Calcium in PDB 8xru: The Crystal Structure of A GH3 Enzyme CCBGL3B with Glycerol

The structure of The Crystal Structure of A GH3 Enzyme CCBGL3B with Glycerol, PDB code: 8xru 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)	19.85 / 2.02
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	162.992, 182.048, 145.284, 90, 102.01, 90
R / Rfree (%)	20.5 / 23.5

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

Calcium binding site 1 out of 2 in the The Crystal Structure of A GH3 Enzyme CCBGL3B with Glycerol


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 Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:44.5 occ:1.00 O A:VAL692 2.1 30.1 1.0 OD1 A:ASP690 2.2 30.9 1.0 O A:HOH1034 2.2 30.7 1.0 O A:HOH948 2.2 28.9 1.0 O A:HOH990 2.2 28.5 1.0 O A:HOH906 2.3 33.1 1.0 CG A:ASP690 3.1 33.4 1.0 C A:VAL692 3.3 27.2 1.0 OD2 A:ASP690 3.4 31.2 1.0 N A:VAL692 3.9 29.9 1.0 O A:HOH1187 4.0 36.9 1.0 O A:PRO740 4.0 32.0 1.0 O A:GLU742 4.1 30.5 1.0 CA A:VAL692 4.2 28.2 1.0 O A:GLU739 4.2 31.3 1.0 O A:HOH1047 4.3 30.9 1.0 N A:THR693 4.3 28.8 1.0 CA A:THR693 4.4 30.1 1.0 CB A:ASP690 4.5 30.6 1.0 CG2 A:THR693 4.5 28.8 1.0 CB A:GLU739 4.6 34.2 1.0 CA A:GLY741 4.6 31.7 1.0 N A:THR691 4.6 29.8 1.0 OE1 A:GLU739 4.6 30.6 1.0 CB A:VAL692 4.6 28.8 1.0 N A:GLU742 4.7 30.9 1.0 CZ A:PHE743 4.7 33.7 1.0 C A:PRO740 4.7 33.6 1.0 C A:ASP690 4.8 31.4 1.0 C A:GLY741 4.8 34.6 1.0 CE1 A:PHE743 4.8 32.9 1.0 CA A:ASP690 4.9 29.5 1.0 C A:GLU739 4.9 34.4 1.0 N A:GLY741 4.9 34.3 1.0

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


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 Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:44.7 occ:1.00 O B:VAL692 2.1 29.2 1.0 OD1 B:ASP690 2.1 28.4 1.0 O B:HOH1148 2.2 29.0 1.0 O B:HOH996 2.2 28.9 1.0 O B:HOH918 2.2 26.2 1.0 O B:HOH945 2.3 30.9 1.0 CG B:ASP690 3.0 29.8 1.0 C B:VAL692 3.2 28.9 1.0 OD2 B:ASP690 3.3 28.3 1.0 N B:VAL692 3.8 28.0 1.0 CA B:VAL692 4.0 27.9 1.0 O B:GLU742 4.1 28.5 1.0 N B:THR693 4.2 30.1 1.0 O B:HOH964 4.2 42.8 1.0 O B:HOH1366 4.3 29.5 1.0 CA B:THR693 4.3 27.8 1.0 O B:PRO740 4.3 31.7 1.0 CB B:ASP690 4.4 29.9 1.0 N B:THR691 4.4 27.5 1.0 O B:GLU739 4.4 30.3 1.0 CG2 B:THR693 4.5 28.4 1.0 CB B:VAL692 4.5 29.0 1.0 OE1 B:GLU739 4.5 29.2 1.0 C B:ASP690 4.6 29.1 1.0 CB B:GLU739 4.6 30.8 1.0 CA B:GLY741 4.7 33.4 1.0 CA B:ASP690 4.8 28.1 1.0 N B:GLU742 4.8 30.6 1.0 C B:THR691 4.9 27.3 1.0 CZ B:PHE743 4.9 31.9 1.0 C B:PRO740 4.9 29.3 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