Calcium in PDB 4nuq: Crystal Structure of Mouse N-Cadherin EC1-2 W2F

The structure of Crystal Structure of Mouse N-Cadherin EC1-2 W2F, PDB code: 4nuq was solved by X.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.91 / 2.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.587, 86.245, 46.722, 90.00, 98.52, 90.00
R / Rfree (%)	21.2 / 25.3

The binding sites of Calcium atom in the Crystal Structure of Mouse N-Cadherin EC1-2 W2F (pdb code 4nuq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Mouse N-Cadherin EC1-2 W2F, PDB code: 4nuq:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Mouse N-Cadherin EC1-2 W2F


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 Mouse N-Cadherin EC1-2 W2F within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:49.2 occ:1.00 OE1 A:GLU11 2.2 48.0 1.0 OD1 A:ASP67 2.3 47.0 1.0 OD2 A:ASP103 2.3 51.4 1.0 O A:HOH413 2.4 51.1 1.0 OE1 A:GLU69 2.4 46.0 1.0 O A:HOH448 2.4 51.7 1.0 CG A:ASP103 3.0 52.9 1.0 OD1 A:ASP103 3.1 46.7 1.0 CG A:ASP67 3.3 51.0 1.0 CD A:GLU11 3.3 53.7 1.0 CD A:GLU69 3.6 46.2 1.0 OE2 A:GLU11 3.7 54.0 1.0 CA A:CA302 3.9 47.1 1.0 N A:ARG68 4.0 47.1 1.0 CB A:ASP67 4.1 47.4 1.0 CA A:ASP67 4.1 51.0 1.0 OD2 A:ASP67 4.1 47.4 1.0 N A:GLU69 4.3 43.5 1.0 O A:HOH479 4.3 58.8 1.0 OD1 A:ASN104 4.4 46.1 1.0 C A:ASP67 4.4 48.0 1.0 CB A:GLU69 4.4 47.5 1.0 ND2 A:ASN12 4.4 57.3 1.0 OE2 A:GLU69 4.4 44.8 1.0 CG A:GLU69 4.5 44.4 1.0 CB A:ASP103 4.5 46.0 1.0 OD1 A:ASN12 4.6 64.3 1.0 CG A:GLU11 4.6 47.2 1.0 CG A:ASN12 4.9 57.8 1.0 CA A:GLU69 5.0 46.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Mouse N-Cadherin EC1-2 W2F


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 Mouse N-Cadherin EC1-2 W2F within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:47.1 occ:1.00 OD1 A:ASP100 2.3 52.9 1.0 OE2 A:GLU69 2.4 44.8 1.0 OD1 A:ASP103 2.4 46.7 1.0 OD1 A:ASP136 2.5 48.5 1.0 OE2 A:GLU11 2.5 54.0 1.0 O A:MET101 2.5 49.8 1.0 OE1 A:GLU69 2.5 46.0 1.0 CD A:GLU69 2.8 46.2 1.0 CG A:ASP100 3.4 58.0 1.0 CD A:GLU11 3.5 53.7 1.0 CG A:ASP136 3.5 52.4 1.0 CG A:ASP103 3.5 52.9 1.0 C A:MET101 3.7 52.1 1.0 OE1 A:GLU11 3.8 48.0 1.0 N A:MET101 3.9 42.6 1.0 CA A:CA301 3.9 49.2 1.0 OD1 A:ASN104 4.0 46.1 1.0 OD2 A:ASP100 4.0 56.2 1.0 CB A:ASP136 4.1 49.6 1.0 OD2 A:ASP103 4.1 51.4 1.0 N A:ASP103 4.1 59.5 1.0 NE A:ARG68 4.2 54.2 1.0 CA A:ASP136 4.2 50.3 1.0 CG A:GLU69 4.2 44.4 1.0 CA A:MET101 4.4 50.6 1.0 OD2 A:ASP136 4.5 50.4 1.0 NH2 A:ARG68 4.6 47.2 1.0 CB A:ASP100 4.6 50.3 1.0 CA A:ASP100 4.7 52.3 1.0 CB A:ASP103 4.7 46.0 1.0 C A:ASP100 4.7 51.0 1.0 N A:ASN102 4.8 51.5 1.0 CB A:ARG68 4.8 43.5 1.0 CA A:ASP103 4.8 53.6 1.0 CG A:GLU11 4.8 47.2 1.0 CZ A:ARG68 4.9 52.9 1.0 CA A:ASN102 4.9 52.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Mouse N-Cadherin EC1-2 W2F


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 Mouse N-Cadherin EC1-2 W2F within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:50.5 occ:1.00 O A:ASN142 2.3 54.8 1.0 O A:ASN104 2.3 56.9 1.0 OD1 A:ASN102 2.3 56.5 1.0 OD2 A:ASP136 2.4 50.4 1.0 OD2 A:ASP194 2.5 54.3 1.0 OD2 A:ASP134 2.5 58.1 1.0 OD1 A:ASP134 2.6 50.3 1.0 CG A:ASP134 2.9 63.3 1.0 CG A:ASP194 3.4 55.1 1.0 CG A:ASP136 3.5 52.4 1.0 C A:ASN142 3.5 50.1 1.0 CG A:ASN102 3.5 60.0 1.0 C A:ASN104 3.5 57.9 1.0 CB A:ASP194 3.9 52.4 1.0 CB A:ASP136 3.9 49.6 1.0 ND2 A:ASN102 4.1 52.5 1.0 N A:ASN104 4.3 54.3 1.0 CA A:ASN142 4.3 61.5 1.0 OD1 A:ASP194 4.3 54.2 1.0 CA A:ASN104 4.3 49.0 1.0 CB A:ASP134 4.4 55.2 1.0 N A:GLY143 4.5 56.5 1.0 CD1 A:LEU203 4.5 53.1 1.0 N A:ARG105 4.5 54.2 1.0 CB A:ASN142 4.6 54.5 1.0 OD1 A:ASP136 4.6 48.5 1.0 CA A:GLY143 4.6 59.3 1.0 CA A:ARG105 4.6 59.3 1.0 CB A:ASN104 4.6 52.5 1.0 CB A:ASN102 4.7 54.1 1.0 CA A:ASN102 4.8 52.8 1.0 N A:ASP136 4.9 51.2 1.0 C A:ARG105 4.9 54.8 1.0

J.Vendome, K.Felsovalyi, H.Song, Z.Yang, X.Jin, J.Brasch, O.J.Harrison, G.Ahlsen, F.Bahna, A.Kaczynska, P.S.Katsamba, D.Edmond, W.L.Hubbell, L.Shapiro, B.Honig. Structural and Energetic Determinants of Adhesive Binding Specificity in Type I Cadherins. Proc.Natl.Acad.Sci.Usa V. 111 E4175 2014.
ISSN: ISSN 0027-8424
PubMed: 25253890
DOI: 10.1073/PNAS.1416737111