Calcium in PDB 3bc9: Alpha-Amylase B in Complex with Acarbose

All present enzymatic activity of Alpha-Amylase B in Complex with Acarbose:
3.2.1.1;

The structure of Alpha-Amylase B in Complex with Acarbose, PDB code: 3bc9 was solved by T.-C.Tan, B.N.Mijts, K.Swaminathan, B.K.C.Patel, C.Divne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	227.850, 77.240, 50.380, 90.00, 98.63, 90.00
R / Rfree (%)	15.1 / 17.8

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

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Alpha-Amylase B in Complex with Acarbose (pdb code 3bc9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Alpha-Amylase B in Complex with Acarbose, PDB code: 3bc9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Alpha-Amylase B 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 Alpha-Amylase B in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:11.4 occ:1.00 OD1 A:ASP305 2.3 11.2 1.0 OE1 A:GLU323 2.3 13.9 1.0 O A:SER303 2.4 13.1 1.0 OD1 A:ASP321 2.4 11.6 1.0 O A:HOH1021 2.5 13.7 1.0 OD2 A:ASP283 2.5 10.0 1.0 OD1 A:ASP283 2.6 12.2 1.0 CG A:ASP283 2.9 10.6 1.0 CG A:ASP321 3.3 12.0 1.0 CG A:ASP305 3.3 10.8 1.0 CD A:GLU323 3.4 15.2 1.0 C A:SER303 3.6 11.5 1.0 OD2 A:ASP321 3.8 15.0 1.0 CG A:GLU323 4.0 15.6 1.0 OD2 A:ASP305 4.0 10.9 1.0 CB A:GLU323 4.0 15.3 1.0 N A:ASP305 4.0 10.9 1.0 N A:SER303 4.1 13.7 1.0 CB A:ASP321 4.1 12.6 1.0 C A:TRP304 4.2 11.5 1.0 OG A:SER303 4.3 23.0 1.0 CA A:ASP321 4.3 11.3 1.0 CA A:ASP305 4.4 10.9 1.0 CB A:ASP283 4.4 11.4 1.0 CB A:ASP305 4.4 12.6 1.0 OE2 A:GLU323 4.4 17.0 1.0 CA A:SER303 4.4 13.3 1.0 NA A:NA704 4.5 11.0 1.0 N A:TRP304 4.5 11.6 1.0 N A:GLU323 4.5 11.7 1.0 CA A:TRP304 4.5 11.0 1.0 O A:TRP304 4.7 12.8 1.0 C A:ASP321 4.8 11.7 1.0 N A:TYR322 4.8 11.9 1.0 CA A:GLU323 4.9 13.6 1.0 CB A:SER303 4.9 17.8 1.0 O A:HOH1092 4.9 19.4 1.0 OD2 A:ASP313 5.0 12.0 1.0

Calcium binding site 2 out of 4 in the Alpha-Amylase B 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 Alpha-Amylase B in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:10.6 occ:1.00 OD1 A:ASN232 2.3 13.0 1.0 OD1 A:ASP313 2.3 11.8 1.0 O A:HIS354 2.3 10.7 1.0 OD1 A:ASP319 2.3 11.8 1.0 O A:ASP313 2.4 11.4 1.0 O A:HOH1029 2.4 12.5 1.0 CG A:ASP319 3.2 13.5 1.0 C A:ASP313 3.3 10.7 1.0 CG A:ASP313 3.3 11.3 1.0 OD2 A:ASP319 3.4 12.0 1.0 CG A:ASN232 3.4 12.5 1.0 C A:HIS354 3.6 10.9 1.0 CA A:ASP313 3.7 10.2 1.0 O A:HOH1023 3.8 13.1 1.0 O A:ASN232 4.0 11.4 1.0 CB A:ASP313 4.1 9.1 1.0 O A:HOH1008 4.1 12.5 1.0 ND2 A:ASN232 4.1 11.7 1.0 CB A:HIS354 4.2 10.5 1.0 OD2 A:ASP313 4.2 12.0 1.0 NA A:NA704 4.3 11.0 1.0 N A:TYR314 4.4 10.5 1.0 CA A:HIS354 4.4 10.9 1.0 N A:ILE355 4.4 9.9 1.0 CB A:ASN232 4.5 12.4 1.0 CA A:ILE355 4.6 11.0 1.0 CB A:ASP319 4.6 12.2 1.0 CA A:ASN232 4.7 10.8 1.0 C A:ASN232 4.7 11.3 1.0 CA A:TYR314 4.7 10.9 1.0 O A:VAL320 4.8 11.0 1.0 CG1 A:ILE355 4.9 14.4 1.0

Calcium binding site 3 out of 4 in the Alpha-Amylase B 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 Alpha-Amylase B in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:14.6 occ:1.00 O A:ALA419 2.3 14.0 1.0 O A:HOH1083 2.3 19.4 1.0 O A:ALA517 2.3 15.2 1.0 OD1 A:ASP518 2.4 16.2 1.0 OD1 A:ASP541 2.5 17.9 1.0 OD2 A:ASP541 2.5 15.5 1.0 CG A:ASP541 2.8 13.9 1.0 C A:ALA517 3.4 13.7 1.0 CG A:ASP518 3.5 18.8 1.0 C A:ALA419 3.5 13.6 1.0 CA A:ASP518 3.8 15.1 1.0 N A:ALA419 3.9 14.4 1.0 N A:ASP518 4.0 14.7 1.0 CB A:ASP518 4.2 16.3 1.0 CB A:ASP541 4.3 13.8 1.0 CA A:ALA419 4.3 14.7 1.0 CG A:MET421 4.4 14.0 1.0 CB A:ALA517 4.4 16.0 1.0 CA A:ALA517 4.4 13.7 1.0 N A:TYR420 4.5 14.3 1.0 OD2 A:ASP518 4.5 25.7 1.0 O A:HOH1427 4.5 31.6 1.0 C A:GLY418 4.6 14.5 1.0 N A:MET421 4.6 12.1 1.0 CA A:GLY418 4.6 14.4 1.0 CA A:TYR420 4.6 13.2 1.0 O A:HOH1557 4.8 44.5 1.0

Calcium binding site 4 out of 4 in the Alpha-Amylase B 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 Alpha-Amylase B in Complex with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:31.0 occ:1.00 OD1 A:ASP533 2.2 22.3 1.0 O A:VAL530 2.2 28.6 1.0 O A:HOH1409 2.3 31.5 1.0 O A:HOH1400 2.3 34.6 1.0 O A:PHE527 2.4 27.8 1.0 O A:HOH1404 2.6 29.5 1.0 CG A:ASP533 3.5 19.1 1.0 C A:VAL530 3.5 26.4 1.0 C A:PHE527 3.5 27.1 1.0 N A:PHE527 3.8 22.3 1.0 OD2 A:ASP533 4.0 22.0 1.0 C A:GLY526 4.1 21.1 1.0 O A:HOH1539 4.2 41.6 1.0 CA A:GLY526 4.2 20.1 1.0 N A:ASP533 4.2 18.6 1.0 N A:VAL530 4.2 28.8 1.0 CA A:PHE527 4.3 24.4 1.0 CA A:VAL530 4.3 26.6 1.0 N A:GLY532 4.3 22.7 1.0 O A:ASP533 4.4 18.5 1.0 N A:ALA531 4.4 25.4 1.0 CB A:VAL530 4.5 26.1 1.0 N A:PRO528 4.5 29.6 1.0 CA A:ALA531 4.5 24.4 1.0 O A:SER525 4.6 20.0 1.0 C A:ALA531 4.6 23.6 1.0 CB A:ASP533 4.6 16.5 1.0 C A:ASP533 4.7 16.9 1.0 CA A:PRO528 4.7 31.0 1.0 CA A:ASP533 4.7 16.7 1.0 C A:PRO528 4.7 31.3 1.0 O A:PRO528 4.8 33.0 1.0 O A:GLY526 4.8 22.8 1.0 CB A:PHE527 4.9 25.0 1.0 CG1 A:VAL530 4.9 24.6 1.0 OE1 A:GLN556 5.0 24.7 1.0

T.-C.Tan, B.N.Mijts, K.Swaminathan, B.K.C.Patel, C.Divne. Crystal Structure of the Polyextremophilic Alpha-Amylase Amyb From Halothermothrix Orenii: Details of A Productive Enzyme-Substrate Complex and An N Domain with A Role in Binding Raw Starch J.Mol.Biol. V. 378 850 2008.
ISSN: ISSN 0022-2836
PubMed: 18387632
DOI: 10.1016/J.JMB.2008.02.041