Calcium in PDB 8xrt: The Crystal Structure of A GH3 Enzyme CCBGL3B

The structure of The Crystal Structure of A GH3 Enzyme CCBGL3B, PDB code: 8xrt 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)	19.93 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	164.594, 178.757, 267.336, 90, 100.76, 90
R / Rfree (%)	18.9 / 22.5

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca801 b:54.0 occ:1.00 O E:HOH905 2.2 40.9 1.0 O E:HOH1026 2.2 41.9 1.0 O E:VAL692 2.2 39.2 1.0 O E:HOH907 2.3 39.6 1.0 OD1 E:ASP690 2.3 43.2 1.0 O E:HOH916 2.3 39.3 1.0 CG E:ASP690 3.2 41.0 1.0 C E:VAL692 3.4 39.0 1.0 OD2 E:ASP690 3.5 42.0 1.0 O E:PRO740 3.8 37.9 1.0 O E:GLU742 3.9 42.6 1.0 N E:VAL692 3.9 33.4 1.0 CG2 E:VAL692 4.1 39.4 1.0 O E:GLU739 4.1 42.9 1.0 O E:HOH1168 4.2 43.3 1.0 CA E:VAL692 4.2 37.4 1.0 O E:HOH1058 4.3 35.1 1.0 N E:THR693 4.4 35.1 1.0 N E:THR691 4.5 35.3 1.0 CA E:THR693 4.5 39.6 1.0 CB E:ASP690 4.6 42.1 1.0 CA E:GLY741 4.6 36.2 1.0 C E:PRO740 4.6 39.3 1.0 N E:GLU742 4.6 40.4 1.0 CG2 E:THR693 4.6 40.3 1.0 C E:ASP690 4.6 38.1 1.0 OE2 E:GLU739 4.7 48.3 1.0 C E:GLY741 4.7 39.7 1.0 CB E:VAL692 4.8 38.9 1.0 CA E:ASP690 4.8 40.7 1.0 C E:GLU742 4.9 42.9 1.0 C E:GLU739 4.9 45.3 1.0 CE1 E:PHE743 4.9 35.5 1.0 N E:GLY741 4.9 35.6 1.0 CZ E:PHE743 5.0 45.4 1.0 C E:THR691 5.0 39.9 1.0 CB E:GLU739 5.0 42.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca801 b:55.5 occ:1.00 O F:VAL692 2.1 40.9 1.0 O F:HOH975 2.2 42.1 1.0 OD1 F:ASP690 2.2 38.3 1.0 O F:HOH916 2.3 43.2 1.0 O F:HOH925 2.4 45.6 1.0 O F:HOH933 2.4 41.5 1.0 CG F:ASP690 3.1 35.9 1.0 OD2 F:ASP690 3.2 33.9 1.0 C F:VAL692 3.3 41.0 1.0 O F:PRO740 4.0 40.7 1.0 N F:VAL692 4.0 38.4 1.0 O F:GLU742 4.1 35.1 1.0 CA F:VAL692 4.2 35.4 1.0 O F:GLU739 4.3 43.1 1.0 N F:THR693 4.3 37.3 1.0 O F:HOH1018 4.4 41.9 1.0 CA F:THR693 4.4 37.1 1.0 OE1 F:GLU739 4.5 40.9 1.0 CB F:ASP690 4.5 36.4 1.0 CB F:GLU739 4.6 32.8 1.0 CA F:GLY741 4.6 33.6 1.0 CG2 F:THR693 4.6 35.4 1.0 C F:PRO740 4.6 41.4 1.0 CB F:VAL692 4.6 41.4 1.0 N F:GLU742 4.7 36.9 1.0 N F:THR691 4.8 39.0 1.0 C F:ASP690 4.8 41.2 1.0 CZ F:PHE743 4.8 42.0 1.0 C F:GLY741 4.9 36.8 1.0 C F:GLU739 4.9 41.8 1.0 N F:GLY741 4.9 38.9 1.0 CA F:ASP690 5.0 36.8 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:71.0 occ:1.00 O A:VAL692 2.1 52.3 1.0 OD1 A:ASP690 2.1 53.2 1.0 O A:HOH911 2.4 52.6 1.0 O A:HOH903 2.4 53.7 1.0 O A:HOH932 2.5 54.0 1.0 O A:HOH916 2.5 51.0 1.0 CG A:ASP690 3.1 52.3 1.0 C A:VAL692 3.3 54.4 1.0 OD2 A:ASP690 3.4 51.2 1.0 N A:VAL692 3.8 45.3 1.0 O A:GLU742 3.9 51.5 1.0 CA A:VAL692 4.1 52.4 1.0 O A:PRO740 4.2 56.6 1.0 O A:GLU739 4.2 55.0 1.0 N A:THR693 4.3 55.7 1.0 OE1 A:GLU739 4.3 55.7 1.0 CA A:THR693 4.4 54.0 1.0 O A:HOH1024 4.4 56.2 1.0 CG2 A:THR693 4.4 55.7 1.0 CB A:ASP690 4.5 44.2 1.0 O A:HOH1022 4.6 52.4 1.0 CB A:VAL692 4.6 51.9 1.0 C A:ASP690 4.6 51.0 1.0 N A:THR691 4.6 51.1 1.0 N A:GLU742 4.6 54.5 1.0 CA A:GLY741 4.7 51.2 1.0 CG A:GLU739 4.7 55.4 1.0 C A:PRO740 4.7 52.9 1.0 CA A:ASP690 4.8 47.7 1.0 C A:GLY741 4.8 55.1 1.0 CD A:GLU739 4.9 57.4 1.0 C A:GLU742 4.9 55.3 1.0 CZ A:PHE743 4.9 51.2 1.0 N A:GLY741 4.9 51.6 1.0 O A:ASP690 4.9 51.8 1.0 CG1 A:VAL692 5.0 52.4 1.0 C A:THR691 5.0 47.7 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:74.5 occ:1.00 OD1 B:ASP690 2.1 62.1 1.0 O B:VAL692 2.2 72.8 1.0 O B:HOH903 2.3 65.2 1.0 O B:HOH937 2.4 65.9 1.0 O B:HOH925 2.4 68.0 1.0 O B:HOH1049 2.4 67.8 1.0 CG B:ASP690 3.0 62.8 1.0 OD2 B:ASP690 3.2 60.4 1.0 C B:VAL692 3.4 65.9 1.0 N B:VAL692 3.9 61.2 1.0 O B:GLU742 4.1 64.0 1.0 O B:PRO740 4.2 69.3 1.0 CA B:VAL692 4.2 63.7 1.0 CA B:GLY741 4.2 62.5 1.0 N B:THR693 4.4 64.9 1.0 CB B:ASP690 4.4 57.9 1.0 O B:GLU739 4.4 65.3 1.0 CA B:THR693 4.4 65.6 1.0 N B:GLU742 4.5 66.2 1.0 N B:THR691 4.5 65.4 1.0 CG2 B:THR693 4.6 56.5 1.0 C B:GLY741 4.6 65.0 1.0 OE1 B:GLU739 4.6 65.3 1.0 CB B:GLU739 4.7 63.6 1.0 C B:PRO740 4.7 66.0 1.0 C B:ASP690 4.7 64.3 1.0 N B:GLY741 4.7 60.9 1.0 CB B:VAL692 4.7 67.6 1.0 CA B:ASP690 4.8 60.5 1.0 CZ B:PHE743 4.9 63.1 1.0 CE1 B:PHE743 4.9 65.7 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca801 b:84.6 occ:1.00 O C:VAL692 2.3 74.0 1.0 O C:HOH956 2.4 66.8 1.0 OD1 C:ASP690 2.4 77.4 1.0 O C:HOH915 2.5 73.2 1.0 O C:HOH913 2.6 69.7 1.0 CG C:ASP690 3.4 74.3 1.0 O C:HOH1002 3.4 74.4 1.0 C C:VAL692 3.5 75.3 1.0 OD2 C:ASP690 3.6 77.5 1.0 O C:PRO740 3.8 71.5 1.0 CA C:GLY741 3.8 72.6 1.0 N C:VAL692 4.1 74.6 1.0 N C:GLU742 4.2 81.4 1.0 CA C:VAL692 4.3 75.1 1.0 C C:PRO740 4.4 72.4 1.0 C C:GLY741 4.4 77.2 1.0 N C:GLY741 4.4 69.5 1.0 N C:THR693 4.5 70.5 1.0 O C:GLU742 4.5 77.9 1.0 CB C:VAL692 4.6 72.1 1.0 CA C:THR693 4.7 64.6 1.0 O C:GLU739 4.8 76.3 1.0 CB C:ASP690 4.8 65.1 1.0 N C:THR691 4.8 74.2 1.0 OE1 C:GLU739 4.8 75.0 1.0 CE1 C:PHE743 5.0 74.0 1.0 CB C:GLU739 5.0 69.3 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca801 b:71.3 occ:1.00 O D:VAL692 2.1 60.9 1.0 OD1 D:ASP690 2.2 58.5 1.0 O D:HOH911 2.3 61.0 1.0 O D:HOH923 2.3 56.6 1.0 O D:HOH938 2.4 59.9 1.0 O D:HOH945 2.4 57.8 1.0 CG D:ASP690 3.1 58.4 1.0 C D:VAL692 3.2 56.8 1.0 OD2 D:ASP690 3.2 59.8 1.0 N D:VAL692 3.9 62.1 1.0 N D:THR693 4.1 53.6 1.0 CA D:VAL692 4.1 56.7 1.0 OE1 D:GLU739 4.1 66.7 1.0 CA D:THR693 4.2 59.4 1.0 O D:PRO740 4.2 66.2 1.0 CB D:GLU739 4.4 60.0 1.0 CB D:ASP690 4.5 52.9 1.0 O D:GLU739 4.5 60.8 1.0 CG2 D:THR693 4.5 55.9 1.0 CA D:GLY741 4.6 62.9 1.0 N D:THR691 4.6 55.4 1.0 CB D:VAL692 4.6 53.3 1.0 O D:GLU742 4.6 62.7 1.0 C D:ASP690 4.8 57.0 1.0 C D:PRO740 4.8 65.7 1.0 C D:GLU739 4.9 63.4 1.0 CB D:THR693 4.9 57.4 1.0 CA D:ASP690 5.0 54.6 1.0 N D:GLY741 5.0 63.7 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