Calcium in PDB 3ubh: Crystal Structure of Drosophila N-Cadherin EC1-4

The structure of Crystal Structure of Drosophila N-Cadherin EC1-4, PDB code: 3ubh 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 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.499, 126.656, 62.009, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 27.6

The binding sites of Calcium atom in the Crystal Structure of Drosophila N-Cadherin EC1-4 (pdb code 3ubh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Drosophila N-Cadherin EC1-4, PDB code: 3ubh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Drosophila N-Cadherin EC1-4


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 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca852 b:50.6 occ:1.00 OE2 A:GLU450 2.1 56.1 1.0 OD1 A:ASP496 2.2 53.9 1.0 OE2 A:GLU539 2.3 59.0 1.0 OD2 A:ASP538 2.4 64.7 1.0 OE1 A:GLU498 2.5 51.5 1.0 CG A:ASP496 3.0 55.0 1.0 OD1 A:ASP538 3.1 61.2 1.0 CG A:ASP538 3.1 62.4 1.0 CD A:GLU450 3.2 53.2 1.0 CD A:GLU539 3.4 55.9 1.0 OD2 A:ASP496 3.6 58.4 1.0 CD A:GLU498 3.7 56.0 1.0 CA A:ASP496 3.9 49.3 1.0 CG A:GLU539 3.9 54.5 1.0 OE1 A:GLU450 3.9 55.0 1.0 CB A:ASP496 4.0 51.6 1.0 CG A:GLU450 4.1 50.3 1.0 N A:TYR497 4.1 50.1 1.0 CA A:CA853 4.2 57.0 1.0 N A:GLU498 4.3 56.4 1.0 C A:ASP496 4.4 50.1 1.0 CB A:GLU498 4.4 61.2 1.0 OE1 A:GLU539 4.4 56.4 1.0 CG A:GLU498 4.4 60.6 1.0 O A:TRP495 4.6 47.1 1.0 CB A:ASP538 4.6 62.4 1.0 OE2 A:GLU498 4.6 56.5 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Drosophila N-Cadherin EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Drosophila N-Cadherin EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca853 b:57.0 occ:1.00 O A:VAL536 2.1 52.6 1.0 OD2 A:ASP573 2.3 64.0 1.0 OD1 A:ASP535 2.3 54.4 1.0 OE2 A:GLU498 2.3 56.5 1.0 OD1 A:ASP538 2.4 61.2 1.0 OE1 A:GLU498 2.6 51.5 1.0 CD A:GLU498 2.8 56.0 1.0 OE1 A:GLU450 2.8 55.0 1.0 C A:VAL536 3.3 53.6 1.0 CG A:ASP535 3.5 57.4 1.0 OE2 A:GLU450 3.5 56.1 1.0 CG A:ASP573 3.5 60.2 1.0 CD A:GLU450 3.5 53.2 1.0 CG A:ASP538 3.5 62.4 1.0 N A:VAL536 3.6 51.8 1.0 N A:ASP538 4.0 58.2 1.0 OD2 A:ASP535 4.0 61.2 1.0 CA A:VAL536 4.1 52.2 1.0 CA A:CA852 4.2 50.6 1.0 N A:ASN537 4.2 55.7 1.0 OD2 A:ASP538 4.3 64.7 1.0 CB A:TYR497 4.3 52.3 1.0 CG A:GLU498 4.3 60.6 1.0 OD1 A:ASP573 4.4 59.5 1.0 CA A:ASN537 4.4 57.7 1.0 CB A:ASP573 4.4 58.9 1.0 CB A:ASP538 4.5 62.4 1.0 C A:ASP535 4.6 53.1 1.0 CA A:ASP535 4.7 53.5 1.0 CB A:ASP535 4.7 56.7 1.0 CA A:ASP573 4.7 58.8 1.0 C A:ASN537 4.7 56.6 1.0 CG A:GLU539 4.7 54.5 1.0 CD2 A:TYR497 4.8 57.2 1.0 CA A:ASP538 4.8 58.9 1.0 CB A:VAL536 4.9 50.1 1.0 CG A:TYR497 4.9 54.0 1.0 N A:GLU498 5.0 56.4 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Drosophila N-Cadherin EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Drosophila N-Cadherin EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca854 b:48.2 occ:1.00 OD2 A:ASP622 2.3 52.2 1.0 OD2 A:ASP571 2.3 49.1 1.0 O A:GLU539 2.4 49.1 1.0 OE1 A:GLN633 2.4 55.3 1.0 OD1 A:ASN537 2.4 64.0 1.0 OD1 A:ASP571 2.5 51.3 1.0 OD1 A:ASP573 2.6 59.5 1.0 CG A:ASP571 2.7 49.5 1.0 CG A:ASN537 3.4 64.2 1.0 CG A:ASP622 3.4 52.8 1.0 CD A:GLN633 3.5 57.1 1.0 CG A:ASP573 3.5 60.2 1.0 C A:GLU539 3.6 49.7 1.0 ND2 A:ASN537 3.7 68.2 1.0 CB A:ASP573 3.8 58.9 1.0 NE2 A:GLN633 3.8 59.6 1.0 CB A:ASP622 3.9 51.7 1.0 N A:GLU539 4.2 53.8 1.0 CB A:ASP571 4.3 47.4 1.0 CA A:GLU539 4.4 51.8 1.0 OD1 A:ASP622 4.5 53.2 1.0 N A:PRO540 4.5 49.1 1.0 CA A:PRO540 4.6 47.1 1.0 CB A:ASN537 4.6 60.8 1.0 N A:ASP573 4.7 55.6 1.0 C A:PRO540 4.7 45.4 1.0 OD2 A:ASP573 4.7 64.0 1.0 C A:ASN537 4.7 56.6 1.0 CA A:ASN537 4.8 57.7 1.0 CG A:GLN633 4.8 58.0 1.0 N A:ASP538 4.8 58.2 1.0 N A:PRO541 4.8 44.0 1.0 CA A:ASP573 4.9 58.8 1.0 CB A:HIS576 4.9 51.9 1.0 CD A:PRO541 4.9 44.5 1.0 CB A:GLU539 4.9 51.4 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Drosophila N-Cadherin EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Drosophila N-Cadherin EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca855 b:61.1 occ:1.00 OD2 A:ASP713 2.1 78.1 1.0 OD2 A:ASP751 2.2 61.5 1.0 OE1 A:GLU715 2.5 65.8 1.0 OE1 A:GLU662 2.6 69.8 1.0 CG A:ASP751 3.0 60.3 1.0 OD1 A:ASP751 3.2 61.1 1.0 CD A:GLU662 3.3 66.0 1.0 CG A:ASP713 3.3 84.3 1.0 OE2 A:GLU662 3.6 65.3 1.0 CD A:GLU715 3.7 68.7 1.0 OD1 A:ASP713 4.1 90.2 1.0 CA A:CA856 4.2 56.4 1.0 CA A:ASP713 4.2 78.8 1.0 N A:PHE714 4.3 70.7 1.0 CB A:ASP713 4.3 85.2 1.0 CB A:GLU715 4.3 79.0 1.0 ND2 A:ASN752 4.3 59.6 1.0 N A:GLU715 4.3 75.7 1.0 CB A:ASP751 4.4 59.5 1.0 CG A:GLU715 4.4 73.7 1.0 C A:ASP713 4.6 76.7 1.0 CG A:GLU662 4.6 64.5 1.0 OE2 A:GLU715 4.6 67.7 1.0 CA A:GLU715 5.0 80.4 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Drosophila N-Cadherin EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Drosophila N-Cadherin EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca856 b:56.4 occ:1.00 OD1 A:ASP748 2.2 62.9 1.0 O A:VAL749 2.4 58.8 1.0 OE2 A:GLU662 2.4 65.3 1.0 OD1 A:ASP785 2.5 64.1 1.0 OE1 A:GLU715 2.5 65.8 1.0 OD1 A:ASP751 2.5 61.1 1.0 OE2 A:GLU715 2.6 67.7 1.0 CD A:GLU715 2.8 68.7 1.0 CG A:ASP748 3.5 61.5 1.0 CG A:ASP785 3.5 61.9 1.0 CG A:ASP751 3.5 60.3 1.0 CD A:GLU662 3.5 66.0 1.0 C A:VAL749 3.5 57.9 1.0 N A:VAL749 3.8 56.7 1.0 OE1 A:GLU662 3.9 69.8 1.0 OD2 A:ASP751 4.0 61.5 1.0 CB A:ASP785 4.0 63.5 1.0 N A:ASP751 4.1 58.7 1.0 CA A:CA855 4.2 61.1 1.0 CA A:ASP785 4.2 65.2 1.0 OD2 A:ASP748 4.2 63.1 1.0 CG A:GLU715 4.3 73.7 1.0 CA A:VAL749 4.3 56.8 1.0 ND2 A:ASN752 4.3 59.6 1.0 CA A:ASP748 4.4 58.0 1.0 CB A:ASP748 4.4 60.0 1.0 OD2 A:ASP785 4.4 59.8 1.0 C A:ASP748 4.5 56.4 1.0 N A:ASN750 4.6 60.8 1.0 CB A:PHE714 4.6 64.2 1.0 CB A:ASP751 4.7 59.5 1.0 CA A:ASN750 4.7 59.5 1.0 CG2 A:VAL749 4.8 58.5 1.0 CD2 A:PHE714 4.8 62.8 1.0 CG A:GLU662 4.8 64.5 1.0 CA A:ASP751 4.8 58.4 1.0 C A:ASN750 4.9 58.4 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Drosophila N-Cadherin EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Drosophila N-Cadherin EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca857 b:52.9 occ:1.00 O A:ASN789 2.3 58.9 1.0 OD1 A:ASN750 2.3 59.4 1.0 O A:ASN752 2.3 54.7 1.0 OD2 A:ASP785 2.3 59.8 1.0 OD2 A:ASP783 2.4 60.6 1.0 OD1 A:ASP783 2.7 62.3 1.0 OD2 A:ASP832 2.7 59.4 1.0 CG A:ASP783 2.9 61.6 1.0 CG A:ASP785 3.4 61.9 1.0 C A:ASN789 3.5 61.2 1.0 C A:ASN752 3.5 54.4 1.0 CG A:ASN750 3.5 59.2 1.0 CG A:ASP832 3.6 59.5 1.0 CB A:ASP785 3.8 63.5 1.0 CB A:ASP832 4.0 59.4 1.0 ND2 A:ASN750 4.1 60.3 1.0 CA A:ASN752 4.2 55.7 1.0 CA A:ASN789 4.3 62.7 1.0 CB A:ASN789 4.3 62.4 1.0 N A:ASN752 4.3 56.5 1.0 CB A:ASP783 4.4 62.0 1.0 CB A:ASN752 4.4 56.6 1.0 N A:ALA790 4.5 63.7 1.0 N A:ALA753 4.5 53.5 1.0 OD1 A:ASP785 4.5 64.1 1.0 OD1 A:ASP832 4.5 60.7 1.0 CA A:ALA753 4.7 52.8 1.0 CB A:ASN750 4.7 59.9 1.0 CA A:ALA790 4.7 63.4 1.0 CA A:ASN750 4.8 59.5 1.0 CD A:PRO754 4.8 52.3 1.0 N A:ASP785 4.9 64.0 1.0 C A:ALA753 5.0 52.3 1.0 CA A:ASP785 5.0 65.2 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