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Sodium in PDB 6gxv: Amylase in Complex with Acarbose

Protein crystallography data

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

Other elements in 6gxv:

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

Calcium (Ca) 6 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 6gxv

Go back to Sodium Binding Sites List in 6gxv
Sodium binding site 1 out of 2 in the Amylase in Complex with Acarbose


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 Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:12.3
occ:1.00
OD2 A:ASP163 2.2 13.4 1.0
OD2 A:ASP197 2.3 12.3 1.0
OD2 A:ASP203 2.3 13.1 1.0
OD2 A:ASP186 2.4 12.4 1.0
O A:ILE204 2.4 11.6 1.0
OD1 A:ASP197 2.9 12.2 1.0
CG A:ASP197 2.9 12.9 1.0
CG A:ASP186 3.1 12.7 1.0
CG A:ASP163 3.3 13.3 1.0
C A:ILE204 3.5 13.3 1.0
CG A:ASP203 3.5 14.1 1.0
O A:HOH823 3.6 9.6 1.0
CB A:ASP163 3.6 13.1 1.0
O A:HOH650 3.6 12.1 1.0
OD1 A:ASP186 3.7 13.7 1.0
CA A:ASP205 3.9 13.0 1.0
CB A:ASP186 4.0 12.7 1.0
N A:ASP205 4.0 13.2 1.0
CA A:CA501 4.1 12.0 1.0
OD1 A:ASP203 4.2 13.1 1.0
N A:ASP186 4.3 13.8 1.0
N A:TYR206 4.3 12.4 1.0
CB A:ASP197 4.4 12.8 1.0
OD1 A:ASP163 4.4 13.1 1.0
O A:ASP203 4.5 13.1 1.0
CA A:CA503 4.5 15.5 1.0
C A:ASP203 4.5 13.2 1.0
N A:ILE204 4.6 12.8 1.0
CB A:ASP203 4.6 13.3 1.0
CA A:ILE204 4.7 13.3 1.0
C A:ASP205 4.7 13.0 1.0
CA A:ASP186 4.8 12.8 1.0
CA A:ASP163 4.9 13.8 1.0
OD1 A:ASP205 5.0 14.1 1.0
N A:ASP163 5.0 13.2 1.0

Sodium binding site 2 out of 2 in 6gxv

Go back to Sodium Binding Sites List in 6gxv
Sodium binding site 2 out of 2 in the Amylase in Complex with Acarbose


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 Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na507

b:13.0
occ:1.00
OD2 B:ASP163 2.3 14.2 1.0
OD2 B:ASP197 2.3 12.4 1.0
OD2 B:ASP203 2.3 13.3 1.0
O B:ILE204 2.4 12.1 1.0
OD2 B:ASP186 2.4 13.4 1.0
OD1 B:ASP197 2.8 13.1 1.0
CG B:ASP197 2.9 13.7 1.0
CG B:ASP186 3.1 13.8 1.0
CG B:ASP163 3.3 13.7 1.0
C B:ILE204 3.5 13.5 1.0
CG B:ASP203 3.5 12.7 1.0
O B:HOH629 3.5 10.4 1.0
O B:HOH801 3.6 10.4 1.0
CB B:ASP163 3.7 12.9 1.0
OD1 B:ASP186 3.7 13.6 1.0
CB B:ASP186 3.9 14.3 1.0
CA B:ASP205 3.9 14.3 1.0
N B:ASP205 4.1 13.7 1.0
CA B:CA506 4.1 13.0 1.0
OD1 B:ASP203 4.1 11.7 1.0
N B:TYR206 4.3 14.4 1.0
N B:ASP186 4.3 15.4 1.0
CB B:ASP197 4.4 12.4 1.0
OD1 B:ASP163 4.5 14.8 1.0
CA B:CA508 4.5 15.8 1.0
N B:ILE204 4.6 13.3 1.0
O B:ASP203 4.6 14.4 1.0
C B:ASP203 4.6 13.8 1.0
CB B:ASP203 4.6 12.9 1.0
C B:ASP205 4.7 14.1 1.0
CA B:ILE204 4.7 13.5 1.0
CA B:ASP186 4.8 14.8 1.0
CA B:ASP163 5.0 14.1 1.0

Reference:

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
Page generated: Tue Oct 8 09:08:32 2024

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