Calcium in PDB 3k8m: Crystal Structure of Susg with Acarbose

The structure of Crystal Structure of Susg with Acarbose, PDB code: 3k8m was solved by N.M.Koropatkin, T.J.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.50
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	127.709, 127.709, 127.987, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.7

The binding sites of Calcium atom in the Crystal Structure of Susg with Acarbose (pdb code 3k8m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Susg with Acarbose, PDB code: 3k8m:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Susg with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Susg with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca700 b:44.0 occ:1.00 OD1 A:ASP77 2.3 44.6 1.0 OD1 A:ASP75 2.4 50.2 1.0 OD1 A:ASP81 2.4 34.3 1.0 O A:TYR79 2.5 32.4 1.0 OD1 A:ASP73 2.8 38.9 1.0 CG A:ASP77 2.9 42.8 1.0 OD2 A:ASP77 2.9 46.4 1.0 CG A:ASP75 3.3 49.4 1.0 OD2 A:ASP75 3.4 51.6 1.0 CG A:ASP81 3.5 35.3 1.0 C A:TYR79 3.6 31.7 1.0 CB A:ASP81 3.8 33.4 1.0 CG A:ASP73 3.9 38.3 1.0 O A:GLY80 4.0 30.4 1.0 CB A:ASP77 4.2 42.4 1.0 N A:TYR79 4.3 35.2 1.0 C A:GLY80 4.3 30.8 1.0 CA A:TYR79 4.3 32.5 1.0 CB A:TYR79 4.3 31.3 1.0 OD2 A:ASP81 4.6 39.8 1.0 N A:ASP77 4.6 43.3 1.0 N A:ASP75 4.6 44.1 1.0 N A:GLY80 4.6 32.3 1.0 OD2 A:ASP73 4.7 39.9 1.0 CB A:ASP75 4.7 45.4 1.0 N A:ASP81 4.7 31.9 1.0 CB A:ASP73 4.7 36.7 1.0 CA A:ASP73 4.7 35.9 1.0 N A:SER74 4.8 38.7 1.0 CA A:GLY80 4.8 31.4 1.0 CA A:ASP77 4.9 41.0 1.0 CA A:ASP81 4.9 32.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Susg with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Susg with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca710 b:51.0 occ:1.00 O A:HOH805 2.3 41.3 1.0 OD1 A:ASN153 2.5 38.3 1.0 OD2 A:ASP352 2.6 38.7 1.0 O A:ILE393 2.6 30.1 1.0 O A:HOH806 2.7 45.4 1.0 O A:HIS392 2.7 33.1 1.0 O A:HOH807 2.8 41.5 1.0 C A:ILE393 3.4 28.1 1.0 CG A:ASP352 3.6 33.7 1.0 CG A:ASN153 3.6 35.6 1.0 CA A:ILE393 3.7 29.1 1.0 C A:HIS392 3.8 31.7 1.0 CB A:ASP352 3.9 28.5 1.0 N A:ILE393 4.2 29.9 1.0 O A:ASN153 4.2 23.7 1.0 ND2 A:ASN153 4.3 35.6 1.0 N A:TYR394 4.5 26.4 1.0 OD1 A:ASP352 4.7 36.1 1.0 O A:LEU353 4.7 27.2 1.0 CB A:ASN153 4.8 31.3 1.0 CB A:HIS344 4.8 33.6 1.0 CD2 A:HIS342 4.9 20.4 1.0 CA A:ASP352 4.9 27.1 1.0 CA A:TYR394 5.0 26.6 1.0 NE2 A:HIS342 5.0 20.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Susg with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Susg with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca800 b:72.0 occ:1.00 O B:TYR79 2.2 51.7 1.0 OD1 B:ASP77 2.2 67.0 1.0 OD1 B:ASP75 2.5 71.7 1.0 OD1 B:ASP81 3.0 57.0 1.0 CG B:ASP77 3.0 66.0 1.0 OD2 B:ASP77 3.2 66.5 1.0 CG B:ASP75 3.2 70.8 1.0 OD2 B:ASP75 3.2 71.5 1.0 C B:TYR79 3.3 51.6 1.0 OD1 B:ASP73 3.3 66.8 1.0 CG B:ASP73 3.5 66.8 1.0 OD2 B:ASP73 3.6 66.0 1.0 CG B:ASP81 3.8 56.0 1.0 CA B:TYR79 4.0 51.7 1.0 CB B:TYR79 4.0 48.3 1.0 N B:TYR79 4.0 54.3 1.0 CB B:ASP81 4.1 53.2 1.0 C B:GLY80 4.3 49.9 1.0 O B:GLY80 4.3 50.4 1.0 N B:GLY80 4.3 50.9 1.0 CB B:ASP77 4.5 63.9 1.0 CB B:ASP73 4.5 65.3 1.0 CA B:ASP73 4.5 64.0 1.0 N B:ASP81 4.6 49.1 1.0 N B:ASP75 4.6 66.9 1.0 CA B:GLY80 4.6 50.0 1.0 CB B:ASP75 4.6 68.8 1.0 N B:SER74 4.7 63.2 1.0 N B:ASP77 4.8 64.1 1.0 OD2 B:ASP81 4.9 57.7 1.0 CA B:ASP81 5.0 50.0 1.0 CA B:ASP75 5.0 67.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Susg with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Susg with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca810 b:72.4 occ:1.00 O B:HIS392 2.5 46.2 1.0 OD2 B:ASP352 2.7 50.2 1.0 O B:ILE393 2.7 38.6 1.0 OD1 B:ASN153 2.8 47.2 1.0 C B:ILE393 3.6 38.9 1.0 CG B:ASP352 3.7 46.1 1.0 C B:HIS392 3.7 43.9 1.0 CG B:ASN153 3.9 46.6 1.0 CA B:ILE393 4.0 38.5 1.0 CB B:ASP352 4.1 41.0 1.0 ND2 B:ASN153 4.2 45.2 1.0 NE2 B:HIS342 4.2 47.3 1.0 CB B:HIS344 4.4 45.4 1.0 N B:ILE393 4.4 42.1 1.0 CD2 B:HIS342 4.4 45.3 1.0 N B:TYR394 4.5 39.0 1.0 N B:HIS395 4.6 43.6 1.0 ND1 B:HIS344 4.7 52.0 1.0 C B:TYR394 4.7 40.2 1.0 CG B:HIS344 4.8 49.5 1.0 OD1 B:ASP352 4.8 48.4 1.0 CA B:TYR394 4.8 38.4 1.0 CA B:HIS392 4.9 43.4 1.0 O B:ASN153 4.9 37.4 1.0 CB B:HIS392 4.9 43.3 1.0

N.M.Koropatkin, T.J.Smith. Susg: A Unique Cell-Membrane-Associated Alpha-Amylase From A Prominent Human Gut Symbiont Targets Complex Starch Molecules. Structure V. 18 200 2010.
ISSN: ISSN 0969-2126
PubMed: 20159465
DOI: 10.1016/J.STR.2009.12.010