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

Protein crystallography data

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

Calcium Binding Sites:

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 1d0b

Go back to Calcium Binding Sites List in 1d0b
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 1d0b

Go back to Calcium Binding Sites List in 1d0b
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

Reference:

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
Page generated: Mon Jul 7 14:17:07 2025

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