Calcium in PDB 7scm: Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2

The structure of Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2, PDB code: 7scm was solved by C.R.Nisler, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.93 / 2.27
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.109, 73.109, 381.934, 90, 90, 120
R / Rfree (%)	19 / 23.8

The structure of Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2 also contains other interesting chemical elements:

Sodium	(Na)	3 atoms
Potassium	(K)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2 (pdb code 7scm). 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 Ancestral Amniote Cadherin-23 EC1-2, PDB code: 7scm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Ancestral Amniote Cadherin-23 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 Ancestral Amniote Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:19.5 occ:1.00 O A:VAL100 2.2 19.9 1.0 OE2 A:GLU19 2.3 20.6 1.0 OE2 A:GLU71 2.3 25.2 1.0 OD1 A:ASP135 2.4 19.8 1.0 OD1 A:ASP99 2.4 21.1 1.0 OD1 A:ASP102 2.5 22.8 1.0 OE1 A:GLU71 2.6 24.3 1.0 CD A:GLU71 2.8 27.0 1.0 CD A:GLU19 3.4 22.8 1.0 CG A:ASP99 3.4 24.8 1.0 C A:VAL100 3.5 24.0 1.0 CG A:ASP135 3.5 25.1 1.0 CG A:ASP102 3.5 26.2 1.0 OE1 A:GLU19 3.8 22.1 1.0 NA A:NA305 3.8 28.9 1.0 OD2 A:ASP99 3.9 24.1 1.0 N A:VAL100 3.9 26.8 1.0 ND2 A:ASN103 4.0 23.0 1.0 OD2 A:ASP102 4.1 27.7 1.0 N A:ASP102 4.1 22.1 1.0 CG A:GLU71 4.3 27.4 1.0 CB A:ASP135 4.3 24.4 1.0 CA A:VAL100 4.3 26.8 1.0 CA A:ASP135 4.4 25.6 1.0 NE A:ARG70 4.5 28.7 1.0 OD2 A:ASP135 4.5 20.3 1.0 N A:ASN101 4.5 21.9 1.0 CB A:ASP99 4.6 24.2 1.0 CA A:ASP99 4.6 23.9 1.0 C A:ASP99 4.7 23.6 1.0 CG A:GLU19 4.7 23.9 1.0 CB A:ASP102 4.7 24.0 1.0 CA A:ASN101 4.8 23.4 1.0 CB A:ARG70 4.8 26.6 1.0 NH2 A:ARG70 4.9 31.5 1.0 CA A:ASP102 4.9 23.5 1.0 CG2 A:VAL100 5.0 31.3 1.0 C A:ASN101 5.0 22.5 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Ancestral Amniote Cadherin-23 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 Ancestral Amniote Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:22.2 occ:1.00 OD1 A:ASN101 2.2 21.8 1.0 O A:ASN103 2.3 25.3 1.0 OD2 A:ASP184 2.3 25.3 1.0 OD2 A:ASP135 2.3 20.3 1.0 OD2 A:ASP133 2.4 22.4 1.0 OD1 A:ASP133 2.4 23.4 1.0 O A:GLY139 2.4 25.7 1.0 CG A:ASP133 2.7 23.9 1.0 CG A:ASP184 3.3 27.9 1.0 CG A:ASN101 3.4 22.1 1.0 CG A:ASP135 3.4 25.1 1.0 C A:ASN103 3.4 23.3 1.0 C A:GLY139 3.6 27.1 1.0 CB A:ASP135 3.7 24.4 1.0 CB A:ASP184 3.8 28.2 1.0 ND2 A:ASN101 3.9 23.6 1.0 CA A:ASN103 4.1 22.6 1.0 CB A:ASP133 4.2 23.8 1.0 N A:ASN103 4.2 23.2 1.0 CB A:ASN103 4.3 23.0 1.0 CA A:GLY139 4.3 28.3 1.0 OD1 A:ASP184 4.4 26.3 1.0 N A:ALA104 4.4 22.9 1.0 OD1 A:ASP135 4.5 19.8 1.0 N A:GLY140 4.6 26.1 1.0 CB A:ASN101 4.6 22.5 1.0 CA A:ALA104 4.7 23.9 1.0 CA A:ASN101 4.7 23.4 1.0 CA A:GLY140 4.8 26.6 1.0 CD1 A:LEU191 4.9 32.5 1.0 CA A:ASP135 4.9 25.6 1.0 C A:ALA104 4.9 22.2 1.0 N A:ASP135 4.9 25.1 1.0 C A:ASN101 5.0 22.5 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Ancestral Amniote Cadherin-23 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 Ancestral Amniote Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:37.1 occ:1.00 OD2 A:ASP38 2.2 37.8 1.0 O A:ARG2 2.2 33.1 1.0 OD2 A:ASP84 2.4 44.9 1.0 OD1 A:ASN1 2.4 47.7 1.0 OD2 A:ASP34 2.5 36.8 1.0 OD1 A:ASP34 2.6 35.9 1.0 OD2 A:ASP36 2.6 52.0 1.0 CG A:ASP34 2.9 34.9 1.0 CG A:ASP38 3.4 44.1 1.0 CG A:ASN1 3.4 53.9 1.0 CG A:ASP84 3.4 38.0 1.0 C A:ARG2 3.5 43.4 1.0 CG A:ASP36 3.5 50.4 1.0 CB A:ASP36 3.7 48.0 1.0 ND2 A:ASN1 3.8 49.1 1.0 CB A:ASP84 3.9 36.7 1.0 N A:ARG2 4.0 52.5 1.0 CB A:ASP38 4.1 44.4 1.0 OD1 A:ASP38 4.3 45.2 1.0 CA A:ARG2 4.3 50.5 1.0 CB A:ASP34 4.4 35.1 1.0 N A:LEU3 4.5 38.5 1.0 OD1 A:ASP84 4.5 37.1 1.0 OE1 A:GLN86 4.6 68.2 1.0 CA A:LEU3 4.6 40.9 1.0 CB A:ASN1 4.7 53.6 1.0 N A:ASP36 4.7 49.3 1.0 OD1 A:ASP36 4.7 61.6 1.0 C A:ASN1 4.7 54.0 1.0 CD A:PRO4 4.7 37.9 1.0 C A:LEU3 4.8 41.5 1.0 N A:PRO4 4.8 36.4 1.0 CA A:ASP36 4.8 47.5 1.0 CA A:ASN1 4.9 54.9 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Ancestral Amniote Cadherin-23 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 Ancestral Amniote Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:28.4 occ:1.00 OD1 B:ASN101 2.2 26.1 1.0 O B:ASN103 2.2 33.8 1.0 OD2 B:ASP184 2.3 22.1 1.0 OD2 B:ASP135 2.4 27.8 1.0 OD2 B:ASP133 2.4 22.3 1.0 O B:GLY139 2.4 30.3 1.0 OD1 B:ASP133 2.4 23.0 1.0 CG B:ASP133 2.7 23.7 1.0 CG B:ASP184 3.3 27.3 1.0 CG B:ASP135 3.4 30.5 1.0 CG B:ASN101 3.4 25.4 1.0 C B:ASN103 3.4 31.5 1.0 C B:GLY139 3.5 31.2 1.0 CB B:ASP135 3.6 30.5 1.0 CB B:ASP184 3.7 28.2 1.0 ND2 B:ASN101 4.0 22.6 1.0 CB B:ASP133 4.2 24.6 1.0 CA B:ASN103 4.2 30.8 1.0 CA B:GLY139 4.2 32.5 1.0 N B:ASN103 4.3 31.1 1.0 CB B:ASN103 4.3 30.3 1.0 N B:ALA104 4.5 31.0 1.0 OD1 B:ASP184 4.5 21.9 1.0 N B:GLY140 4.5 32.0 1.0 OD1 B:ASP135 4.5 26.4 1.0 CB B:ASN101 4.6 23.2 1.0 CA B:GLY140 4.7 30.8 1.0 CA B:ALA104 4.7 27.5 1.0 CA B:ASN101 4.7 24.4 1.0 C B:ALA104 4.8 26.3 1.0 CA B:ASP135 4.9 32.5 1.0 N B:ASP135 4.9 29.9 1.0 CD1 B:LEU191 4.9 34.2 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Ancestral Amniote Cadherin-23 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 Ancestral Amniote Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:24.9 occ:1.00 O B:VAL100 2.3 23.6 1.0 OE2 B:GLU19 2.3 27.3 1.0 OE1 B:GLU71 2.4 30.9 1.0 OD1 B:ASP135 2.4 26.4 1.0 OD1 B:ASP102 2.4 30.7 1.0 OE2 B:GLU71 2.4 31.5 1.0 OD1 B:ASP99 2.4 29.0 1.0 CD B:GLU71 2.7 31.8 1.0 CD B:GLU19 3.4 28.6 1.0 CG B:ASP99 3.4 31.4 1.0 CG B:ASP102 3.4 31.3 1.0 CG B:ASP135 3.5 30.5 1.0 C B:VAL100 3.5 24.5 1.0 OE1 B:GLU19 3.8 27.7 1.0 OD2 B:ASP102 3.8 33.1 1.0 N B:VAL100 3.8 24.9 1.0 NA B:NA305 3.9 37.1 1.0 OD2 B:ASP99 3.9 31.1 1.0 ND2 B:ASN103 3.9 30.2 1.0 N B:ASP102 4.2 25.1 1.0 CB B:ASP135 4.2 30.5 1.0 CG B:GLU71 4.2 34.2 1.0 CA B:ASP135 4.3 32.5 1.0 CA B:VAL100 4.3 25.9 1.0 OD2 B:ASP135 4.4 27.8 1.0 NE B:ARG70 4.4 37.1 1.0 CA B:ASP99 4.5 27.8 1.0 N B:ASN101 4.5 23.2 1.0 CB B:ASP99 4.6 29.5 1.0 C B:ASP99 4.7 26.9 1.0 CG B:GLU19 4.7 28.6 1.0 CB B:ASP102 4.7 27.6 1.0 NH2 B:ARG70 4.8 36.0 1.0 CA B:ASN101 4.8 24.4 1.0 CA B:ASP102 5.0 28.5 1.0 CB B:ARG70 5.0 34.6 1.0 CG2 B:VAL100 5.0 28.8 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Ancestral Amniote Cadherin-23 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 Ancestral Amniote Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:56.0 occ:1.00 O B:ARG2 2.2 50.2 1.0 OD2 B:ASP36 2.4 57.2 1.0 OD2 B:ASP38 2.4 47.4 1.0 OD2 B:ASP34 2.5 52.5 1.0 OD1 B:ASP34 2.6 48.9 1.0 OD1 B:ASN1 2.7 58.7 1.0 OD2 B:ASP84 2.7 52.9 1.0 CG B:ASP34 2.9 47.6 1.0 CG B:ASN1 3.3 58.2 1.0 C B:ARG2 3.4 65.5 1.0 CG B:ASP36 3.4 57.6 1.0 ND2 B:ASN1 3.5 49.5 1.0 CG B:ASP38 3.6 54.3 1.0 CG B:ASP84 3.7 51.0 1.0 N B:ARG2 3.8 68.5 1.0 CB B:ASP84 3.9 51.7 1.0 CB B:ASP36 3.9 51.8 1.0 CA B:ARG2 4.2 70.7 1.0 CB B:ASP34 4.4 46.5 1.0 N B:LEU3 4.4 65.5 1.0 CB B:ASP38 4.4 56.0 1.0 OD1 B:ASP38 4.4 51.2 1.0 OD1 B:ASP36 4.4 73.1 1.0 CB B:ASN1 4.6 63.6 1.0 C B:ASN1 4.6 67.3 1.0 CA B:LEU3 4.7 65.6 1.0 CD B:PRO4 4.8 49.8 1.0 N B:ASP36 4.8 57.3 1.0 OD1 B:ASP84 4.8 50.3 1.0 CA B:ASN1 4.8 67.3 1.0 NE2 B:GLN86 4.8 80.5 1.0 C B:LEU3 4.8 58.0 1.0 N B:PRO4 4.9 50.9 1.0 CA B:ASP36 4.9 54.0 1.0

C.R.Nisler, M.Sotomayor. Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2 To Be Published.