Calcium in PDB 3k8l: Crystal Structure of Susg-D498N Mutant with Maltoheptaose

The structure of Crystal Structure of Susg-D498N Mutant with Maltoheptaose, PDB code: 3k8l 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)	50.00 / 2.30
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	128.041, 128.041, 130.483, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.6

The binding sites of Calcium atom in the Crystal Structure of Susg-D498N Mutant with Maltoheptaose (pdb code 3k8l). 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-D498N Mutant with Maltoheptaose, PDB code: 3k8l:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Susg-D498N Mutant with Maltoheptaose


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-D498N Mutant with Maltoheptaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca700 b:31.6 occ:1.00 O A:TYR79 2.4 25.4 1.0 OD1 A:ASP75 2.4 39.7 1.0 OD1 A:ASP77 2.5 28.4 1.0 OD1 A:ASP73 2.5 28.8 1.0 OD1 A:ASP81 2.6 24.4 1.0 O A:HOH17 2.6 17.9 1.0 O A:HOH870 2.6 28.3 1.0 CG A:ASP77 3.1 32.1 1.0 OD2 A:ASP77 3.1 34.0 1.0 CG A:ASP75 3.3 37.4 1.0 C A:TYR79 3.6 24.8 1.0 OD2 A:ASP75 3.6 39.4 1.0 CG A:ASP81 3.6 24.1 1.0 CG A:ASP73 3.6 28.2 1.0 CB A:ASP81 3.9 22.7 1.0 O A:GLY80 4.2 22.8 1.0 N A:TYR79 4.2 26.6 1.0 CA A:TYR79 4.3 25.2 1.0 C A:GLY80 4.3 23.1 1.0 N A:ASP75 4.3 32.4 1.0 CB A:TYR79 4.3 24.2 1.0 N A:SER74 4.4 28.3 1.0 OD2 A:ASP73 4.5 28.1 1.0 CB A:ASP73 4.5 26.0 1.0 CB A:ASP77 4.5 31.3 1.0 CA A:ASP73 4.5 26.2 1.0 N A:ASP77 4.5 33.0 1.0 N A:GLY80 4.6 23.3 1.0 N A:ASP81 4.6 22.9 1.0 CB A:ASP75 4.6 33.9 1.0 OD2 A:ASP81 4.7 23.3 1.0 CA A:GLY80 4.8 22.6 1.0 CA A:ASP75 4.8 32.9 1.0 CA A:ASP81 4.9 22.7 1.0 O A:HOH981 4.9 45.3 1.0 C A:ASP73 4.9 27.6 1.0 CA A:ASP77 5.0 32.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Susg-D498N Mutant with Maltoheptaose


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-D498N Mutant with Maltoheptaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca710 b:16.9 occ:1.00 OD2 A:ASP352 2.3 17.6 1.0 OD1 A:ASN153 2.3 21.8 1.0 O A:HIS392 2.4 16.5 1.0 O A:HOH1 2.4 17.4 1.0 O A:HOH3 2.4 16.8 1.0 O A:HOH2 2.4 13.9 1.0 O A:ILE393 2.4 19.6 1.0 C A:ILE393 3.3 18.7 1.0 CG A:ASP352 3.4 16.5 1.0 CG A:ASN153 3.4 20.2 1.0 C A:HIS392 3.5 17.1 1.0 CA A:ILE393 3.6 18.4 1.0 CB A:ASP352 4.0 15.2 1.0 N A:ILE393 4.0 17.7 1.0 ND2 A:ASN153 4.0 17.9 1.0 O A:ASN153 4.3 18.6 1.0 ND1 A:HIS344 4.3 28.8 1.0 N A:TYR394 4.4 18.9 1.0 OD1 A:ASP352 4.4 19.2 1.0 CB A:ASN153 4.6 17.9 1.0 O A:HOH718 4.6 20.3 1.0 NE2 A:HIS342 4.6 17.8 1.0 CB A:HIS344 4.7 23.0 1.0 CA A:HIS392 4.7 18.6 1.0 C A:TYR394 4.8 18.8 1.0 N A:HIS395 4.8 20.1 1.0 CD2 A:HIS342 4.8 16.2 1.0 CA A:TYR394 4.9 18.9 1.0 CB A:HIS392 4.9 18.0 1.0 O A:LEU353 4.9 15.9 1.0 CA A:ASN153 5.0 19.1 1.0 CG A:HIS344 5.0 28.3 1.0 CB A:ILE393 5.0 19.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Susg-D498N Mutant with Maltoheptaose


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-D498N Mutant with Maltoheptaose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca800 b:37.9 occ:1.00 O B:TYR79 2.3 36.7 1.0 OD1 B:ASP73 2.4 45.2 1.0 OD2 B:ASP75 2.4 53.2 1.0 OD1 B:ASP77 2.6 47.0 1.0 OD1 B:ASP81 2.6 37.0 1.0 OD1 B:ASP75 2.9 53.3 1.0 CG B:ASP75 2.9 52.7 1.0 OD2 B:ASP77 3.1 44.9 1.0 CG B:ASP77 3.2 47.2 1.0 C B:TYR79 3.5 37.1 1.0 CG B:ASP81 3.5 37.5 1.0 CG B:ASP73 3.6 46.6 1.0 CB B:ASP81 3.8 36.0 1.0 O B:GLY80 4.1 34.6 1.0 N B:TYR79 4.2 39.7 1.0 CA B:TYR79 4.2 37.2 1.0 C B:GLY80 4.2 34.8 1.0 CB B:TYR79 4.3 34.5 1.0 CB B:ASP75 4.3 50.7 1.0 CB B:ASP73 4.3 44.8 1.0 N B:ASP75 4.4 49.2 1.0 CA B:ASP73 4.4 43.1 1.0 OD2 B:ASP73 4.5 47.1 1.0 N B:GLY80 4.5 35.9 1.0 N B:ASP81 4.5 33.5 1.0 N B:SER74 4.5 43.1 1.0 OD2 B:ASP81 4.6 40.4 1.0 CB B:ASP77 4.6 47.1 1.0 N B:ASP77 4.7 48.1 1.0 CA B:GLY80 4.7 34.9 1.0 CA B:ASP81 4.8 34.4 1.0 CA B:ASP75 4.8 50.7 1.0 N B:GLY76 4.9 50.0 1.0 C B:ASP73 4.9 42.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Susg-D498N Mutant with Maltoheptaose


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-D498N Mutant with Maltoheptaose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca810 b:29.7 occ:1.00 O B:HOH6 2.3 26.8 1.0 O B:HOH4 2.3 24.6 1.0 O B:ILE393 2.3 29.0 1.0 OD1 B:ASN153 2.4 21.7 1.0 OD2 B:ASP352 2.4 31.5 1.0 O B:HIS392 2.5 27.6 1.0 O B:HOH5 2.6 25.9 1.0 C B:ILE393 3.2 28.1 1.0 CA B:ILE393 3.5 28.8 1.0 CG B:ASP352 3.5 28.4 1.0 CG B:ASN153 3.5 20.2 1.0 C B:HIS392 3.5 28.1 1.0 CB B:ASP352 3.9 27.0 1.0 N B:ILE393 4.0 28.2 1.0 ND2 B:ASN153 4.1 20.5 1.0 O B:ASN153 4.2 20.7 1.0 N B:TYR394 4.4 27.8 1.0 ND1 B:HIS344 4.6 39.0 1.0 OD1 B:ASP352 4.6 28.6 1.0 CB B:HIS344 4.7 33.5 1.0 O B:HOH802 4.7 46.7 1.0 NE2 B:HIS342 4.7 30.8 1.0 CB B:ASN153 4.7 20.3 1.0 CA B:HIS392 4.8 27.9 1.0 CD2 B:HIS342 4.8 29.9 1.0 N B:HIS395 4.8 29.2 1.0 C B:TYR394 4.8 27.9 1.0 CA B:TYR394 4.8 27.9 1.0 CB B:ILE393 4.9 27.4 1.0 O B:LEU353 4.9 28.4 1.0 CB B:HIS392 4.9 27.8 1.0 CA B:ASP352 5.0 26.0 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