Calcium in PDB 1d0b: Internalin B Leucine Rich Repeat Domain

The structure of Internalin B Leucine Rich Repeat Domain, PDB code: 1d0b was solved by M.Marino, L.Braun, P.Cossart, P.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.86
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.410, 56.920, 84.350, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 23.5

The binding sites of Calcium atom in the Internalin B Leucine Rich Repeat Domain (pdb code 1d0b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Internalin B Leucine Rich Repeat Domain, PDB code: 1d0b:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Internalin B Leucine Rich Repeat Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Internalin B Leucine Rich Repeat Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca249 b:17.1 occ:1.00 O A:PRO49 2.4 17.6 1.0 OD1 A:ASP51 2.4 16.1 1.0 O A:HOH267 2.4 22.9 1.0 O A:HOH263 2.4 20.4 1.0 O A:HOH264 2.5 17.4 1.0 O A:HOH266 2.5 12.9 1.0 O A:HOH265 2.6 30.5 1.0 CG A:ASP51 3.4 15.4 1.0 C A:PRO49 3.5 17.6 1.0 O A:HOH338 3.7 37.9 1.0 OD2 A:ASP51 3.9 19.2 1.0 CA A:PRO49 4.0 18.2 1.0 O A:HOH291 4.1 18.0 1.0 N A:ASP51 4.2 16.1 1.0 O A:HOH323 4.3 23.8 1.0 CA A:ASP51 4.5 16.6 1.0 N A:ASP50 4.6 13.8 1.0 CB A:ASP51 4.6 16.0 1.0 O A:HOH393 4.6 35.7 1.0 C A:ASP50 4.6 16.4 1.0 O A:PHE48 4.6 12.8 1.0 O A:LYS45 4.7 18.4 1.0 CA A:ASP50 4.9 12.6 1.0

Calcium binding site 2 out of 2 in the Internalin B Leucine Rich Repeat Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Internalin B Leucine Rich Repeat Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca250 b:44.4 occ:1.00 OD2 A:ASP59 2.5 27.2 1.0 O A:HOH268 2.5 32.8 1.0 O A:HOH397 2.5 38.7 1.0 O A:HOH269 2.6 42.2 1.0 OE2 A:GLU55 2.7 26.1 1.0 OD1 A:ASP59 2.8 25.3 1.0 CG A:ASP59 2.9 24.4 1.0 CD A:GLU55 3.9 31.6 1.0 CB A:ASP59 4.4 18.2 1.0 CG A:GLU55 4.5 25.6 1.0 NZ A:LYS58 4.6 29.8 1.0 OE1 A:GLU55 4.9 20.8 1.0 CE A:LYS58 4.9 23.5 1.0

M.Marino, L.Braun, P.Cossart, P.Ghosh. Structure of the Lnlb Leucine-Rich Repeats, A Domain That Triggers Host Cell Invasion By the Bacterial Pathogen L. Monocytogenes. Mol.Cell V. 4 1063 1999.
ISSN: ISSN 1097-2765
PubMed: 10635330
DOI: 10.1016/S1097-2765(00)80234-8