Calcium in PDB 6ulm: Crystal Structure of Human Cadherin 17 EC1-2

The structure of Crystal Structure of Human Cadherin 17 EC1-2, PDB code: 6ulm was solved by M.E.Gray, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.53 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.394, 81.609, 106.813, 90, 90, 90
R / Rfree (%)	20.6 / 25.7

The binding sites of Calcium atom in the Crystal Structure of Human Cadherin 17 EC1-2 (pdb code 6ulm). 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 Human Cadherin 17 EC1-2, PDB code: 6ulm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Human Cadherin 17 EC1-2


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 Human Cadherin 17 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:21.0 occ:1.00 OE2 B:GLU18 2.2 25.5 1.0 OD1 B:ASP99 2.2 21.5 1.0 OD1 B:ASP96 2.2 22.4 1.0 OD1 B:ASP132 2.3 23.3 1.0 O B:ILE97 2.4 22.6 1.0 OE2 B:GLU65 2.5 23.6 1.0 OE1 B:GLU65 2.8 24.1 1.0 CD B:GLU65 3.0 26.5 1.0 CD B:GLU18 3.3 24.7 1.0 CG B:ASP96 3.3 22.6 1.0 CG B:ASP99 3.3 25.8 1.0 CG B:ASP132 3.4 22.5 1.0 C B:ILE97 3.6 25.8 1.0 OE1 B:GLU18 3.7 18.8 1.0 OD2 B:ASP96 3.8 21.0 1.0 ND2 B:ASN100 3.8 20.2 1.0 N B:ILE97 3.9 21.9 1.0 OD2 B:ASP99 3.9 23.6 1.0 CA B:CA302 3.9 24.6 1.0 N B:ASP99 4.0 23.9 1.0 CB B:ASP132 4.1 19.6 1.0 CA B:ASP132 4.2 22.2 1.0 OD2 B:ASP132 4.4 19.9 1.0 CA B:ILE97 4.4 24.4 1.0 CG B:GLU65 4.4 24.9 1.0 NE B:ARG64 4.4 23.4 1.0 CB B:ASP99 4.5 24.8 1.0 CB B:ASP96 4.5 20.6 1.0 CG1 B:ILE97 4.6 30.7 1.0 CG B:GLU18 4.6 23.6 1.0 CA B:ASP96 4.6 21.6 1.0 N B:ASN98 4.6 25.4 1.0 CA B:ASP99 4.7 22.2 1.0 C B:ASP96 4.7 22.3 1.0 CB B:ARG64 4.8 23.9 1.0 CA B:ASN98 4.9 24.3 1.0 C B:ASN98 4.9 22.8 1.0 C B:ASP99 5.0 20.2 1.0 N B:ASP132 5.0 18.9 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Human Cadherin 17 EC1-2


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 Human Cadherin 17 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:24.6 occ:1.00 OD2 B:ASP99 2.1 23.6 1.0 OE1 B:GLU65 2.2 24.1 1.0 OE1 B:GLU18 2.3 18.8 1.0 OD1 B:ASP63 2.4 19.1 1.0 O B:HOH500 2.5 18.3 1.0 O B:HOH494 2.6 25.0 1.0 CG B:ASP99 2.9 25.8 1.0 OD1 B:ASP99 3.1 21.5 1.0 CD B:GLU18 3.3 24.7 1.0 CG B:ASP63 3.5 20.2 1.0 CD B:GLU65 3.5 26.5 1.0 OE2 B:GLU18 3.6 25.5 1.0 CA B:CA301 3.9 21.0 1.0 O B:HOH469 4.0 42.9 1.0 O B:HOH422 4.1 26.2 1.0 OD2 B:ASP63 4.2 22.3 1.0 N B:ARG64 4.3 20.3 1.0 CB B:ASP63 4.3 20.1 1.0 ND2 B:ASN100 4.3 20.2 1.0 CA B:ASP63 4.3 20.7 1.0 CB B:GLU65 4.3 22.6 1.0 O B:HOH443 4.3 30.3 1.0 O B:HOH449 4.3 21.7 1.0 CB B:ASP99 4.3 24.8 1.0 OE2 B:GLU65 4.3 23.6 1.0 CG B:GLU65 4.4 24.9 1.0 N B:GLU65 4.4 21.5 1.0 C B:ASP63 4.5 22.2 1.0 CG B:GLU18 4.6 23.6 1.0 CB B:GLU18 4.9 21.1 1.0 CA B:GLU65 5.0 24.4 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Human Cadherin 17 EC1-2


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 Human Cadherin 17 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:20.0 occ:1.00 O B:ASN100 2.3 18.4 1.0 OD2 B:ASP193 2.3 24.1 1.0 OD2 B:ASP132 2.4 19.9 1.0 OD1 B:ASN98 2.4 24.7 1.0 O B:ASN138 2.4 20.7 1.0 OD2 B:ASP130 2.4 20.4 1.0 OD1 B:ASP130 2.7 18.3 1.0 CG B:ASP130 2.9 22.4 1.0 CG B:ASP193 3.3 23.7 1.0 CG B:ASP132 3.4 22.5 1.0 CG B:ASN98 3.5 26.1 1.0 C B:ASN100 3.5 23.9 1.0 C B:ASN138 3.6 22.4 1.0 CB B:ASP193 3.7 22.3 1.0 CB B:ASP132 3.7 19.6 1.0 ND2 B:ASN98 4.1 29.2 1.0 N B:ASN100 4.2 19.3 1.0 CA B:ASN100 4.3 21.4 1.0 CB B:ASP130 4.4 17.9 1.0 CA B:ASN138 4.4 23.6 1.0 OD1 B:ASP193 4.4 19.9 1.0 CD2 B:PHE202 4.5 27.3 1.0 CB B:ASN100 4.5 23.1 1.0 OD1 B:ASP132 4.6 23.3 1.0 N B:ARG101 4.6 27.3 1.0 N B:GLY139 4.6 22.2 1.0 CD B:PRO102 4.6 22.8 1.0 CB B:ASN98 4.7 25.2 1.0 CA B:ASN98 4.8 24.3 1.0 CB B:ASN138 4.8 26.6 1.0 CA B:GLY139 4.8 25.8 1.0 CA B:ARG101 4.8 31.3 1.0 N B:PRO102 4.8 21.6 1.0 C B:ARG101 4.8 25.6 1.0 N B:ASP132 4.9 18.9 1.0 CA B:ASP132 4.9 22.2 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Human Cadherin 17 EC1-2


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 Human Cadherin 17 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:34.1 occ:1.00 OD1 A:ASP63 2.2 38.5 1.0 O A:HOH429 2.2 33.6 1.0 OD2 A:ASP99 2.3 28.8 1.0 OE1 A:GLU65 2.3 29.8 1.0 O A:HOH469 2.4 39.9 1.0 OE1 A:GLU18 2.4 29.7 1.0 CG A:ASP99 3.1 26.7 1.0 CD A:GLU18 3.2 29.3 1.0 OD1 A:ASP99 3.3 24.9 1.0 CG A:ASP63 3.3 40.0 1.0 CD A:GLU65 3.5 34.2 1.0 OE2 A:GLU18 3.5 26.3 1.0 CA A:CA302 3.9 27.9 1.0 O A:HOH436 3.9 33.4 1.0 OD2 A:ASP63 4.1 43.1 1.0 O A:HOH449 4.1 29.4 1.0 CB A:GLU65 4.1 43.0 1.0 N A:GLU65 4.1 35.2 1.0 CB A:ASP63 4.2 38.3 1.0 N A:ARG64 4.2 31.6 1.0 CA A:ASP63 4.2 34.1 1.0 CG A:GLU65 4.3 40.5 1.0 C A:ASP63 4.4 33.7 1.0 OE2 A:GLU65 4.4 36.5 1.0 ND2 A:ASN100 4.5 30.1 1.0 CB A:ASP99 4.5 26.2 1.0 CG A:GLU18 4.6 29.1 1.0 CA A:GLU65 4.8 43.7 1.0 CB A:GLU18 4.9 28.5 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Human Cadherin 17 EC1-2


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 Human Cadherin 17 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:27.9 occ:1.00 OD1 A:ASP96 2.2 28.3 1.0 OE2 A:GLU18 2.3 26.3 1.0 OD1 A:ASP99 2.3 24.9 1.0 OD1 A:ASP132 2.4 26.5 1.0 O A:ILE97 2.5 25.5 1.0 OE2 A:GLU65 2.6 36.5 1.0 OE1 A:GLU65 2.7 29.8 1.0 CD A:GLU65 2.9 34.2 1.0 CG A:ASP96 3.3 29.9 1.0 CD A:GLU18 3.4 29.3 1.0 CG A:ASP99 3.4 26.7 1.0 CG A:ASP132 3.4 24.7 1.0 ND2 A:ASN100 3.7 30.1 1.0 C A:ILE97 3.7 25.4 1.0 OE1 A:GLU18 3.8 29.7 1.0 N A:ILE97 3.8 23.8 1.0 OD2 A:ASP96 3.9 31.5 1.0 OD2 A:ASP99 3.9 28.8 1.0 CA A:CA301 3.9 34.1 1.0 CB A:ASP132 4.0 23.5 1.0 N A:ASP99 4.1 25.2 1.0 CA A:ASP132 4.2 24.6 1.0 CG A:GLU65 4.3 40.5 1.0 OD2 A:ASP132 4.4 26.5 1.0 CA A:ILE97 4.4 25.1 1.0 NE A:ARG64 4.4 32.1 1.0 CB A:ASP96 4.5 27.1 1.0 CA A:ASP96 4.5 26.3 1.0 CB A:ASP99 4.6 26.2 1.0 CG1 A:ILE97 4.6 27.7 1.0 CG A:GLU18 4.6 29.1 1.0 C A:ASP96 4.7 25.1 1.0 CA A:ASP99 4.8 26.0 1.0 O A:HOH469 4.8 39.9 1.0 N A:ASN98 4.8 25.9 1.0 CB A:ARG64 4.8 29.4 1.0 NH1 A:ARG64 4.8 37.1 1.0 C A:ASN98 5.0 27.2 1.0 CA A:ASN98 5.0 26.7 1.0 CG A:ASN100 5.0 31.4 1.0 C A:ASP99 5.0 26.6 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Human Cadherin 17 EC1-2


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 Human Cadherin 17 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:18.7 occ:1.00 OD2 A:ASP193 2.3 20.2 1.0 O A:ASN100 2.3 24.5 1.0 OD2 A:ASP132 2.4 26.5 1.0 O A:ASN138 2.4 21.4 1.0 OD2 A:ASP130 2.4 19.3 1.0 OD1 A:ASN98 2.4 24.7 1.0 OD1 A:ASP130 2.5 20.3 1.0 CG A:ASP130 2.8 24.1 1.0 CG A:ASP193 3.3 18.8 1.0 CG A:ASP132 3.4 24.7 1.0 CG A:ASN98 3.5 24.8 1.0 C A:ASN100 3.5 25.8 1.0 C A:ASN138 3.6 23.1 1.0 CB A:ASP193 3.7 17.9 1.0 CB A:ASP132 3.7 23.5 1.0 ND2 A:ASN98 4.1 23.1 1.0 N A:ASN100 4.2 28.8 1.0 CA A:ASN100 4.3 26.8 1.0 CB A:ASP130 4.3 21.8 1.0 CA A:ASN138 4.4 21.0 1.0 OD1 A:ASP193 4.4 18.0 1.0 OD1 A:ASP132 4.5 26.5 1.0 CB A:ASN100 4.5 27.3 1.0 N A:GLY139 4.6 23.0 1.0 N A:ARG101 4.6 26.0 1.0 CD2 A:PHE202 4.7 29.6 1.0 CD A:PRO102 4.7 20.0 1.0 N A:PRO102 4.7 20.2 1.0 CB A:ASN98 4.7 24.9 1.0 CB A:ASN138 4.8 20.2 1.0 CA A:GLY139 4.8 24.3 1.0 CA A:ASN98 4.8 26.7 1.0 C A:ARG101 4.8 22.1 1.0 N A:ASP132 4.8 26.9 1.0 CA A:ARG101 4.9 26.7 1.0 CA A:ASP132 4.9 24.6 1.0

M.E.Gray, M.Sotomayor. Crystal Structure of the Nonclassical Cadherin-17 N-Terminus and Implications For Its Adhesive Binding Mechanism. Acta Crystallogr.,Sect.F V. 77 85 2021.
ISSN: ESSN 2053-230X
PubMed: 33682793
DOI: 10.1107/S2053230X21002247