Calcium in PDB 4xxw: Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant

The structure of Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant, PDB code: 4xxw was solved by Y.Narui, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.26
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	157.746, 57.789, 155.264, 90.00, 99.17, 90.00
R / Rfree (%)	18.7 / 23.3

The structure of Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant (pdb code 4xxw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant, PDB code: 4xxw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant


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 Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:40.8 occ:1.00 OD2 B:ASP85 2.2 36.7 1.0 OD1 B:ASP83 2.2 39.5 1.0 OD2 B:ASP121 2.3 40.5 1.0 O B:HOH1224 2.4 39.2 1.0 OE1 B:GLU27 2.5 39.2 1.0 OE2 B:GLU28 2.6 50.4 1.0 CG B:ASP121 3.2 38.5 1.0 OD1 B:ASP121 3.3 36.4 1.0 CD B:GLU27 3.3 37.4 1.0 CG B:ASP85 3.3 38.6 1.0 CG B:ASP83 3.3 42.2 1.0 CD B:GLU28 3.5 52.7 1.0 OE2 B:GLU27 3.7 34.6 1.0 CB B:ASP85 3.9 41.1 1.0 CA B:CA1002 4.0 34.2 1.0 CG B:GLU28 4.2 50.3 1.0 OD2 B:ASP83 4.2 43.7 1.0 ND2 B:ASN122 4.2 36.1 1.0 CB B:ASP83 4.2 42.4 1.0 N B:ASP85 4.3 41.0 1.0 OE1 B:GLU28 4.3 57.4 1.0 OD1 B:ASP85 4.3 37.0 1.0 O B:HOH1122 4.4 51.7 1.0 CA B:ASP83 4.4 42.0 1.0 N B:ARG84 4.4 38.8 1.0 CG B:GLU27 4.5 37.8 1.0 O B:HOH1113 4.5 52.3 1.0 CB B:ASP121 4.7 38.8 1.0 CA B:ASP85 4.8 41.4 1.0 C B:ASP83 4.8 41.0 1.0

Calcium binding site 2 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant


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 Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:34.2 occ:1.00 OE2 B:GLU27 2.3 34.6 1.0 OD1 B:ASP159 2.3 38.1 1.0 OD1 B:ASP121 2.4 36.4 1.0 O B:ARG119 2.4 35.6 1.0 OD1 B:ASP118 2.4 36.2 1.0 OD2 B:ASP85 2.5 36.7 1.0 OD1 B:ASP85 2.5 37.0 1.0 CG B:ASP85 2.8 38.6 1.0 CD B:GLU27 3.3 37.4 1.0 CG B:ASP159 3.3 37.7 1.0 CG B:ASP118 3.5 36.5 1.0 C B:ARG119 3.5 39.5 1.0 CG B:ASP121 3.6 38.5 1.0 N B:ARG119 3.7 40.4 1.0 OE1 B:GLU27 3.7 39.2 1.0 ND2 B:ASN122 4.0 36.1 1.0 CA B:CA1001 4.0 40.8 1.0 CB B:ASP159 4.1 36.1 1.0 OD2 B:ASP121 4.1 40.5 1.0 N B:ASP121 4.1 36.6 1.0 CA B:ARG119 4.2 42.1 1.0 OD2 B:ASP118 4.2 35.6 1.0 OD2 B:ASP159 4.2 37.9 1.0 CA B:ASP159 4.3 36.6 1.0 O B:HOH1193 4.3 32.1 1.0 CB B:ASP85 4.4 41.1 1.0 CB B:ARG119 4.5 47.5 1.0 C B:ASP118 4.6 37.9 1.0 CA B:ASP118 4.6 35.7 1.0 CG B:GLU27 4.6 37.8 1.0 CB B:ASP118 4.6 35.9 1.0 N B:ASN120 4.6 39.2 1.0 CB B:ASP121 4.8 38.8 1.0 CA B:ASN120 4.8 37.4 1.0 CA B:ASP121 4.9 37.4 1.0

Calcium binding site 3 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant


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 Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:30.3 occ:1.00 OD1 B:ASN120 2.2 33.8 1.0 OD2 B:ASP157 2.3 32.3 1.0 O B:ASN163 2.3 31.2 1.0 O B:ASN122 2.3 32.5 1.0 OD2 B:ASP159 2.4 37.9 1.0 OD2 B:ASP215 2.5 32.1 1.0 OD1 B:ASP157 2.7 31.4 1.0 CG B:ASP157 2.8 32.5 1.0 CG B:ASN120 3.4 35.8 1.0 CG B:ASP159 3.5 37.7 1.0 CG B:ASP215 3.5 32.9 1.0 C B:ASN122 3.5 33.2 1.0 C B:ASN163 3.5 32.6 1.0 CB B:ASP159 3.7 36.1 1.0 CB B:ASP215 3.8 32.3 1.0 ND2 B:ASN120 3.9 36.1 1.0 N B:ASN122 4.3 34.2 1.0 CB B:ASP157 4.3 31.8 1.0 CA B:ASN122 4.3 34.4 1.0 CA B:ASN163 4.3 32.9 1.0 CB B:ASN163 4.4 33.6 1.0 N B:SER123 4.5 33.5 1.0 N B:GLY164 4.5 33.4 1.0 CB B:ASN122 4.6 34.3 1.0 OD1 B:ASP215 4.6 36.0 1.0 CD B:ARG224 4.6 44.7 1.0 CB B:ASN120 4.6 37.0 1.0 OD1 B:ASP159 4.6 38.1 1.0 CA B:SER123 4.7 32.6 1.0 CA B:ASN120 4.7 37.4 1.0 CA B:GLY164 4.7 34.4 1.0 C B:SER123 4.9 32.0 1.0 C B:ASN120 4.9 38.0 1.0 N B:ASP159 4.9 36.4 1.0 CA B:ASP159 5.0 36.6 1.0

Calcium binding site 4 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant


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 Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:54.7 occ:1.00 OE1 A:GLU27 2.2 57.5 1.0 OD2 A:ASP121 2.3 71.9 1.0 OD2 A:ASP85 2.3 52.3 1.0 OE2 A:GLU28 2.4 66.1 1.0 OD1 A:ASP83 2.4 67.6 1.0 O A:HOH1164 2.4 45.7 1.0 CG A:ASP121 3.2 67.3 1.0 CD A:GLU27 3.3 56.5 1.0 CD A:GLU28 3.3 67.4 1.0 CG A:ASP83 3.4 67.5 1.0 CG A:ASP85 3.4 53.9 1.0 OD1 A:ASP121 3.5 62.6 1.0 OE2 A:GLU27 3.7 54.5 1.0 CG A:GLU28 3.8 64.7 1.0 CB A:ASP85 4.0 56.7 1.0 CA A:CA1002 4.1 56.7 1.0 CB A:ASP83 4.2 66.2 1.0 OE1 A:GLU28 4.2 72.5 1.0 ND2 A:ASN122 4.2 62.0 1.0 OD2 A:ASP83 4.2 71.1 1.0 N A:ASP85 4.2 56.3 1.0 CA A:ASP83 4.3 61.6 1.0 N A:ARG84 4.4 54.9 1.0 CG A:GLU27 4.5 55.5 1.0 OD1 A:ASP85 4.5 52.4 1.0 CB A:ASP121 4.6 67.9 1.0 C A:ASP83 4.7 58.6 1.0 CA A:ASP85 4.8 57.5 1.0 O A:HOH1147 4.9 49.6 1.0

Calcium binding site 5 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant


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 Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:56.7 occ:1.00 OD1 A:ASP85 2.3 52.4 1.0 OD1 A:ASP159 2.4 61.8 1.0 OD1 A:ASP118 2.4 51.5 1.0 OD1 A:ASP121 2.4 62.6 1.0 OD2 A:ASP85 2.4 52.3 1.0 OE2 A:GLU27 2.4 54.5 1.0 O A:ARG119 2.7 51.9 1.0 CG A:ASP85 2.7 53.9 1.0 CG A:ASP159 3.4 59.4 1.0 CG A:ASP118 3.4 51.6 1.0 CD A:GLU27 3.5 56.5 1.0 CG A:ASP121 3.6 67.3 1.0 C A:ARG119 3.8 52.9 1.0 OD2 A:ASP118 3.8 51.2 1.0 OE1 A:GLU27 3.8 57.5 1.0 CB A:ASP159 3.9 57.6 1.0 N A:ARG119 3.9 53.8 1.0 ND2 A:ASN122 3.9 62.0 1.0 OD2 A:ASP121 4.1 71.9 1.0 CA A:CA1001 4.1 54.7 1.0 CA A:ASP159 4.1 59.1 1.0 CB A:ASP85 4.2 56.7 1.0 O A:HOH1133 4.3 41.0 1.0 N A:ASP121 4.3 59.7 1.0 OD2 A:ASP159 4.4 58.9 1.0 CA A:ARG119 4.4 56.0 1.0 CB A:ASP118 4.6 50.9 1.0 CA A:ASP118 4.7 51.3 1.0 CG A:GLU27 4.8 55.5 1.0 C A:ASP118 4.8 52.1 1.0 CB A:ASP121 4.8 67.9 1.0 N A:ASN120 4.8 57.6 1.0 CB A:ARG119 4.9 59.2 1.0 CA A:ASN120 5.0 56.0 1.0 N A:ASP85 5.0 56.3 1.0

Calcium binding site 6 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant


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 Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:50.9 occ:1.00 OD1 A:ASN120 2.2 48.9 1.0 O A:ASN122 2.2 53.3 1.0 OD2 A:ASP157 2.3 50.9 1.0 OD2 A:ASP215 2.3 52.9 1.0 OD2 A:ASP159 2.3 58.9 1.0 O A:ASN163 2.5 48.0 1.0 OD1 A:ASP157 2.7 56.5 1.0 CG A:ASP157 2.8 52.7 1.0 CG A:ASN120 3.3 52.2 1.0 C A:ASN122 3.3 57.1 1.0 CG A:ASP215 3.3 52.5 1.0 CG A:ASP159 3.4 59.4 1.0 C A:ASN163 3.6 46.5 1.0 ND2 A:ASN120 3.8 53.6 1.0 CB A:ASP215 3.8 49.8 1.0 CB A:ASP159 3.8 57.6 1.0 CA A:ASN122 4.2 59.8 1.0 N A:ASN122 4.2 60.1 1.0 N A:SER123 4.3 58.6 1.0 CB A:ASP157 4.3 53.2 1.0 CA A:ASN163 4.4 46.8 1.0 OD1 A:ASP215 4.4 55.7 1.0 CB A:ASN122 4.4 59.6 1.0 CB A:ASN163 4.4 47.0 1.0 CA A:SER123 4.5 58.3 1.0 OD1 A:ASP159 4.5 61.8 1.0 CB A:ASN120 4.6 54.1 1.0 N A:GLY164 4.6 46.8 1.0 CD A:ARG224 4.7 71.8 1.0 CA A:ASN120 4.7 56.0 1.0 CA A:GLY164 4.8 47.1 1.0 CD A:PRO124 4.8 53.0 1.0 C A:SER123 4.8 56.3 1.0 C A:ASN120 4.9 58.7 1.0 N A:ASP159 5.0 58.6 1.0

Calcium binding site 7 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant


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 Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1001 b:33.5 occ:1.00 OD2 C:ASP40 2.2 35.0 1.0 OD1 C:ASN3 2.3 43.0 1.0 O C:ARG4 2.3 33.7 1.0 OD2 C:ASP38 2.3 31.8 1.0 OD2 C:ASP86 2.4 35.8 1.0 OD2 C:ASP36 2.4 33.1 1.0 OD1 C:ASP36 2.7 33.0 1.0 CG C:ASP36 2.9 33.3 1.0 CG C:ASN3 3.3 44.9 1.0 CG C:ASP40 3.4 34.4 1.0 CG C:ASP38 3.4 32.1 1.0 CG C:ASP86 3.4 39.3 1.0 C C:ARG4 3.5 35.9 1.0 ND2 C:ASN3 3.7 44.1 1.0 CB C:ASP38 3.8 32.4 1.0 CB C:ASP86 3.9 39.1 1.0 CB C:ASP40 4.0 33.6 1.0 N C:ARG4 4.1 40.6 1.0 CA C:ARG4 4.3 38.9 1.0 OD1 C:ASP40 4.4 35.9 1.0 CB C:ASP36 4.4 33.2 1.0 N C:LEU5 4.4 36.0 1.0 OD1 C:ASP86 4.5 43.8 1.0 OD1 C:ASP38 4.5 30.8 1.0 CA C:LEU5 4.5 36.5 1.0 CB C:ASN3 4.7 45.5 1.0 NE2 C:GLN88 4.7 67.3 1.0 CB C:ARG4 4.7 38.1 1.0 C C:ASN3 4.8 45.4 1.0 CD C:PRO6 4.8 35.8 1.0 N C:ASP38 4.8 32.0 1.0 C C:LEU5 4.8 35.0 1.0 N C:PRO6 4.9 35.1 1.0 CA C:ASN3 4.9 47.5 1.0 CA C:ASP38 4.9 32.2 1.0

Calcium binding site 8 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant


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 Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1002 b:38.6 occ:1.00 OD1 C:ASP71 2.2 39.3 1.0 OE1 C:GLU21 2.3 33.5 1.0 OE1 C:GLU73 2.3 35.1 1.0 OD2 C:ASP104 2.3 38.2 1.0 O C:HOH1183 2.5 36.1 1.0 O C:HOH1171 2.6 29.4 1.0 OD1 C:ASP104 3.0 35.3 1.0 CG C:ASP104 3.0 36.3 1.0 CD C:GLU21 3.1 33.4 1.0 OE2 C:GLU21 3.3 32.3 1.0 CG C:ASP71 3.4 42.5 1.0 CD C:GLU73 3.5 36.4 1.0 CA C:CA1003 3.9 32.6 1.0 N C:ARG72 4.1 38.5 1.0 O C:HOH1205 4.1 38.8 1.0 O C:HOH1104 4.1 39.2 1.0 OD2 C:ASP71 4.2 43.5 1.0 OD1 C:ASN105 4.2 32.5 1.0 CA C:ASP71 4.2 41.4 1.0 CG C:GLU73 4.3 38.5 1.0 CB C:ASP71 4.4 42.1 1.0 OE2 C:GLU73 4.4 36.5 1.0 N C:GLU73 4.4 39.8 1.0 O C:HOH1172 4.4 36.7 1.0 C C:ASP71 4.4 39.8 1.0 CB C:GLU73 4.5 39.4 1.0 CG C:GLU21 4.5 33.4 1.0 CB C:ASP104 4.5 35.6 1.0

Calcium binding site 9 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant


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 Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1003 b:32.6 occ:1.00 OE2 C:GLU21 2.3 32.3 1.0 OD1 C:ASP137 2.4 32.1 1.0 OE2 C:GLU73 2.4 36.5 1.0 O C:VAL102 2.4 30.4 1.0 OD1 C:ASP101 2.4 35.7 1.0 OD1 C:ASP104 2.4 35.3 1.0 OE1 C:GLU73 2.6 35.1 1.0 CD C:GLU73 2.9 36.4 1.0 CG C:ASP101 3.2 35.6 1.0 CG C:ASP104 3.4 36.3 1.0 CD C:GLU21 3.5 33.4 1.0 OD2 C:ASP101 3.5 37.2 1.0 CG C:ASP137 3.6 31.7 1.0 C C:VAL102 3.6 31.5 1.0 N C:VAL102 3.9 33.0 1.0 CA C:CA1002 3.9 38.6 1.0 OD2 C:ASP104 4.0 38.2 1.0 OE1 C:GLU21 4.0 33.5 1.0 OD1 C:ASN105 4.0 32.5 1.0 N C:ASP104 4.1 33.6 1.0 CB C:ASP137 4.1 31.1 1.0 CA C:ASP137 4.3 32.0 1.0 CA C:VAL102 4.4 32.7 1.0 CG C:GLU73 4.4 38.5 1.0 CB C:ASP101 4.5 34.4 1.0 CB C:ASP104 4.5 35.6 1.0 N C:ASN103 4.6 31.5 1.0 OD2 C:ASP137 4.6 30.9 1.0 CA C:ASP101 4.7 34.0 1.0 CA C:ASN103 4.7 31.7 1.0 C C:ASP101 4.7 33.9 1.0 CA C:ASP104 4.7 34.3 1.0 CB C:ARG72 4.7 38.0 1.0 CG C:GLU21 4.8 33.4 1.0 NH2 C:ARG72 4.8 41.5 1.0 NE C:ARG72 4.8 39.5 1.0 C C:ASN103 4.9 33.5 1.0 CG2 C:VAL102 4.9 34.6 1.0

Calcium binding site 10 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant


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 Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1- 2 Splice Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1004 b:25.4 occ:1.00 OD2 C:ASP186 2.3 26.9 1.0 OD2 C:ASP137 2.3 30.9 1.0 OD1 C:ASN103 2.3 26.4 1.0 O C:ASN105 2.3 28.9 1.0 O C:GLY141 2.3 29.2 1.0 OD2 C:ASP135 2.4 25.6 1.0 OD1 C:ASP135 2.4 25.6 1.0 CG C:ASP135 2.7 26.9 1.0 CG C:ASP186 3.3 28.1 1.0 CG C:ASN103 3.3 28.3 1.0 CG C:ASP137 3.3 31.7 1.0 C C:ASN105 3.5 30.4 1.0 C C:GLY141 3.5 30.3 1.0 ND2 C:ASN103 3.6 27.5 1.0 CB C:ASP186 3.7 27.6 1.0 CB C:ASP137 3.7 31.1 1.0 N C:ASN105 4.2 31.9 1.0 CA C:ASN105 4.3 31.3 1.0 OD1 C:ASP186 4.3 27.5 1.0 CB C:ASP135 4.4 27.0 1.0 CA C:GLY141 4.4 30.2 1.0 CB C:ASN105 4.4 31.1 1.0 OD1 C:ASP137 4.5 32.1 1.0 N C:GLY142 4.5 31.1 1.0 N C:ALA106 4.5 31.1 1.0 CB C:ASN103 4.7 30.0 1.0 CA C:GLY142 4.7 31.6 1.0 N C:ASP137 4.7 31.2 1.0 CA C:ALA106 4.7 31.1 1.0 CA C:ASP137 4.8 32.0 1.0 CD1 C:LEU193 4.9 33.0 1.0 CB C:LEU193 4.9 31.6 1.0 C C:ALA106 5.0 31.0 1.0 CA C:ASN103 5.0 31.7 1.0

Y.Narui, M.Sotomayor. Tuning Inner-Ear Tip-Link Affinity Through Alternatively Spliced Variants of Protocadherin-15. Biochemistry V. 57 1702 2018.
ISSN: ISSN 1520-4995
PubMed: 29443515
DOI: 10.1021/ACS.BIOCHEM.7B01075