690 2.2 36.4 1.0 O B:HOH992 2.3 31.3 1.0 O B:HOH1000 2.3 32.7 1.0 O B:HOH904 2.3 36.4 1.0 O B:HOH911 2.4 36.8 1.0 CG B:ASP690 2.9 38.0 1.0 OD2 B:ASP690 3.0 37.3 1.0 C B:VAL692 3.3 32.9 1.0 N B:VAL692 4.0 33.8 1.0 O B:GLU739 4.0 38.8 1.0 N B:THR693 4.1 31.2 1.0 CA B:THR693 4.2 36.6 1.0 O B:PRO740 4.2 40.4 1.0 CA B:VAL692 4.2 34.3 1.0 CG2 B:THR693 4.4 32.4 1.0 CB B:ASP690 4.4 36.5 1.0 O B:GLU742 4.4 40.5 1.0 CB B:GLU739 4.4 35.2 1.0 OE1 B:GLU739 4.4 38.7 1.0 CA B:GLY741 4.6 34.4 1.0 C B:ASP690 4.7 35.9 1.0 N B:THR691 4.7 33.1 1.0 C B:PRO740 4.7 35.7 1.0 C B:GLU739 4.7 42.5 1.0 CZ B:PHE743 4.8 38.9 1.0 CB B:VAL692 4.8 33.7 1.0 CA B:ASP690 4.8 37.9 1.0 CB B:THR693 4.9 38.7 1.0 N B:GLY741 4.9 31.1 1.0 C B:GLY741 5.0 34.3 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca802 b:50.4 occ:1.00 O C:HOH946 2.2 31.9 1.0 OD1 C:ASP690 2.3 33.3 1.0 O C:VAL692 2.3 32.1 1.0 O C:HOH1010 2.3 33.6 1.0 O C:HOH938 2.5 36.0 1.0 CG C:ASP690 3.1 34.6 1.0 OD2 C:ASP690 3.3 32.8 1.0 C C:VAL692 3.5 29.0 1.0 O C:GLU739 3.6 37.1 1.0 O C:PRO740 3.8 33.0 1.0 O C:GLU742 4.0 38.4 1.0 N C:VAL692 4.1 32.8 1.0 O C:HOH1094 4.2 39.5 1.0 CA C:GLY741 4.3 29.2 1.0 O C:HOH973 4.3 29.4 1.0 OE1 C:GLU739 4.3 45.0 1.0 CA C:VAL692 4.3 31.0 1.0 C C:PRO740 4.3 30.6 1.0 N C:THR693 4.5 27.8 1.0 CB C:ASP690 4.5 35.7 1.0 C C:GLU739 4.5 39.9 1.0 N C:GLY741 4.5 27.6 1.0 C C:GLY741 4.6 31.7 1.0 N C:GLU742 4.6 33.6 1.0 CA C:THR693 4.6 31.2 1.0 CG2 C:THR693 4.6 30.5 1.0 CZ C:PHE743 4.6 33.1 1.0 CB C:VAL692 4.7 37.7 1.0 N C:THR691 4.7 32.0 1.0 CB C:GLU739 4.7 36.8 1.0 C C:ASP690 4.8 34.0 1.0 CE1 C:PHE743 4.8 27.5 1.0 CG C:GLU739 4.8 42.2 1.0 CA C:ASP690 4.9 36.7 1.0 CG1 C:VAL692 4.9 29.8 1.0 C C:GLU742 5.0 36.6 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca802 b:53.0 occ:1.00 O F:VAL692 2.1 38.9 1.0 O F:HOH969 2.2 34.5 1.0 O F:HOH915 2.3 31.8 1.0 O F:HOH1184 2.3 47.6 1.0 O F:HOH913 2.4 38.2 1.0 OD1 F:ASP690 2.4 36.9 1.0 C F:VAL692 3.3 34.5 1.0 CG F:ASP690 3.4 34.6 1.0 OD2 F:ASP690 3.6 34.7 1.0 O F:PRO740 3.8 34.3 1.0 N F:VAL692 4.0 31.1 1.0 O F:GLU739 4.1 41.1 1.0 CA F:GLY741 4.1 30.3 1.0 CA F:VAL692 4.2 30.5 1.0 O F:GLU742 4.3 29.2 1.0 N F:THR693 4.3 34.3 1.0 C F:PRO740 4.3 37.5 1.0 CA F:THR693 4.4 36.1 1.0 CB F:GLU739 4.5 39.2 1.0 N F:GLY741 4.5 32.3 1.0 O F:HOH1276 4.6 46.9 1.0 OE1 F:GLU739 4.6 46.0 1.0 CB F:VAL692 4.6 37.4 1.0 C F:GLY741 4.7 33.1 1.0 C F:GLU739 4.7 39.0 1.0 N F:GLU742 4.7 32.1 1.0 CB F:ASP690 4.8 32.3 1.0 N F:THR691 4.9 38.3 1.0 CG2 F:THR693 4.9 31.4 1.0 CZ F:PHE743 4.9 36.5 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca802 b:58.0 occ:1.00 O D:VAL692 2.2 47.6 1.0 O D:HOH908 2.3 47.2 1.0 OD1 D:ASP690 2.4 47.0 1.0 O D:HOH907 2.4 45.3 1.0 O D:HOH963 2.4 50.6 1.0 O D:HOH1149 2.4 53.6 1.0 CG D:ASP690 3.3 46.3 1.0 C D:VAL692 3.4 48.7 1.0 OD2 D:ASP690 3.4 48.2 1.0 O D:PRO740 3.7 46.3 1.0 N D:VAL692 4.0 43.1 1.0 CA D:VAL692 4.2 47.5 1.0 O D:HOH1038 4.2 45.9 1.0 O D:GLU742 4.2 46.6 1.0 CA D:GLY741 4.3 45.4 1.0 O D:GLU739 4.3 48.5 1.0 N D:THR693 4.3 47.8 1.0 OE1 D:GLU739 4.4 50.6 1.0 C D:PRO740 4.4 44.7 1.0 CB D:VAL692 4.4 50.3 1.0 CA D:THR693 4.5 44.3 1.0 N D:GLU742 4.6 45.7 1.0 C D:GLY741 4.6 47.3 1.0 CB D:GLU739 4.7 43.0 1.0 N D:GLY741 4.7 44.5 1.0 CB D:ASP690 4.7 42.6 1.0 CG2 D:THR693 4.8 43.7 1.0 N D:THR691 4.9 42.0 1.0 C D:GLU739 4.9 49.8 1.0 CE1 D:PHE743 5.0 45.7 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca802 b:58.9 occ:1.00 O E:VAL692 2.1 46.0 1.0 O E:HOH934 2.2 50.9 1.0 OD1 E:ASP690 2.3 40.5 1.0 O E:HOH944 2.3 40.2 1.0 O E:HOH974 2.4 44.3 1.0 O E:HOH912 2.5 47.1 1.0 CG E:ASP690 3.2 40.2 1.0 C E:VAL692 3.4 46.1 1.0 OD2 E:ASP690 3.5 42.2 1.0 N E:VAL692 3.9 41.3 1.0 O E:PRO740 4.0 45.0 1.0 O E:GLU742 4.0 42.5 1.0 OE1 E:GLU739 4.0 52.8 1.0 O E:GLU739 4.1 47.8 1.0 CA E:VAL692 4.2 42.8 1.0 N E:THR693 4.3 47.5 1.0 CA E:GLY741 4.5 39.4 1.0 CA E:THR693 4.5 44.2 1.0 CB E:ASP690 4.6 40.5 1.0 CB E:VAL692 4.6 44.3 1.0 O E:HOH995 4.6 40.1 1.0 C E:PRO740 4.6 43.4 1.0 CB E:GLU739 4.7 48.9 1.0 CG2 E:THR693 4.7 40.1 1.0 C E:GLY741 4.7 42.5 1.0 N E:GLU742 4.7 37.3 1.0 N E:THR691 4.7 39.2 1.0 CG E:GLU739 4.7 53.5 1.0 CD E:GLU739 4.8 54.3 1.0 CZ E:PHE743 4.8 37.6 1.0 C E:ASP690 4.8 37.1 1.0 N E:GLY741 4.9 39.6 1.0 C E:GLU739 4.9 46.9 1.0 CG1 E:VAL692 4.9 45.5 1.0 CA E:ASP690 5.0 39.0 1.0 CE1 E:PHE743 5.0 39.6 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