Calcium in PDB 6uax: Crystal Structure of A GH128 (Subgroup II) Endo-Beta-1,3-Glucanase From Sorangium Cellulosum (SCGH128_II)

The structure of Crystal Structure of A GH128 (Subgroup II) Endo-Beta-1,3-Glucanase From Sorangium Cellulosum (SCGH128_II), PDB code: 6uax was solved by C.R.Santos, P.A.C.R.Costa, M.N.Domingues, E.A.Lima, F.Mandelli, P.S.Vieira, M.T.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.55 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.756, 65.628, 86.551, 90.00, 95.96, 90.00
R / Rfree (%)	12.9 / 16.7

The structure of Crystal Structure of A GH128 (Subgroup II) Endo-Beta-1,3-Glucanase From Sorangium Cellulosum (SCGH128_II) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of A GH128 (Subgroup II) Endo-Beta-1,3-Glucanase From Sorangium Cellulosum (SCGH128_II) (pdb code 6uax). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A GH128 (Subgroup II) Endo-Beta-1,3-Glucanase From Sorangium Cellulosum (SCGH128_II), PDB code: 6uax:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of A GH128 (Subgroup II) Endo-Beta-1,3-Glucanase From Sorangium Cellulosum (SCGH128_II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A GH128 (Subgroup II) Endo-Beta-1,3-Glucanase From Sorangium Cellulosum (SCGH128_II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:13.1 occ:1.00 OE1 A:GLN264 2.3 16.7 1.0 O A:HOH765 2.3 29.5 1.0 O A:HOH577 2.3 26.2 1.0 O A:ASP262 2.4 11.6 1.0 OD2 A:ASP305 2.5 9.2 1.0 O A:HOH732 2.5 15.7 1.0 O A:HOH532 2.5 32.0 1.0 O A:HOH855 2.6 36.7 1.0 CG A:ASP305 3.3 9.3 1.0 CD A:GLN264 3.5 11.3 1.0 OD1 A:ASP305 3.5 14.8 1.0 C A:ASP262 3.6 9.8 1.0 NE2 A:GLN264 4.2 22.5 1.0 N A:GLN264 4.2 7.3 1.0 CA A:ASP262 4.5 11.9 1.0 N A:ASN263 4.5 9.4 1.0 CA A:ASN263 4.5 8.9 1.0 CG A:GLN264 4.6 11.2 1.0 CB A:ASP262 4.6 15.8 1.0 O A:HOH786 4.7 37.8 1.0 O A:HOH883 4.7 31.5 1.0 CB A:ASP305 4.8 9.3 1.0 O A:HOH868 4.8 40.9 1.0 CB A:GLN264 4.8 9.5 1.0 O A:GLU301 4.8 9.4 1.0 OE1 A:GLU301 4.8 27.5 1.0 C A:ASN263 4.9 8.0 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of A GH128 (Subgroup II) Endo-Beta-1,3-Glucanase From Sorangium Cellulosum (SCGH128_II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A GH128 (Subgroup II) Endo-Beta-1,3-Glucanase From Sorangium Cellulosum (SCGH128_II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:28.1 occ:1.00 O A:GLY155 2.2 15.1 0.4 O A:HOH867 2.3 33.3 1.0 O A:HOH567 2.3 36.5 1.0 O A:HOH522 2.3 38.7 1.0 O A:HOH872 2.5 23.0 1.0 O A:HOH749 2.7 45.8 1.0 C A:GLY155 3.4 11.6 0.4 OD1 A:ASN156 3.7 20.4 0.6 N A:ASN156 4.0 11.3 0.6 CA A:GLY155 4.2 10.6 0.4 CG A:ASN156 4.3 17.9 0.6 N A:ASN156 4.4 12.1 0.4 CA A:GLY155 4.4 9.1 0.6 ND2 A:ASN156 4.5 23.4 0.6 CA A:ASN156 4.6 11.8 0.4 CB A:ASN156 4.6 15.6 0.4 C A:GLY155 4.7 10.1 0.6 OD1 A:ASN156 4.8 15.9 0.4 CA A:ASN156 4.8 11.7 0.6

Calcium binding site 3 out of 3 in the Crystal Structure of A GH128 (Subgroup II) Endo-Beta-1,3-Glucanase From Sorangium Cellulosum (SCGH128_II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A GH128 (Subgroup II) Endo-Beta-1,3-Glucanase From Sorangium Cellulosum (SCGH128_II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:15.2 occ:1.00 OE1 B:GLN264 2.2 17.5 1.0 O B:ASP262 2.3 10.8 0.4 O B:HOH536 2.3 21.7 1.0 O B:HOH736 2.4 21.3 1.0 O B:ASP262 2.4 9.9 0.6 O B:HOH646 2.4 16.3 1.0 O B:HOH560 2.5 23.9 1.0 OD2 B:ASP305 2.5 11.5 1.0 CG B:ASP305 3.4 10.6 1.0 CD B:GLN264 3.4 15.7 1.0 C B:ASP262 3.5 11.1 0.4 C B:ASP262 3.5 10.1 0.6 OD1 B:ASP305 3.6 16.6 1.0 N B:GLN264 4.2 11.2 1.0 CA B:ASP262 4.3 11.3 0.6 NE2 B:GLN264 4.3 16.9 1.0 CA B:ASP262 4.4 13.0 0.4 O B:HOH724 4.4 29.3 1.0 OE1 B:GLU301 4.5 16.9 1.0 N B:ASN263 4.5 11.1 1.0 CG B:GLN264 4.5 11.8 1.0 CB B:ASP262 4.5 10.8 0.6 CA B:ASN263 4.5 8.9 1.0 CB B:ASP262 4.7 13.1 0.4 CB B:GLN264 4.7 10.5 1.0 O B:GLU301 4.8 9.2 1.0 O B:HOH508 4.8 24.4 1.0 CB B:ASP305 4.9 9.5 1.0 O B:HOH761 4.9 26.5 1.0 C B:ASN263 4.9 10.7 1.0

C.R.Santos, E.A.Lima, F.Mandelli, M.T.Murakami. Structural Insights Into Beta-1,3-Glucan Cleavage By A Glycoside Hydrolase Family Nat.Chem.Biol. 2020.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-020-0554-5