Calcium in PDB 3ubf: Crystal Structure of Drosophila N-Cadherin EC1-3, I

The structure of Crystal Structure of Drosophila N-Cadherin EC1-3, I, PDB code: 3ubf was solved by X.Jin, M.A.Walker, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	96.289, 96.289, 148.196, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 27.9

The structure of Crystal Structure of Drosophila N-Cadherin EC1-3, I also contains other interesting chemical elements:

Zinc

(Zn)

18 atoms

The binding sites of Calcium atom in the Crystal Structure of Drosophila N-Cadherin EC1-3, I (pdb code 3ubf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Drosophila N-Cadherin EC1-3, I, PDB code: 3ubf:

Calcium binding site 1 out of 1 in the Crystal Structure of Drosophila N-Cadherin EC1-3, I


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 Drosophila N-Cadherin EC1-3, I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca754 b:51.4 occ:1.00 OE1 A:GLU498 2.3 45.3 1.0 O A:HOH115 2.3 9.1 1.0 OE2 A:GLU450 2.3 55.2 1.0 O A:HOH165 2.5 2.0 1.0 OD2 A:ASP575 2.8 61.2 1.0 OD1 A:ASP496 3.0 57.6 1.0 CD A:GLU450 3.0 53.5 1.0 OE1 A:GLU450 3.0 53.0 1.0 CD A:GLU498 3.1 48.0 1.0 ZN A:ZN1 3.3 45.2 1.0 OE2 A:GLU498 3.4 46.9 1.0 ZN A:ZN19 3.5 95.0 1.0 CG A:ASP575 3.6 56.9 1.0 CB A:ASP575 3.6 53.1 1.0 CG A:ASP496 4.0 55.4 1.0 N A:TYR497 4.2 46.8 1.0 CG A:GLU498 4.3 52.3 1.0 ZN A:ZN7 4.3 64.6 1.0 CG A:GLU450 4.5 50.9 1.0 N A:GLU498 4.5 50.0 1.0 O A:HOH107 4.5 8.1 1.0 OD1 A:ASP535 4.5 53.7 1.0 CA A:ASP496 4.6 48.9 1.0 OD1 A:ASP573 4.7 51.4 1.0 CB A:GLU498 4.7 54.0 1.0 OD2 A:ASP535 4.7 56.2 1.0 CB A:TYR497 4.7 45.4 1.0 C A:ASP496 4.7 47.9 1.0 OD2 A:ASP496 4.8 58.9 1.0 OD1 A:ASP575 4.8 58.0 1.0 CB A:ASP496 4.9 51.9 1.0 CG A:ASP535 4.9 54.4 1.0 CA A:TYR497 5.0 46.0 1.0 OD2 A:ASP573 5.0 49.5 1.0

X.Jin, M.A.Walker, K.Felsovalyi, J.Vendome, F.Bahna, S.Mannepalli, F.Cosmanescu, G.Ahlsen, B.Honig, L.Shapiro. Crystal Structures of Drosophila N-Cadherin Ectodomain Regions Reveal A Widely Used Class of CA2+-Free Interdomain Linkers. Proc.Natl.Acad.Sci.Usa V. 109 E127 2012.
ISSN: ISSN 0027-8424
PubMed: 22171007
DOI: 10.1073/PNAS.1117538108