Calcium 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:

Sodium

(Na)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Amylase in Complex with Branched Ligand (pdb code 6gya). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Amylase in Complex with Branched Ligand, PDB code: 6gya:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Amylase in Complex with Branched Ligand


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 Branched Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:54.3 occ:1.00 O A:ASP197 2.2 51.3 1.0 OD1 A:ASP203 2.3 66.6 1.0 O A:HOH607 2.3 58.1 1.0 OD1 A:ASN106 2.3 48.4 1.0 OD1 A:ASP197 2.4 62.0 1.0 O A:HIS238 2.4 48.3 1.0 OD2 A:ASP203 2.8 71.0 1.0 CG A:ASP203 2.8 60.2 1.0 C A:ASP197 3.2 57.4 1.0 CG A:ASP197 3.4 61.1 1.0 CG A:ASN106 3.4 51.0 1.0 C A:HIS238 3.6 54.4 1.0 CA A:ASP197 3.7 61.3 1.0 NA A:NA502 3.8 59.1 1.0 O A:HOH602 3.9 42.1 1.0 O A:HOH622 3.9 62.7 1.0 O A:ASN106 3.9 57.6 1.0 ND2 A:ASN106 3.9 51.3 1.0 CB A:ASP197 4.1 59.6 1.0 CB A:HIS238 4.2 50.3 1.0 OD2 A:ASP197 4.2 54.2 1.0 N A:TYR198 4.3 57.3 1.0 CB A:ASP203 4.3 57.2 1.0 CA A:HIS238 4.4 55.1 1.0 N A:ILE239 4.6 54.2 1.0 CB A:ASN106 4.6 48.6 1.0 CA A:TYR198 4.7 58.7 1.0 O A:ILE204 4.7 63.8 1.0 CA A:ASN106 4.7 48.5 1.0 C A:ASN106 4.7 50.2 1.0 CA A:ILE239 4.7 55.6 1.0 CG1 A:ILE239 4.9 53.3 1.0

Calcium binding site 2 out of 12 in the Amylase in Complex with Branched Ligand


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 Branched Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:62.3 occ:1.00 O A:ALA184 2.2 69.5 1.0 OD1 A:ASP163 2.3 67.9 1.0 OD1 A:ASP205 2.3 66.5 1.0 OD1 A:ASP186 2.3 67.2 1.0 OD2 A:ASP207 2.7 65.3 1.0 OD2 A:ASP163 2.7 65.2 1.0 CG A:ASP163 2.8 62.9 1.0 CG A:ASP205 3.0 73.9 1.0 C A:ALA184 3.5 68.8 1.0 CG A:ASP207 3.5 64.3 1.0 OD2 A:ASP205 3.5 72.1 1.0 CG A:ASP186 3.6 64.1 1.0 CB A:ASP207 3.7 64.0 1.0 N A:ALA184 3.9 78.8 1.0 CB A:ASP205 4.0 72.5 1.0 N A:ASP186 4.1 58.6 1.0 O A:HOH601 4.1 46.3 1.0 CA A:ALA184 4.2 73.5 1.0 CB A:ASP163 4.3 64.5 1.0 C A:TRP185 4.3 59.4 1.0 CA A:ASP205 4.4 64.9 1.0 CA A:ASP186 4.4 57.9 1.0 OD2 A:ASP186 4.4 56.2 1.0 N A:TRP185 4.5 63.1 1.0 N A:ASP207 4.5 70.9 1.0 OD1 A:ASP207 4.6 69.1 1.0 CB A:ASP186 4.6 62.3 1.0 CB A:ALA184 4.6 77.5 1.0 CA A:TRP185 4.7 60.0 1.0 CA A:ASP207 4.7 66.2 1.0 O A:TRP185 4.7 62.0 1.0 C A:ASP205 4.9 62.9 1.0 O A:HOH621 4.9 89.4 1.0 N A:TYR206 4.9 60.1 1.0 C A:LYS183 5.0 80.8 1.0

Calcium binding site 3 out of 12 in the Amylase in Complex with Branched Ligand


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 Branched Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:48.8 occ:1.00 O A:TYR306 2.1 49.2 1.0 OD1 A:ASP408 2.3 55.5 1.0 OD1 A:ASP431 2.3 40.2 1.0 O A:GLY304 2.5 51.8 1.0 O A:GLN407 2.5 50.6 1.0 OD2 A:ASP431 2.7 46.7 1.0 CG A:ASP431 2.8 43.1 1.0 C A:TYR306 3.3 53.9 1.0 C A:GLN407 3.4 58.5 1.0 C A:GLY304 3.4 52.5 1.0 CG A:ASP408 3.5 61.8 1.0 O A:HOH645 3.6 48.2 1.0 C A:TYR305 3.7 49.2 1.0 N A:TYR306 3.8 51.4 1.0 CA A:TYR305 3.9 50.4 1.0 N A:TYR305 4.0 52.7 1.0 CA A:ASP408 4.0 59.9 1.0 O A:TYR305 4.0 53.3 1.0 N A:ASP408 4.1 55.9 1.0 CB A:GLN407 4.2 71.8 1.0 CA A:TYR306 4.2 52.8 1.0 N A:ASP307 4.3 51.0 1.0 CB A:ASP431 4.4 41.2 1.0 CB A:ASP408 4.4 62.3 1.0 CA A:GLN407 4.4 62.4 1.0 OD2 A:ASP408 4.4 68.9 1.0 CA A:ASP307 4.5 51.8 1.0 CG A:MET308 4.6 45.6 1.0 CA A:GLY304 4.6 48.9 1.0 N A:MET308 4.6 52.9 1.0 O A:HOH659 4.8 43.2 1.0 CB A:TYR306 4.9 51.4 1.0 O A:HOH623 4.9 33.7 1.0

Calcium binding site 4 out of 12 in the Amylase in Complex with Branched Ligand


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 Branched Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:64.5 occ:1.00 O B:ASP197 2.3 63.4 1.0 OD1 B:ASP203 2.3 92.6 1.0 OD1 B:ASN106 2.3 88.1 1.0 OD1 B:ASP197 2.3 72.3 1.0 O B:HIS238 2.4 65.4 1.0 OD2 B:ASP203 2.7 90.8 1.0 CG B:ASP203 2.8 78.2 1.0 C B:ASP197 3.3 68.9 1.0 CG B:ASP197 3.4 66.7 1.0 CG B:ASN106 3.4 68.4 1.0 C B:HIS238 3.6 57.5 1.0 NA B:NA502 3.6 74.2 1.0 CA B:ASP197 3.8 67.4 1.0 O B:ASN106 3.9 74.8 1.0 ND2 B:ASN106 4.0 66.7 1.0 O B:HOH601 4.1 65.0 1.0 CB B:ASP197 4.1 65.0 1.0 OD2 B:ASP197 4.2 62.8 1.0 CB B:HIS238 4.3 64.2 1.0 CB B:ASP203 4.3 66.3 1.0 N B:TYR198 4.4 68.9 1.0 CA B:HIS238 4.5 61.2 1.0 O B:ILE204 4.5 74.2 1.0 CB B:ASN106 4.6 54.7 1.0 N B:ILE239 4.6 57.2 1.0 CA B:ILE239 4.7 62.6 1.0 CA B:ASN106 4.7 52.8 1.0 C B:ASN106 4.7 60.0 1.0 CA B:TYR198 4.8 68.8 1.0

Calcium binding site 5 out of 12 in the Amylase in Complex with Branched Ligand


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 Branched Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:71.8 occ:1.00 OD1 B:ASP205 1.9 72.3 1.0 OD1 B:ASP163 2.0 88.2 1.0 OD2 B:ASP163 2.4 87.3 1.0 CG B:ASP163 2.4 77.6 1.0 CG B:ASP205 2.5 82.8 1.0 O B:ALA184 2.7 83.6 1.0 OD1 B:ASP186 2.7 80.3 1.0 OD2 B:ASP207 3.1 77.5 1.0 OD2 B:ASP205 3.1 79.8 1.0 CB B:ASP205 3.5 79.9 1.0 CG B:ASP186 3.8 80.4 1.0 CG B:ASP207 3.8 70.5 1.0 CA B:ASP205 3.8 76.1 1.0 C B:ALA184 3.9 91.1 1.0 CB B:ASP163 3.9 71.2 1.0 CB B:ASP207 4.1 68.7 1.0 N B:ALA184 4.2 96.4 1.0 OD2 B:ASP186 4.3 79.5 1.0 C B:ASP205 4.4 74.2 1.0 N B:ASP186 4.5 74.9 1.0 N B:ASP207 4.5 76.9 1.0 N B:TYR206 4.6 73.3 1.0 CA B:ALA184 4.6 96.7 1.0 C B:TRP185 4.7 73.9 1.0 CA B:ASP163 4.7 72.3 1.0 OD1 B:ASP207 4.7 74.6 1.0 N B:TRP185 4.8 84.0 1.0 O B:HOH611 4.9 58.2 1.0 CA B:TRP185 4.9 76.5 1.0 CA B:ASP186 4.9 71.8 1.0 CD B:LYS183 4.9 73.4 1.0 NA B:NA502 4.9 74.2 1.0 CB B:ASP186 4.9 73.8 1.0 CA B:ASP207 5.0 75.5 1.0

Calcium binding site 6 out of 12 in the Amylase in Complex with Branched Ligand


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 Branched Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:53.3 occ:1.00 O B:TYR306 2.1 51.6 1.0 OD1 B:ASP408 2.3 51.3 1.0 OD1 B:ASP431 2.4 44.3 1.0 O B:GLY304 2.4 53.4 1.0 O B:GLN407 2.5 52.8 1.0 OD2 B:ASP431 2.7 46.7 1.0 CG B:ASP431 2.9 45.0 1.0 C B:TYR306 3.3 53.6 1.0 C B:GLN407 3.4 55.6 1.0 C B:GLY304 3.5 52.5 1.0 CG B:ASP408 3.6 57.5 1.0 C B:TYR305 3.7 55.0 1.0 N B:TYR306 3.8 56.4 1.0 CA B:TYR305 3.9 52.9 1.0 O B:TYR305 4.0 60.4 1.0 N B:TYR305 4.0 53.2 1.0 CA B:ASP408 4.0 54.8 1.0 N B:ASP408 4.1 52.0 1.0 CB B:GLN407 4.1 74.6 1.0 CA B:TYR306 4.2 51.1 1.0 N B:ASP307 4.3 54.3 1.0 CA B:GLN407 4.4 62.2 1.0 CB B:ASP408 4.4 58.0 1.0 CB B:ASP431 4.4 45.8 1.0 OD2 B:ASP408 4.4 63.4 1.0 CA B:ASP307 4.5 56.2 1.0 CA B:GLY304 4.6 46.5 1.0 N B:MET308 4.6 52.2 1.0 CG B:MET308 4.6 51.8 1.0 CB B:TYR306 5.0 54.9 1.0 O B:HOH628 5.0 46.3 1.0

Calcium binding site 7 out of 12 in the Amylase in Complex with Branched Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Amylase in Complex with Branched Ligand within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:59.8 occ:1.00 O C:ASP197 2.2 53.8 1.0 OD1 C:ASP203 2.3 60.8 1.0 O C:HOH617 2.3 69.8 1.0 OD1 C:ASN106 2.3 65.2 1.0 OD1 C:ASP197 2.3 61.9 1.0 O C:HIS238 2.4 47.0 1.0 OD2 C:ASP203 2.7 66.0 1.0 CG C:ASP203 2.9 54.6 1.0 C C:ASP197 3.2 52.5 1.0 CG C:ASP197 3.3 61.2 1.0 CG C:ASN106 3.4 63.0 1.0 C C:HIS238 3.6 56.1 1.0 CA C:ASP197 3.7 59.8 1.0 NA C:NA502 3.8 64.9 1.0 ND2 C:ASN106 4.0 53.1 1.0 O C:ASN106 4.0 71.0 1.0 CB C:ASP197 4.1 63.7 1.0 O C:HOH633 4.1 62.1 1.0 OD2 C:ASP197 4.2 54.0 1.0 CB C:HIS238 4.2 54.5 1.0 N C:TYR198 4.3 51.9 1.0 O C:HOH623 4.3 41.6 1.0 CB C:ASP203 4.4 53.5 1.0 CA C:HIS238 4.4 53.0 1.0 N C:ILE239 4.6 58.1 1.0 CB C:ASN106 4.6 58.4 1.0 O C:ILE204 4.6 76.2 1.0 CA C:ILE239 4.6 64.8 1.0 CA C:TYR198 4.7 53.2 1.0 CA C:ASN106 4.7 55.9 1.0 C C:ASN106 4.8 57.4 1.0

Calcium binding site 8 out of 12 in the Amylase in Complex with Branched Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Amylase in Complex with Branched Ligand within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:65.1 occ:1.00 OD2 C:ASP207 2.2 63.8 1.0 O C:ALA184 2.3 78.2 1.0 OD1 C:ASP163 2.3 74.2 1.0 OD1 C:ASP205 2.3 69.6 1.0 OD1 C:ASP186 2.4 60.9 1.0 OD2 C:ASP163 2.7 60.8 1.0 CG C:ASP163 2.8 64.7 1.0 CG C:ASP205 3.1 73.6 1.0 CG C:ASP207 3.2 70.9 1.0 C C:ALA184 3.5 76.8 1.0 CG C:ASP186 3.5 68.3 1.0 OD2 C:ASP205 3.6 70.8 1.0 N C:ALA184 3.9 71.5 1.0 CB C:ASP207 3.9 73.2 1.0 CB C:ASP205 4.1 69.6 1.0 CA C:ALA184 4.2 74.2 1.0 OD2 C:ASP186 4.2 68.8 1.0 OD1 C:ASP207 4.2 75.2 1.0 N C:ASP186 4.2 66.3 1.0 CB C:ASP163 4.3 63.8 1.0 C C:TRP185 4.4 66.8 1.0 CA C:ASP205 4.4 72.6 1.0 O C:HOH646 4.5 45.3 1.0 N C:TRP185 4.5 70.6 1.0 CA C:ASP186 4.5 61.0 1.0 N C:ASP207 4.5 75.7 1.0 CB C:ALA184 4.6 72.8 1.0 CB C:ASP186 4.6 62.1 1.0 CA C:TRP185 4.8 69.2 1.0 O C:TRP185 4.8 64.1 1.0 CA C:ASP207 4.8 79.2 1.0 C C:ASP205 4.9 62.6 1.0 N C:TYR206 4.9 61.8 1.0 C C:LYS183 4.9 68.5 1.0

Calcium binding site 9 out of 12 in the Amylase in Complex with Branched Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Amylase in Complex with Branched Ligand within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:54.2 occ:1.00 O C:TYR306 2.2 62.8 1.0 OD1 C:ASP408 2.3 53.3 1.0 OD1 C:ASP431 2.4 39.9 1.0 O C:GLY304 2.4 53.2 1.0 O C:GLN407 2.5 58.8 1.0 OD2 C:ASP431 2.7 53.8 1.0 CG C:ASP431 2.9 46.8 1.0 C C:TYR306 3.4 52.5 1.0 C C:GLN407 3.4 68.3 1.0 C C:GLY304 3.4 53.2 1.0 CG C:ASP408 3.5 57.8 1.0 C C:TYR305 3.8 49.4 1.0 CA C:TYR305 3.9 52.6 1.0 N C:TYR306 3.9 45.5 1.0 N C:TYR305 4.0 52.2 1.0 CA C:ASP408 4.0 56.5 1.0 N C:ASP408 4.1 60.9 1.0 O C:TYR305 4.1 48.3 1.0 CB C:GLN407 4.1 69.1 1.0 CA C:TYR306 4.3 45.4 1.0 N C:ASP307 4.3 55.3 1.0 CA C:GLN407 4.4 70.4 1.0 CB C:ASP408 4.4 52.7 1.0 OD2 C:ASP408 4.4 63.6 1.0 CB C:ASP431 4.5 47.8 1.0 CA C:ASP307 4.5 56.9 1.0 CA C:GLY304 4.6 55.3 1.0 N C:MET308 4.6 58.5 1.0 CG C:MET308 4.7 61.4 1.0 O C:HOH647 4.8 29.4 1.0 CB C:TYR306 5.0 48.6 1.0

Calcium binding site 10 out of 12 in the Amylase in Complex with Branched Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Amylase in Complex with Branched Ligand within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca501 b:59.0 occ:1.00 O D:ASP197 2.2 59.5 1.0 O D:HOH648 2.3 60.8 1.0 OD1 D:ASP197 2.3 68.3 1.0 OD1 D:ASN106 2.3 64.5 1.0 OD1 D:ASP203 2.4 74.0 1.0 O D:HIS238 2.4 47.4 1.0 OD2 D:ASP203 2.7 59.2 1.0 CG D:ASP203 2.9 54.6 1.0 C D:ASP197 3.2 54.6 1.0 CG D:ASP197 3.4 62.2 1.0 CG D:ASN106 3.5 59.6 1.0 C D:HIS238 3.6 52.1 1.0 CA D:ASP197 3.8 55.6 1.0 NA D:NA502 3.8 60.3 1.0 O D:ASN106 4.0 65.3 1.0 ND2 D:ASN106 4.0 51.2 1.0 CB D:ASP197 4.1 59.0 1.0 OD2 D:ASP197 4.2 49.7 1.0 CB D:HIS238 4.2 52.6 1.0 N D:TYR198 4.3 54.4 1.0 O D:HOH611 4.3 68.3 1.0 CB D:ASP203 4.4 54.4 1.0 CA D:HIS238 4.5 53.7 1.0 N D:ILE239 4.6 53.6 1.0 O D:ILE204 4.6 79.0 1.0 CB D:ASN106 4.6 57.3 1.0 CA D:ILE239 4.7 63.5 1.0 CA D:ASN106 4.7 55.5 1.0 CA D:TYR198 4.7 56.7 1.0 C D:ASN106 4.8 57.1 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