Calcium in PDB 3ck8: B. Thetaiotaomicron Susd with Beta-Cyclodextrin

The structure of B. Thetaiotaomicron Susd with Beta-Cyclodextrin, PDB code: 3ck8 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)	60.19 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.670, 73.140, 83.550, 65.06, 71.95, 69.76
R / Rfree (%)	16.9 / 20

The binding sites of Calcium atom in the B. Thetaiotaomicron Susd with Beta-Cyclodextrin (pdb code 3ck8). 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 Beta-Cyclodextrin, PDB code: 3ck8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the B. Thetaiotaomicron Susd with Beta-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 Beta-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca600 b:11.0 occ:1.00 OD1 A:ASP432 2.3 8.2 1.0 O A:ASP430 2.4 11.0 1.0 O A:GLN288 2.4 11.3 1.0 OD2 A:ASP273 2.4 9.2 1.0 O A:HOH1325 2.5 8.4 1.0 O A:HOH939 2.5 8.9 1.0 O A:HOH832 2.6 5.8 1.0 CG A:ASP432 3.3 7.7 1.0 CG A:ASP273 3.3 12.0 1.0 C A:ASP430 3.6 9.1 1.0 C A:GLN288 3.6 10.3 1.0 OD2 A:ASP432 3.9 11.8 1.0 O A:HOH1324 3.9 10.1 1.0 OD1 A:ASP273 4.0 9.8 1.0 N A:GLN288 4.1 7.2 1.0 CB A:ASP273 4.2 10.6 1.0 N A:ASP432 4.2 10.3 1.0 CA A:ASP430 4.3 10.7 1.0 CB A:ASP432 4.4 9.1 1.0 CB A:ASP430 4.5 10.9 1.0 NH2 A:ARG287 4.5 8.2 1.0 CA A:GLN288 4.5 8.3 1.0 O A:HOH1059 4.5 16.3 1.0 O A:HOH1167 4.5 27.8 1.0 C A:THR431 4.5 10.5 1.0 N A:ASP289 4.6 11.4 1.0 CA A:ASP432 4.6 9.2 1.0 CA A:ASP289 4.6 12.3 1.0 O A:ALA270 4.6 9.7 1.0 N A:THR431 4.6 9.4 1.0 NE A:ARG287 4.7 9.7 1.0 OD1 A:ASN272 4.8 9.7 1.0 CA A:THR431 4.8 10.6 1.0 CB A:ASP289 4.9 15.5 1.0 OD2 A:ASP289 4.9 21.9 1.0 O A:HOH981 5.0 15.0 1.0 CB A:GLN288 5.0 5.5 1.0

Calcium binding site 2 out of 4 in the B. Thetaiotaomicron Susd with Beta-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 Beta-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca720 b:12.8 occ:1.00 O A:HOH1048 2.2 13.1 1.0 O1 A:EDO731 2.3 19.5 1.0 O A:HOH1067 2.3 17.2 1.0 OE2 A:GLU274 2.4 12.4 1.0 O A:HOH1050 2.4 15.2 1.0 OE1 A:GLU274 2.5 10.6 1.0 CD A:GLU274 2.8 9.1 1.0 C1 A:EDO731 3.0 19.1 1.0 O2 A:EDO731 3.9 25.2 1.0 C2 A:EDO731 4.1 22.0 1.0 NH1 A:ARG417 4.1 8.5 1.0 CG A:GLU274 4.3 11.8 1.0 O A:HOH1059 4.4 16.3 1.0 O A:HOH1002 4.5 19.1 1.0 O2 A:EDO734 4.7 31.6 1.0 O A:HOH1324 4.7 10.1 1.0 O A:HOH968 4.8 27.4 1.0 CZ A:ARG417 4.8 8.3 1.0 NH2 A:ARG417 4.9 3.6 1.0

Calcium binding site 3 out of 4 in the B. Thetaiotaomicron Susd with Beta-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 Beta-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca700 b:11.7 occ:1.00 OD1 B:ASP432 2.3 10.2 1.0 O B:ASP430 2.4 12.4 1.0 OD2 B:ASP273 2.4 11.9 1.0 O B:GLN288 2.4 12.0 1.0 O B:HOH1549 2.4 9.9 1.0 O B:HOH1374 2.5 5.9 1.0 O B:HOH1550 2.6 11.9 1.0 CG B:ASP432 3.3 11.6 1.0 CG B:ASP273 3.3 12.2 1.0 C B:ASP430 3.6 11.4 1.0 C B:GLN288 3.6 11.7 1.0 OD2 B:ASP432 3.8 12.1 1.0 O B:HOH1417 4.0 12.1 1.0 OD1 B:ASP273 4.0 13.0 1.0 N B:GLN288 4.1 10.8 1.0 CB B:ASP273 4.1 11.5 1.0 N B:ASP432 4.2 9.9 1.0 CA B:ASP430 4.3 11.9 1.0 CB B:ASP432 4.4 10.9 1.0 O B:HOH1596 4.4 24.2 1.0 CB B:ASP430 4.5 10.6 1.0 CA B:GLN288 4.5 11.3 1.0 C B:THR431 4.5 9.9 1.0 NH2 B:ARG287 4.5 7.2 1.0 CA B:ASP432 4.5 8.6 1.0 N B:ASP289 4.6 12.4 1.0 N B:THR431 4.6 10.1 1.0 CA B:ASP289 4.6 13.2 1.0 O B:ALA270 4.6 11.1 1.0 NE B:ARG287 4.7 10.5 1.0 OD1 B:ASN272 4.7 8.9 1.0 CA B:THR431 4.8 10.7 1.0 CB B:ASP289 4.8 16.1 1.0 O B:HOH1740 4.9 14.4 1.0 OD2 B:ASP289 4.9 20.5 1.0

Calcium binding site 4 out of 4 in the B. Thetaiotaomicron Susd with Beta-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 Beta-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca710 b:15.6 occ:1.00 OE1 B:GLU274 2.3 17.4 1.0 O B:HOH1515 2.4 18.9 1.0 O B:HOH1581 2.5 20.6 1.0 O B:HOH1439 2.5 13.6 1.0 OE2 B:GLU274 2.6 14.0 1.0 CD B:GLU274 2.8 14.7 1.0 O B:HOH1690 4.1 39.1 1.0 NH1 B:ARG417 4.1 9.8 1.0 CG B:GLU274 4.3 13.2 1.0 O B:HOH1462 4.6 18.4 1.0 O B:HOH1596 4.6 24.2 1.0 O1 B:EDO744 4.6 32.3 1.0 O B:HOH1417 4.8 12.1 1.0 CZ B:ARG417 4.9 11.6 1.0 NH2 B:ARG417 4.9 10.3 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