Calcium in PDB 6gxv: Amylase in Complex with Acarbose

The structure of Amylase in Complex with Acarbose, PDB code: 6gxv was solved by J.Agirre, O.Moroz, S.Meier, J.Brask, A.Munch, T.Hoff, C.Andersen, K.S.Wilson, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.21 / 2.07
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	180.900, 180.900, 77.850, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 17.6

The structure of Amylase in Complex with Acarbose also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Amylase in Complex with Acarbose (pdb code 6gxv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Amylase in Complex with Acarbose, PDB code: 6gxv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Amylase in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Amylase in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:12.0 occ:1.00 O A:ASP197 2.3 13.0 1.0 O A:HIS238 2.3 11.7 1.0 OD1 A:ASN106 2.3 13.9 1.0 OD1 A:ASP197 2.4 12.2 1.0 OD1 A:ASP203 2.4 13.1 1.0 O A:HOH823 2.4 9.6 1.0 CG A:ASP203 3.2 14.1 1.0 C A:ASP197 3.3 12.1 1.0 OD2 A:ASP203 3.4 13.1 1.0 CG A:ASP197 3.4 12.9 1.0 CG A:ASN106 3.5 13.9 1.0 C A:HIS238 3.5 12.8 1.0 CA A:ASP197 3.7 12.7 1.0 O A:HOH650 3.8 12.1 1.0 CB A:HIS238 4.0 11.7 1.0 NA A:NA502 4.1 12.3 1.0 O A:ASN106 4.1 14.4 1.0 CB A:ASP197 4.1 12.8 1.0 ND2 A:ASN106 4.1 13.0 1.0 CA A:HIS238 4.3 12.4 1.0 O A:HOH681 4.3 10.3 1.0 OD2 A:ASP197 4.3 12.3 1.0 N A:TYR198 4.4 12.7 1.0 N A:ILE239 4.5 13.8 1.0 O A:ILE204 4.6 11.6 1.0 CB A:ASN106 4.6 13.3 1.0 CA A:ILE239 4.6 14.8 1.0 CB A:ASP203 4.7 13.3 1.0 CA A:ASN106 4.8 14.0 1.0 CA A:TYR198 4.8 11.7 1.0 C A:ASN106 4.9 14.3 1.0 CG1 A:ILE239 4.9 17.5 1.0

Calcium binding site 2 out of 6 in the Amylase in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Amylase in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:15.5 occ:1.00 O A:ALA184 2.3 15.8 1.0 OD1 A:ASP205 2.4 14.1 1.0 O A:HOH961 2.4 16.4 1.0 OD1 A:ASP186 2.4 13.7 1.0 OD1 A:ASP163 2.5 13.1 1.0 OD2 A:ASP207 2.6 19.3 1.0 OD2 A:ASP163 2.6 13.4 1.0 CG A:ASP163 2.8 13.3 1.0 CG A:ASP205 3.3 15.0 1.0 CG A:ASP207 3.4 18.0 1.0 CG A:ASP186 3.5 12.7 1.0 C A:ALA184 3.6 15.9 1.0 CB A:ASP207 3.9 16.8 1.0 N A:ASP186 3.9 13.8 1.0 OD2 A:ASP205 4.0 13.5 1.0 O A:HOH649 4.1 21.8 1.0 C A:TRP185 4.1 14.0 1.0 N A:ALA184 4.2 18.2 1.0 OD2 A:ASP186 4.2 12.4 1.0 CB A:ASP205 4.2 14.0 1.0 CA A:ASP205 4.3 13.0 1.0 CA A:ASP186 4.3 12.8 1.0 CB A:ASP163 4.3 13.1 1.0 N A:ASP207 4.4 15.5 1.0 OD1 A:ASP207 4.4 16.2 1.0 CA A:ALA184 4.4 18.0 1.0 CB A:ASP186 4.5 12.7 1.0 NA A:NA502 4.5 12.3 1.0 N A:TRP185 4.5 13.8 1.0 CA A:TRP185 4.6 13.7 1.0 O A:TRP185 4.6 13.8 1.0 O A:HOH1013 4.6 28.8 1.0 C A:ASP205 4.7 13.0 1.0 CA A:ASP207 4.7 16.9 1.0 N A:TYR206 4.8 12.4 1.0 OD2 A:ASP197 4.8 12.3 1.0 CB A:ALA184 4.9 18.4 1.0

Calcium binding site 3 out of 6 in the Amylase in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Amylase in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:29.3 occ:1.00 O A:TYR306 2.3 22.9 1.0 O A:GLY304 2.5 20.0 1.0 O A:HOH862 2.5 41.1 1.0 OD1 A:ASP408 2.5 28.4 1.0 OD1 A:ASP431 2.5 23.1 1.0 OD2 A:ASP431 2.5 20.4 1.0 O A:GLN407 2.7 20.9 1.0 CG A:ASP431 2.8 21.5 1.0 C A:GLY304 3.3 20.4 1.0 C A:TYR306 3.5 20.3 1.0 CG A:ASP408 3.5 27.9 1.0 C A:GLN407 3.6 21.8 1.0 N A:TYR306 3.8 18.1 1.0 CA A:ASP408 3.8 23.4 1.0 O A:HOH716 3.9 55.4 1.0 C A:TYR305 4.0 19.7 1.0 N A:TYR305 4.1 19.6 1.0 N A:ASP408 4.1 22.6 1.0 CG A:MET308 4.2 18.4 1.0 CB A:ASP408 4.2 26.8 1.0 CA A:TYR306 4.2 18.9 1.0 CA A:TYR305 4.2 19.5 1.0 CA A:GLY304 4.2 20.9 1.0 O A:HOH781 4.3 30.0 1.0 CB A:ASP431 4.3 19.0 1.0 OD2 A:ASP408 4.5 33.0 1.0 N A:MET308 4.5 17.9 1.0 N A:ASP307 4.5 19.7 1.0 O A:TYR305 4.5 21.4 1.0 O A:HOH628 4.5 15.5 1.0 CB A:GLN407 4.6 25.2 1.0 CB A:TYR306 4.7 18.9 1.0 CA A:ASP307 4.7 18.9 1.0 CA A:GLN407 4.7 24.5 1.0 CB A:MET308 5.0 18.2 1.0

Calcium binding site 4 out of 6 in the Amylase in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Amylase in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:13.0 occ:1.00 O B:ASP197 2.3 13.5 1.0 OD1 B:ASN106 2.3 13.9 1.0 O B:HIS238 2.3 12.4 1.0 OD1 B:ASP197 2.4 13.1 1.0 OD1 B:ASP203 2.4 11.7 1.0 O B:HOH801 2.4 10.4 1.0 C B:ASP197 3.3 12.7 1.0 CG B:ASP203 3.3 12.7 1.0 CG B:ASN106 3.5 14.0 1.0 CG B:ASP197 3.5 13.7 1.0 OD2 B:ASP203 3.5 13.3 1.0 C B:HIS238 3.5 12.8 1.0 CA B:ASP197 3.7 12.2 1.0 O B:HOH629 3.8 10.4 1.0 O B:ASN106 4.0 13.6 1.0 CB B:HIS238 4.0 13.2 1.0 NA B:NA507 4.1 13.0 1.0 ND2 B:ASN106 4.1 12.6 1.0 CB B:ASP197 4.2 12.4 1.0 O B:HOH775 4.3 13.7 1.0 CA B:HIS238 4.3 13.9 1.0 N B:TYR198 4.3 12.7 1.0 OD2 B:ASP197 4.4 12.4 1.0 N B:ILE239 4.5 11.6 1.0 CB B:ASN106 4.6 13.1 1.0 O B:ILE204 4.6 12.1 1.0 CB B:ASP203 4.7 12.9 1.0 CA B:ILE239 4.7 12.9 1.0 CA B:ASN106 4.7 13.7 1.0 C B:ASN106 4.8 14.4 1.0 CA B:TYR198 4.8 12.0 1.0 CG1 B:ILE239 4.8 12.3 1.0

Calcium binding site 5 out of 6 in the Amylase in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Amylase in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca508 b:15.8 occ:1.00 O B:ALA184 2.3 15.6 1.0 OD1 B:ASP205 2.4 13.0 1.0 O B:HOH971 2.4 13.5 1.0 OD1 B:ASP163 2.4 14.8 1.0 OD1 B:ASP186 2.5 13.6 1.0 OD2 B:ASP207 2.6 16.1 1.0 OD2 B:ASP163 2.6 14.2 1.0 CG B:ASP163 2.8 13.7 1.0 CG B:ASP205 3.3 15.6 1.0 CG B:ASP207 3.5 16.7 1.0 CG B:ASP186 3.5 13.8 1.0 C B:ALA184 3.5 17.0 1.0 N B:ASP186 3.9 15.4 1.0 CB B:ASP207 3.9 16.0 1.0 OD2 B:ASP205 3.9 16.5 1.0 C B:TRP185 4.1 15.1 1.0 OD2 B:ASP186 4.2 13.4 1.0 CB B:ASP205 4.2 14.3 1.0 CA B:ASP205 4.2 14.3 1.0 N B:ALA184 4.2 18.3 1.0 O B:HOH693 4.3 19.8 1.0 CA B:ASP186 4.3 14.8 1.0 CB B:ASP163 4.3 12.9 1.0 N B:ASP207 4.4 15.4 1.0 OD1 B:ASP207 4.4 16.2 1.0 N B:TRP185 4.4 15.2 1.0 CA B:ALA184 4.4 18.2 1.0 CA B:TRP185 4.5 14.9 1.0 NA B:NA507 4.5 13.0 1.0 CB B:ASP186 4.5 14.3 1.0 O B:TRP185 4.6 15.0 1.0 O B:HOH1049 4.6 32.1 1.0 C B:ASP205 4.7 14.1 1.0 O B:HOH943 4.7 32.5 1.0 N B:TYR206 4.7 14.4 1.0 CA B:ASP207 4.8 16.1 1.0 OD2 B:ASP197 4.8 12.4 1.0 CB B:ALA184 4.9 18.8 1.0

Calcium binding site 6 out of 6 in the Amylase in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Amylase in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca509 b:27.2 occ:1.00 O B:TYR306 2.3 19.4 1.0 OD1 B:ASP408 2.4 21.3 1.0 O B:GLY304 2.5 18.9 1.0 OD1 B:ASP431 2.5 17.4 1.0 OD2 B:ASP431 2.6 17.4 1.0 O B:GLN407 2.6 21.2 1.0 CG B:ASP431 2.9 17.0 1.0 C B:GLY304 3.4 19.9 1.0 O B:HOH842 3.5 41.7 1.0 C B:GLN407 3.5 20.4 1.0 C B:TYR306 3.5 18.0 1.0 CG B:ASP408 3.5 21.8 1.0 CA B:ASP408 3.7 19.7 1.0 N B:TYR306 3.8 16.7 1.0 N B:ASP408 4.0 18.6 1.0 C B:TYR305 4.0 17.7 1.0 N B:TYR305 4.1 20.0 1.0 CG B:MET308 4.2 17.0 1.0 CB B:ASP408 4.2 20.1 1.0 CA B:GLY304 4.2 21.1 1.0 CA B:TYR306 4.2 17.0 1.0 O B:HOH844 4.3 20.7 1.0 CA B:TYR305 4.3 19.1 1.0 CB B:ASP431 4.4 16.7 1.0 OD2 B:ASP408 4.5 29.1 1.0 O B:HOH643 4.5 12.6 1.0 N B:MET308 4.5 16.8 1.0 N B:ASP307 4.6 17.8 1.0 O B:TYR305 4.6 17.4 1.0 O B:HOH1015 4.6 44.7 1.0 CA B:GLN407 4.7 20.9 1.0 CB B:GLN407 4.7 21.3 1.0 CB B:TYR306 4.8 16.5 1.0 CA B:ASP307 4.8 18.0 1.0 CG B:GLN407 4.9 22.2 1.0 C B:ASP408 4.9 19.3 1.0 O B:ASP408 5.0 19.0 1.0

J.Agirre, O.Moroz, S.Meier, J.Brask, A.Munch, T.Hoff, C.Andersen, K.S.Wilson, G.J.Davies. The Structure of the Alic GH13 Alpha-Amylase From Alicyclobacillus Sp. Reveals the Accommodation of Starch Branching Points in the Alpha-Amylase Family. Acta Crystallogr D Struct V. 75 1 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 30644839
DOI: 10.1107/S2059798318014900