Calcium in PDB 7sb6: Crystal Structure of Ancestral Mammalian Cadherin-23 EC1-2

The structure of Crystal Structure of Ancestral Mammalian Cadherin-23 EC1-2, PDB code: 7sb6 was solved by C.R.Nisler, Y.Narui, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.53 / 2.59
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	118.446, 168.834, 125.276, 90, 90, 90
R / Rfree (%)	20.4 / 24.6

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

Chlorine	(Cl)	3 atoms
Potassium	(K)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Ancestral Mammalian Cadherin-23 EC1-2 (pdb code 7sb6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of Ancestral Mammalian Cadherin-23 EC1-2, PDB code: 7sb6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Crystal Structure of Ancestral Mammalian 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 Mammalian Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:41.8 occ:1.00 OD1 A:ASP135 2.3 42.5 1.0 OE1 A:GLU19 2.3 43.3 1.0 OD1 A:ASP99 2.4 48.9 1.0 OD1 A:ASP102 2.4 46.8 1.0 O A:VAL100 2.4 40.8 1.0 OE2 A:GLU71 2.5 45.9 1.0 OE1 A:GLU71 2.6 44.6 1.0 CD A:GLU71 2.9 45.9 1.0 CD A:GLU19 3.3 45.1 1.0 CG A:ASP102 3.4 47.9 1.0 CG A:ASP99 3.5 47.1 1.0 CG A:ASP135 3.5 42.2 1.0 OE2 A:GLU19 3.6 46.4 1.0 C A:VAL100 3.6 41.4 1.0 CA A:CA302 3.8 75.6 1.0 OD2 A:ASP102 3.9 49.5 1.0 N A:VAL100 3.9 41.8 1.0 ND2 A:ASN103 4.0 46.6 1.0 N A:ASP102 4.1 44.7 1.0 OD2 A:ASP99 4.1 48.6 1.0 CB A:ASP135 4.1 41.8 1.0 CG A:GLU71 4.3 47.8 1.0 CA A:ASP135 4.4 43.1 1.0 NE A:ARG70 4.4 41.3 1.0 CA A:VAL100 4.5 41.7 1.0 OD2 A:ASP135 4.5 42.0 1.0 CA A:ASP99 4.5 43.5 1.0 CB A:ASP99 4.5 43.7 1.0 N A:ASN101 4.6 41.3 1.0 CB A:ASP102 4.6 47.8 1.0 CG A:GLU19 4.7 46.0 1.0 C A:ASP99 4.7 43.2 1.0 CA A:ASN101 4.7 42.7 1.0 C A:ASN101 4.8 43.4 1.0 CA A:ASP102 4.8 46.1 1.0 NH1 A:ARG70 4.8 44.8 1.0 CB A:ARG70 4.9 42.2 1.0 CG2 A:VAL100 4.9 43.0 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of Ancestral Mammalian 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 Mammalian Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:75.6 occ:1.00 OD2 A:ASP102 2.3 49.5 1.0 OE2 A:GLU71 2.4 45.9 1.0 OE2 A:GLU19 2.5 46.4 1.0 OD1 A:ASP69 2.5 52.4 1.0 O A:HOH429 2.5 41.2 1.0 CG A:ASP102 3.0 47.9 1.0 OD1 A:ASP102 3.1 46.8 1.0 CD A:GLU19 3.3 45.1 1.0 CG A:ASP69 3.4 54.0 1.0 CD A:GLU71 3.6 45.9 1.0 OE1 A:GLU19 3.8 43.3 1.0 CA A:CA301 3.8 41.8 1.0 ND2 A:ASN103 3.9 46.6 1.0 CA A:ASP69 4.0 48.9 1.0 CB A:ASP69 4.1 51.6 1.0 N A:ARG70 4.1 45.7 1.0 N A:GLU71 4.2 45.5 1.0 OD2 A:ASP69 4.2 55.5 1.0 CB A:GLU71 4.3 49.8 1.0 C A:ASP69 4.3 48.2 1.0 CG A:GLU71 4.3 47.8 1.0 CB A:ASP102 4.4 47.8 1.0 OE1 A:GLU71 4.5 44.6 1.0 CG A:GLU19 4.5 46.0 1.0 O A:HOH432 4.6 44.8 1.0 CA A:GLU71 4.9 50.2 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of Ancestral Mammalian 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 Mammalian Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:39.9 occ:1.00 OD1 A:ASN101 2.2 45.2 1.0 O A:GLY139 2.2 42.3 1.0 O A:ASN103 2.3 40.4 1.0 OD2 A:ASP184 2.4 38.5 1.0 OD2 A:ASP133 2.4 42.5 1.0 OD2 A:ASP135 2.4 42.0 1.0 OD1 A:ASP133 2.5 43.6 1.0 CG A:ASP133 2.7 41.7 1.0 CG A:ASN101 3.2 44.2 1.0 CG A:ASP184 3.3 40.4 1.0 CG A:ASP135 3.4 42.2 1.0 C A:GLY139 3.4 42.1 1.0 C A:ASN103 3.5 44.2 1.0 CB A:ASP135 3.6 41.8 1.0 ND2 A:ASN101 3.7 47.1 1.0 CB A:ASP184 3.8 40.9 1.0 CA A:GLY139 4.1 41.8 1.0 N A:ASN103 4.2 44.7 1.0 CB A:ASP133 4.2 41.5 1.0 OD1 A:ASP184 4.2 41.9 1.0 CA A:ASN103 4.3 45.0 1.0 N A:GLY140 4.5 41.9 1.0 CB A:ASN101 4.5 41.6 1.0 CB A:ASN103 4.5 44.2 1.0 N A:ALA104 4.5 46.2 1.0 OD1 A:ASP135 4.5 42.5 1.0 CA A:ASN101 4.7 42.7 1.0 N A:ASP135 4.7 42.8 1.0 CA A:GLY140 4.7 43.6 1.0 CA A:ASP135 4.7 43.1 1.0 CA A:ALA104 4.8 47.5 1.0 CD1 A:LEU191 4.9 47.0 1.0 C A:ASN101 4.9 43.4 1.0 N A:ASP102 4.9 44.7 1.0 CB A:LEU191 5.0 44.1 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of Ancestral Mammalian 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 Mammalian Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:85.9 occ:1.00 OD2 A:ASP34 2.2 73.2 1.0 OD2 A:ASP38 2.3 82.5 1.0 OD2 A:ASP36 2.5 83.4 1.0 OD2 A:ASP84 2.5 84.2 1.0 OD1 A:ASP34 2.5 73.5 1.0 OD1 A:ASN1 2.6 86.8 1.0 O A:ARG2 2.6 75.5 1.0 CG A:ASP34 2.7 72.8 1.0 CG A:ASP84 3.3 83.3 1.0 CB A:ASP84 3.5 81.6 1.0 CG A:ASP38 3.5 84.1 1.0 CG A:ASP36 3.6 80.8 1.0 CG A:ASN1 3.7 87.8 1.0 C A:ARG2 3.8 77.4 1.0 CB A:ASP36 4.0 80.3 1.0 ND2 A:ASN1 4.2 88.3 1.0 CB A:ASP34 4.2 70.0 1.0 CB A:ASP38 4.3 82.6 1.0 N A:ARG2 4.3 83.9 1.0 OD1 A:ASP38 4.4 86.7 1.0 CD A:PRO4 4.5 71.2 1.0 OD1 A:ASP84 4.5 87.8 1.0 OD1 A:ASP36 4.6 81.4 1.0 N A:PRO4 4.7 70.0 1.0 N A:LEU3 4.7 75.6 1.0 CA A:ARG2 4.7 83.1 1.0 CA A:LEU3 4.7 75.0 1.0 C A:LEU3 4.8 71.8 1.0 N A:ASP36 5.0 75.2 1.0 CA A:ASP84 5.0 82.5 1.0 CB A:ASN1 5.0 91.2 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of Ancestral Mammalian 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 Mammalian Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:49.3 occ:1.00 OD1 B:ASP135 2.2 49.6 1.0 OD1 B:ASP99 2.3 51.1 1.0 OE1 B:GLU19 2.3 47.8 1.0 OE1 B:GLU71 2.5 50.0 1.0 O B:VAL100 2.5 51.9 1.0 OE2 B:GLU71 2.6 50.7 1.0 OD1 B:ASP102 2.6 51.8 1.0 CD B:GLU71 2.8 51.1 1.0 CG B:ASP135 3.3 48.9 1.0 CG B:ASP99 3.4 51.2 1.0 CD B:GLU19 3.4 49.2 1.0 C B:VAL100 3.7 49.3 1.0 CG B:ASP102 3.7 54.5 1.0 OE2 B:GLU19 3.8 51.2 1.0 N B:VAL100 3.8 46.8 1.0 ND2 B:ASN103 3.9 56.2 1.0 OD2 B:ASP99 3.9 53.3 1.0 CB B:ASP135 4.0 48.1 1.0 CA B:CA302 4.2 77.0 1.0 OD2 B:ASP102 4.2 60.7 1.0 CA B:ASP135 4.3 49.2 1.0 N B:ASP102 4.3 47.7 1.0 CG B:GLU71 4.3 53.0 1.0 OD2 B:ASP135 4.3 48.0 1.0 CA B:VAL100 4.4 48.1 1.0 NE B:ARG70 4.4 49.8 1.0 CB B:ASP99 4.5 49.1 1.0 CA B:ASP99 4.6 45.5 1.0 C B:ASP99 4.7 45.0 1.0 N B:ASN101 4.7 49.7 1.0 CG B:GLU19 4.7 47.7 1.0 CB B:ASP102 4.8 52.8 1.0 CB B:ARG70 4.9 44.8 1.0 CA B:ASN101 4.9 51.1 1.0 NH1 B:ARG70 4.9 53.3 1.0 CB B:VAL100 5.0 49.2 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of Ancestral Mammalian 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 Mammalian Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:77.0 occ:1.00 O B:HOH422 2.3 44.4 1.0 OD2 B:ASP102 2.5 60.7 1.0 OE2 B:GLU19 2.5 51.2 1.0 OD1 B:ASP69 2.5 53.1 1.0 OE2 B:GLU71 2.7 50.7 1.0 CG B:ASP102 3.2 54.5 1.0 CG B:ASP69 3.3 54.4 1.0 OD1 B:ASP102 3.3 51.8 1.0 CD B:GLU19 3.4 49.2 1.0 OE1 B:GLU19 3.8 47.8 1.0 CD B:GLU71 3.8 51.1 1.0 OD2 B:ASP69 4.0 57.0 1.0 CA B:ASP69 4.1 49.2 1.0 CB B:ASP69 4.1 52.3 1.0 CA B:CA301 4.2 49.3 1.0 ND2 B:ASN103 4.2 56.2 1.0 N B:ARG70 4.3 46.6 1.0 O B:HOH412 4.5 48.2 1.0 C B:ASP69 4.5 49.9 1.0 N B:GLU71 4.5 49.8 1.0 CB B:GLU71 4.5 53.0 1.0 CG B:GLU19 4.5 47.7 1.0 CG B:GLU71 4.6 53.0 1.0 CB B:ASP102 4.7 52.8 1.0 OE1 B:GLU71 4.7 50.0 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of Ancestral Mammalian Cadherin-23 EC1-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Ancestral Mammalian Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:47.6 occ:1.00 O B:GLY139 2.2 41.7 1.0 OD1 B:ASN101 2.3 58.3 1.0 O B:ASN103 2.3 49.2 1.0 OD2 B:ASP184 2.3 51.1 1.0 OD1 B:ASP133 2.4 50.0 1.0 OD2 B:ASP133 2.5 54.4 1.0 OD2 B:ASP135 2.7 48.0 1.0 CG B:ASP133 2.7 52.7 1.0 CG B:ASP184 3.2 50.0 1.0 CG B:ASN101 3.4 55.5 1.0 C B:GLY139 3.4 45.5 1.0 C B:ASN103 3.5 51.6 1.0 CG B:ASP135 3.6 48.9 1.0 CB B:ASP184 3.7 48.2 1.0 CB B:ASP135 3.8 48.1 1.0 ND2 B:ASN101 3.9 56.9 1.0 CB B:ASP133 4.2 52.7 1.0 CA B:GLY139 4.2 48.0 1.0 OD1 B:ASP184 4.2 51.2 1.0 N B:ASN103 4.2 51.5 1.0 CA B:ASN103 4.3 52.2 1.0 N B:GLY140 4.5 46.8 1.0 N B:ALA104 4.5 53.7 1.0 CB B:ASN103 4.6 51.3 1.0 CB B:ASN101 4.6 52.8 1.0 CA B:GLY140 4.7 48.2 1.0 CA B:ALA104 4.8 50.8 1.0 OD1 B:ASP135 4.8 49.6 1.0 CA B:ASN101 4.8 51.1 1.0 N B:ASP135 4.9 49.4 1.0 CA B:ASP135 4.9 49.2 1.0 C B:ASN101 5.0 51.3 1.0 C B:ALA104 5.0 48.1 1.0 CD B:PRO105 5.0 47.4 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of Ancestral Mammalian Cadherin-23 EC1-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Ancestral Mammalian Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:69.4 occ:1.00 OD2 B:ASP84 2.3 77.0 1.0 OD2 B:ASP38 2.4 76.9 1.0 OD2 B:ASP34 2.4 71.9 1.0 O B:ARG2 2.5 74.9 1.0 OD2 B:ASP36 2.7 70.8 1.0 OD1 B:ASP34 2.7 75.5 1.0 CG B:ASP34 2.9 72.2 1.0 ND2 B:ASN1 2.9 88.9 1.0 OD1 B:ASN1 2.9 81.1 1.0 CG B:ASN1 3.2 87.9 1.0 CG B:ASP84 3.3 73.7 1.0 CG B:ASP38 3.6 79.2 1.0 CG B:ASP36 3.7 74.5 1.0 C B:ARG2 3.8 77.4 1.0 CB B:ASP84 3.9 71.3 1.0 CB B:ASP36 3.9 74.4 1.0 N B:ARG2 4.1 87.2 1.0 CB B:ASP38 4.1 75.7 1.0 OD1 B:ASP84 4.3 77.6 1.0 CB B:ASP34 4.4 70.2 1.0 CA B:ARG2 4.5 86.1 1.0 OD1 B:ASP38 4.6 81.4 1.0 CB B:ASN1 4.7 90.0 1.0 N B:LEU3 4.8 71.5 1.0 C B:ASN1 4.9 87.1 1.0 CA B:LEU3 4.9 66.8 1.0 OD1 B:ASP36 4.9 75.2 1.0 N B:ASP36 4.9 73.7 1.0 CA B:ASP36 4.9 75.0 1.0 CD B:PRO4 5.0 57.6 1.0 C B:LEU3 5.0 61.5 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of Ancestral Mammalian Cadherin-23 EC1-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Ancestral Mammalian Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:86.6 occ:1.00 OD2 C:ASP102 2.3 53.4 1.0 O C:HOH418 2.3 51.9 1.0 OE2 C:GLU19 2.4 55.5 1.0 OD1 C:ASP69 2.4 58.9 1.0 OE2 C:GLU71 2.5 53.1 1.0 CG C:ASP102 3.1 52.0 1.0 OD1 C:ASP102 3.3 50.8 1.0 CG C:ASP69 3.3 62.5 1.0 CD C:GLU19 3.4 54.2 1.0 CD C:GLU71 3.7 54.1 1.0 OE1 C:GLU19 3.9 51.1 1.0 O C:HOH417 3.9 48.9 1.0 CB C:ASP69 4.0 61.8 1.0 CA C:ASP69 4.0 58.0 1.0 CA C:CA302 4.1 52.0 1.0 OD2 C:ASP69 4.2 66.2 1.0 ND2 C:ASN103 4.3 56.1 1.0 N C:ARG70 4.3 53.6 1.0 N C:GLU71 4.4 58.3 1.0 CB C:GLU71 4.4 59.3 1.0 C C:ASP69 4.5 56.4 1.0 CG C:GLU19 4.5 52.5 1.0 CB C:ASP102 4.5 50.1 1.0 CG C:GLU71 4.5 56.8 1.0 OE1 C:GLU71 4.6 49.6 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of Ancestral Mammalian Cadherin-23 EC1-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Ancestral Mammalian Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:52.0 occ:1.00 OD1 C:ASP99 2.2 57.5 1.0 OD1 C:ASP135 2.4 55.4 1.0 OE1 C:GLU19 2.4 51.1 1.0 OE1 C:GLU71 2.4 49.6 1.0 O C:VAL100 2.5 51.5 1.0 OD1 C:ASP102 2.5 50.8 1.0 OE2 C:GLU71 2.6 53.1 1.0 CD C:GLU71 2.9 54.1 1.0 CG C:ASP99 3.3 55.7 1.0 CG C:ASP135 3.4 51.2 1.0 CD C:GLU19 3.4 54.2 1.0 CG C:ASP102 3.5 52.0 1.0 C C:VAL100 3.7 51.1 1.0 OE2 C:GLU19 3.8 55.5 1.0 N C:VAL100 3.9 51.8 1.0 OD2 C:ASP99 3.9 58.1 1.0 OD2 C:ASP102 4.0 53.4 1.0 ND2 C:ASN103 4.0 56.1 1.0 CB C:ASP135 4.1 51.0 1.0 N C:ASP102 4.1 47.2 1.0 CA C:CA301 4.1 86.6 1.0 OD2 C:ASP135 4.3 49.3 1.0 CA C:ASP135 4.3 52.6 1.0 CG C:GLU71 4.3 56.8 1.0 CA C:VAL100 4.4 52.2 1.0 CB C:ASP99 4.4 53.8 1.0 CA C:ASP99 4.5 50.7 1.0 NE C:ARG70 4.6 55.3 1.0 CB C:ASP102 4.6 50.1 1.0 C C:ASP99 4.6 49.5 1.0 N C:ASN101 4.7 49.2 1.0 CG C:GLU19 4.8 52.5 1.0 CA C:ASP102 4.8 49.4 1.0 CA C:ASN101 4.8 48.1 1.0 NH1 C:ARG70 4.9 61.1 1.0 CG2 C:VAL100 4.9 57.2 1.0 CB C:ARG70 4.9 53.0 1.0 C C:ASN101 5.0 49.6 1.0

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