Sodium in PDB 6gya: Amylase in Complex with Branched Ligand

The structure of Amylase in Complex with Branched Ligand, PDB code: 6gya 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)	66.86 / 2.95
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	212.180, 212.180, 172.220, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 18.3

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

Calcium

(Ca)

12 atoms

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

Sodium binding site 1 out of 4 in the Amylase in Complex with Branched Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Amylase in Complex with Branched Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:59.1 occ:1.00 O A:ILE204 2.3 63.8 1.0 OD2 A:ASP197 2.7 54.2 1.0 OD2 A:ASP203 2.7 71.0 1.0 OD2 A:ASP163 2.7 65.2 1.0 OD2 A:ASP186 2.7 56.2 1.0 OD1 A:ASP197 3.0 62.0 1.0 CG A:ASP203 3.1 60.2 1.0 OD1 A:ASP203 3.1 66.6 1.0 CG A:ASP197 3.1 61.1 1.0 C A:ILE204 3.2 61.4 1.0 O A:HOH607 3.5 58.1 1.0 CG A:ASP186 3.6 64.1 1.0 CG A:ASP163 3.6 62.9 1.0 CB A:ASP163 3.7 64.5 1.0 O A:HOH622 3.7 62.7 1.0 CA A:CA501 3.8 54.3 1.0 O A:ASP203 3.8 65.5 1.0 N A:ASP205 3.8 70.2 1.0 CA A:ASP205 3.8 64.9 1.0 C A:ASP203 4.0 54.8 1.0 CB A:ASP203 4.0 57.2 1.0 OD1 A:ASP186 4.1 67.2 1.0 N A:ILE204 4.2 50.9 1.0 CA A:ILE204 4.3 54.1 1.0 N A:TYR206 4.5 60.1 1.0 CB A:ASP186 4.5 62.3 1.0 CB A:ASP197 4.6 59.6 1.0 CA A:ASP203 4.6 57.5 1.0 C A:ASP205 4.7 62.9 1.0 N A:ASP163 4.8 59.0 1.0 OD1 A:ASP163 4.8 67.9 1.0 N A:ASP186 4.9 58.6 1.0 CA A:ASP163 4.9 61.9 1.0 CB A:ASP205 4.9 72.5 1.0 O A:ASP197 5.0 51.3 1.0

Sodium binding site 2 out of 4 in the Amylase in Complex with Branched Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Amylase in Complex with Branched Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:74.2 occ:1.00 O B:ILE204 2.3 74.2 1.0 OD2 B:ASP197 2.7 62.8 1.0 OD2 B:ASP203 2.7 90.8 1.0 OD2 B:ASP163 2.7 87.3 1.0 OD1 B:ASP197 3.0 72.3 1.0 OD2 B:ASP186 3.0 79.5 1.0 CG B:ASP203 3.1 78.2 1.0 OD1 B:ASP203 3.1 92.6 1.0 CG B:ASP197 3.1 66.7 1.0 C B:ILE204 3.2 69.6 1.0 O B:HOH601 3.6 65.0 1.0 CG B:ASP163 3.6 77.6 1.0 CA B:CA501 3.6 64.5 1.0 CG B:ASP186 3.7 80.4 1.0 CB B:ASP163 3.7 71.2 1.0 O B:ASP203 3.8 80.8 1.0 N B:ASP205 3.9 75.6 1.0 CA B:ASP205 3.9 76.1 1.0 C B:ASP203 4.0 59.3 1.0 CB B:ASP203 4.1 66.3 1.0 N B:ILE204 4.2 63.9 1.0 OD1 B:ASP186 4.3 80.3 1.0 CA B:ILE204 4.4 67.5 1.0 N B:TYR206 4.5 73.3 1.0 CB B:ASP186 4.5 73.8 1.0 CB B:ASP197 4.6 65.0 1.0 CA B:ASP203 4.6 64.4 1.0 C B:ASP205 4.7 74.2 1.0 N B:ASP163 4.8 62.6 1.0 OD1 B:ASP163 4.8 88.2 1.0 N B:ASP186 4.9 74.9 1.0 CA B:ASP163 4.9 72.3 1.0 O B:ASP197 4.9 63.4 1.0 CB B:ASP205 4.9 79.9 1.0 CA B:CA503 4.9 71.8 1.0 CD2 B:TYR206 4.9 64.0 1.0

Sodium binding site 3 out of 4 in the Amylase in Complex with Branched Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Amylase in Complex with Branched Ligand within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:64.9 occ:1.00 O C:ILE204 2.3 76.2 1.0 OD2 C:ASP197 2.6 54.0 1.0 OD2 C:ASP203 2.7 66.0 1.0 OD2 C:ASP163 2.7 60.8 1.0 OD1 C:ASP197 3.0 61.9 1.0 OD2 C:ASP186 3.1 68.8 1.0 CG C:ASP197 3.2 61.2 1.0 CG C:ASP203 3.2 54.6 1.0 C C:ILE204 3.3 73.8 1.0 O C:HOH617 3.5 69.8 1.0 CG C:ASP186 3.5 68.3 1.0 CG C:ASP163 3.6 64.7 1.0 OD1 C:ASP203 3.7 60.8 1.0 OD1 C:ASP186 3.7 60.9 1.0 CB C:ASP163 3.7 63.8 1.0 CA C:CA501 3.8 59.8 1.0 CA C:ASP205 3.8 72.6 1.0 O C:ASP203 3.8 68.5 1.0 N C:ASP205 3.8 75.8 1.0 O C:HOH633 3.9 62.1 1.0 C C:ASP203 4.0 61.1 1.0 CB C:ASP203 4.1 53.5 1.0 N C:ILE204 4.2 61.4 1.0 CA C:ILE204 4.4 65.3 1.0 N C:TYR206 4.4 61.8 1.0 CB C:ASP186 4.5 62.1 1.0 CB C:ASP197 4.6 63.7 1.0 CA C:ASP203 4.7 55.6 1.0 C C:ASP205 4.7 62.6 1.0 OD1 C:ASP163 4.8 74.2 1.0 N C:ASP163 4.8 67.0 1.0 N C:ASP186 4.8 66.3 1.0 CB C:ASP205 4.9 69.6 1.0 CA C:ASP163 4.9 62.8 1.0 CD2 C:TYR206 5.0 76.6 1.0

Sodium binding site 4 out of 4 in the Amylase in Complex with Branched Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Amylase in Complex with Branched Ligand within 5.0Å range: probe atom residue distance (Å) B Occ D:Na502 b:60.3 occ:1.00 O D:ILE204 2.3 79.0 1.0 OD2 D:ASP197 2.7 49.7 1.0 OD2 D:ASP203 2.7 59.2 1.0 OD2 D:ASP163 2.7 56.0 1.0 OD2 D:ASP186 3.0 59.1 1.0 OD1 D:ASP197 3.0 68.3 1.0 CG D:ASP197 3.2 62.2 1.0 O D:HOH648 3.2 60.8 1.0 C D:ILE204 3.3 76.8 1.0 CG D:ASP203 3.3 54.6 1.0 CG D:ASP186 3.4 63.1 1.0 CG D:ASP163 3.6 64.9 1.0 OD1 D:ASP186 3.7 66.0 1.0 CB D:ASP163 3.7 62.3 1.0 CA D:CA501 3.8 59.0 1.0 CA D:ASP205 3.8 76.8 1.0 N D:ASP205 3.8 75.2 1.0 O D:ASP203 3.8 64.7 1.0 OD1 D:ASP203 3.9 74.0 1.0 C D:ASP203 4.0 59.1 1.0 CB D:ASP203 4.1 54.4 1.0 O D:HOH611 4.2 68.3 1.0 N D:ILE204 4.2 75.4 1.0 CA D:ILE204 4.4 80.9 1.0 N D:TYR206 4.4 66.9 1.0 CB D:ASP186 4.5 59.5 1.0 CB D:ASP197 4.6 59.0 1.0 C D:ASP205 4.6 65.1 1.0 CA D:ASP203 4.7 57.2 1.0 N D:ASP163 4.8 63.6 1.0 OD1 D:ASP163 4.8 72.3 1.0 N D:ASP186 4.8 65.2 1.0 CA D:ASP163 4.9 62.0 1.0 CB D:ASP205 4.9 79.8 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