Calcium in PDB 3ck7: B. Thetaiotaomicron Susd with Alpha-Cyclodextrin

The structure of B. Thetaiotaomicron Susd with Alpha-Cyclodextrin, PDB code: 3ck7 was solved by N.M.Koropatkin, E.C.Martens, J.I.Gordon, T.J.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.50 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.100, 163.300, 123.120, 90.00, 97.20, 90.00
R / Rfree (%)	19.4 / 23.7

The binding sites of Calcium atom in the B. Thetaiotaomicron Susd with Alpha-Cyclodextrin (pdb code 3ck7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the B. Thetaiotaomicron Susd with Alpha-Cyclodextrin, PDB code: 3ck7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the B. Thetaiotaomicron Susd with Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of B. Thetaiotaomicron Susd with Alpha-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca710 b:18.4 occ:1.00 OD1 A:ASP432 2.3 13.1 1.0 O A:ASP430 2.4 5.6 1.0 O A:GLN288 2.4 12.9 1.0 O A:HOH880 2.5 16.6 1.0 OD2 A:ASP273 2.5 18.1 1.0 O A:HOH1012 2.6 7.3 1.0 O A:HOH852 2.7 13.1 1.0 CG A:ASP432 3.3 9.8 1.0 C A:ASP430 3.5 6.4 1.0 C A:GLN288 3.6 11.9 1.0 CG A:ASP273 3.6 14.5 1.0 OD2 A:ASP432 3.9 9.8 1.0 N A:GLN288 4.0 11.1 1.0 N A:ASP432 4.2 6.8 1.0 CA A:ASP430 4.3 7.2 1.0 O A:HOH998 4.4 24.5 1.0 CA A:GLN288 4.4 11.2 1.0 CB A:ASP273 4.4 11.5 1.0 OD1 A:ASP273 4.4 18.2 1.0 CB A:ASP432 4.4 7.8 1.0 CB A:ASP430 4.4 6.5 1.0 C A:THR431 4.4 5.1 1.0 N A:ASP289 4.5 12.3 1.0 N A:THR431 4.5 5.3 1.0 CA A:ASP432 4.6 7.5 1.0 O A:ALA270 4.6 7.5 1.0 CA A:ASP289 4.6 13.2 1.0 CA A:THR431 4.8 5.3 1.0 CB A:GLN288 4.8 10.4 1.0 NH2 A:ARG287 4.8 23.8 1.0 NE A:ARG287 4.9 22.9 1.0 OD1 A:ASN272 4.9 9.6 1.0 O A:THR431 4.9 4.7 1.0 CB A:ASP289 5.0 15.4 1.0

Calcium binding site 2 out of 4 in the B. Thetaiotaomicron Susd with Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of B. Thetaiotaomicron Susd with Alpha-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca720 b:17.0 occ:1.00 O B:ASP430 2.3 9.4 1.0 O B:GLN288 2.3 11.2 1.0 O B:HOH969 2.5 11.3 1.0 OD1 B:ASP432 2.7 8.9 1.0 O B:HOH727 2.8 10.5 1.0 OD2 B:ASP273 3.1 13.1 1.0 CG B:ASP432 3.4 7.8 1.0 C B:ASP430 3.5 8.6 1.0 C B:GLN288 3.5 10.8 1.0 OD2 B:ASP432 3.7 10.3 1.0 CG B:ASP273 3.7 13.2 1.0 N B:GLN288 4.0 9.2 1.0 CA B:ASP430 4.2 9.7 1.0 N B:ASP432 4.2 5.1 1.0 CB B:ASP430 4.2 10.8 1.0 OD1 B:ASP273 4.3 13.5 1.0 CA B:GLN288 4.3 10.4 1.0 CB B:ASP432 4.4 7.2 1.0 CB B:ASP273 4.5 9.7 1.0 C B:THR431 4.5 4.6 1.0 O B:ALA270 4.5 10.1 1.0 N B:ASP289 4.5 10.8 1.0 N B:THR431 4.5 5.0 1.0 CA B:ASP432 4.6 5.9 1.0 NH2 B:ARG287 4.6 21.4 1.0 CA B:ASP289 4.6 11.9 1.0 CB B:GLN288 4.8 10.6 1.0 CA B:THR431 4.8 4.5 1.0 OD1 B:ASN272 4.9 9.3 1.0 NE B:ARG287 4.9 21.2 1.0

Calcium binding site 3 out of 4 in the B. Thetaiotaomicron Susd with Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of B. Thetaiotaomicron Susd with Alpha-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca700 b:21.0 occ:1.00 O C:GLN288 2.3 12.0 1.0 O C:ASP430 2.3 5.2 1.0 O C:HOH817 2.5 6.0 1.0 OD1 C:ASP432 2.5 8.5 1.0 O C:HOH814 2.6 13.3 1.0 OD2 C:ASP273 3.3 14.7 1.0 CG C:ASP432 3.3 9.1 1.0 C C:ASP430 3.5 7.8 1.0 C C:GLN288 3.5 11.7 1.0 OD2 C:ASP432 3.7 10.5 1.0 CG C:ASP273 3.7 12.4 1.0 N C:GLN288 4.1 10.3 1.0 O C:HOH938 4.1 23.6 1.0 CA C:ASP430 4.2 8.4 1.0 N C:ASP432 4.2 7.0 1.0 CB C:ASP273 4.3 11.4 1.0 CB C:ASP430 4.3 9.2 1.0 OD1 C:ASP273 4.3 12.9 1.0 CA C:GLN288 4.3 11.1 1.0 N C:ASP289 4.4 13.5 1.0 CB C:ASP432 4.5 9.6 1.0 C C:THR431 4.5 5.8 1.0 CA C:ASP289 4.5 15.8 1.0 N C:THR431 4.5 6.1 1.0 CA C:ASP432 4.6 8.2 1.0 O C:ALA270 4.6 8.9 1.0 CB C:GLN288 4.8 8.9 1.0 CA C:THR431 4.8 6.8 1.0 OD1 C:ASN272 4.9 9.2 1.0 NE C:ARG287 4.9 22.0 1.0 CB C:ASP289 5.0 18.8 1.0

Calcium binding site 4 out of 4 in the B. Thetaiotaomicron Susd with Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of B. Thetaiotaomicron Susd with Alpha-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca730 b:21.6 occ:1.00 O D:ASP430 2.3 9.1 1.0 O D:HOH836 2.4 13.3 1.0 OD1 D:ASP432 2.4 7.3 1.0 O D:GLN288 2.5 11.3 1.0 O D:HOH766 2.5 9.0 1.0 OD2 D:ASP273 2.9 19.3 1.0 CG D:ASP432 3.2 6.4 1.0 O D:HOH858 3.3 19.4 1.0 C D:ASP430 3.4 8.4 1.0 OD2 D:ASP432 3.6 7.0 1.0 CG D:ASP273 3.6 16.5 1.0 C D:GLN288 3.6 11.7 1.0 N D:ASP432 4.1 6.4 1.0 N D:GLN288 4.1 9.6 1.0 CA D:ASP430 4.2 10.4 1.0 OD1 D:ASP273 4.3 17.6 1.0 CB D:ASP430 4.4 11.2 1.0 CB D:ASP273 4.4 15.3 1.0 O D:ALA270 4.4 12.4 1.0 C D:THR431 4.4 7.3 1.0 CB D:ASP432 4.4 6.3 1.0 N D:THR431 4.4 7.1 1.0 CA D:GLN288 4.4 10.6 1.0 NH2 D:ARG287 4.5 27.3 1.0 CA D:ASP432 4.5 7.5 1.0 N D:ASP289 4.6 11.6 1.0 CA D:THR431 4.7 6.4 1.0 CA D:ASP289 4.7 14.9 1.0 OD1 D:ASN272 4.8 12.8 1.0 NE D:ARG287 4.8 22.6 1.0 CB D:GLN288 4.8 8.7 1.0 O D:THR431 5.0 8.1 1.0

N.M.Koropatkin, E.C.Martens, J.I.Gordon, T.J.Smith. Starch Catabolism By A Prominent Human Gut Symbiont Is Directed By the Recognition of Amylose Helices. Structure V. 16 1105 2008.
ISSN: ISSN 0969-2126
PubMed: 18611383
DOI: 10.1016/J.STR.2008.03.017