Calcium in PDB 5kj4: Crystal Structure of Mouse Protocadherin-15 EC9-10

The structure of Crystal Structure of Mouse Protocadherin-15 EC9-10, PDB code: 5kj4 was solved by R.Araya-Secchi, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.98 / 3.35
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	143.541, 143.541, 95.599, 90.00, 90.00, 120.00
R / Rfree (%)	15.8 / 19.6

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Mouse Protocadherin-15 EC9-10 (pdb code 5kj4). 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 Mouse Protocadherin-15 EC9-10, PDB code: 5kj4:
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 Mouse Protocadherin-15 EC9-10


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 Protocadherin-15 EC9-10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:0.4 occ:1.00 OD2 A:ASP989 2.2 0.4 1.0 O A:ALA939 2.3 0.7 1.0 O A:TYR901 2.3 0.7 1.0 OD1 A:ASN899 2.4 0.0 1.0 OD2 A:ASP933 2.7 0.1 1.0 OD1 A:ASP931 2.8 0.9 1.0 OD2 A:ASP931 2.8 0.3 1.0 CG A:ASP931 3.1 0.9 1.0 CG A:ASP989 3.3 0.2 1.0 CG A:ASN899 3.4 0.4 1.0 C A:ALA939 3.4 0.3 1.0 C A:TYR901 3.5 0.6 1.0 CB A:ASP989 3.8 0.3 1.0 CG A:ASP933 3.8 0.3 1.0 ND2 A:ASN899 3.8 0.6 1.0 CA A:ALA939 4.2 0.3 1.0 N A:TYR901 4.3 0.5 1.0 OD1 A:ASP989 4.4 0.8 1.0 CB A:ASP933 4.4 0.6 1.0 CA A:TYR901 4.4 0.4 1.0 CA A:PRO902 4.4 0.9 1.0 N A:SER940 4.4 0.4 1.0 N A:PRO902 4.4 0.1 1.0 CB A:ALA939 4.5 0.7 1.0 CB A:ASP931 4.5 0.9 1.0 SD A:MET995 4.6 0.2 1.0 CA A:SER940 4.6 0.5 1.0 C A:PRO902 4.7 0.3 1.0 OD1 A:ASP933 4.7 0.1 1.0 CB A:MET995 4.8 0.1 1.0 CB A:ASN899 4.8 0.1 1.0 CB A:TYR901 4.8 0.7 1.0 CD A:PRO903 4.9 0.4 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of Mouse Protocadherin-15 EC9-10


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 Protocadherin-15 EC9-10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:80.7 occ:1.00 OD1 A:ASP1118 1.9 81.4 1.0 OE2 A:GLU1077 2.2 63.1 1.0 OE2 A:GLU1026 2.3 69.6 1.0 OD1 A:ASP1115 2.5 79.0 1.0 O A:GLU1116 2.6 0.7 1.0 CD A:GLU1077 2.9 62.9 1.0 OE1 A:GLU1077 2.9 60.5 1.0 CG A:ASP1118 3.0 84.3 1.0 O A:HOH2105 3.1 32.9 1.0 CD A:GLU1026 3.2 70.2 1.0 OE1 A:GLU1026 3.5 68.4 1.0 OD2 A:ASP1118 3.6 82.0 1.0 N A:ASP1118 3.7 96.0 1.0 CG A:ASP1115 3.7 83.0 1.0 C A:GLU1116 3.7 0.1 1.0 N A:GLU1116 4.1 96.3 1.0 CB A:ASP1118 4.1 88.6 1.0 OD2 A:ASP1115 4.2 84.2 1.0 CG A:GLU1077 4.3 62.8 1.0 CA A:ASP1118 4.4 92.0 1.0 CA A:ASN1117 4.5 0.2 1.0 C A:ASN1117 4.5 0.0 1.0 CA A:GLU1116 4.6 0.2 1.0 N A:ASN1117 4.6 0.5 1.0 CG A:GLU1026 4.6 71.1 1.0 O A:ASP1118 4.7 87.5 1.0 CB A:TYR1076 4.7 60.7 1.0 C A:ASP1118 4.8 89.4 1.0 CA A:CA2003 4.8 66.7 1.0 CB A:ASP1115 4.9 83.5 1.0 C A:ASP1115 4.9 91.5 1.0 CA A:ASP1115 5.0 86.2 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of Mouse Protocadherin-15 EC9-10


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 Protocadherin-15 EC9-10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:66.7 occ:1.00 OD2 A:ASP1118 2.0 82.0 1.0 OE1 A:GLU1026 2.5 68.4 1.0 OD2 A:ASP1075 2.7 68.8 1.0 CG A:ASP1075 3.0 66.4 1.0 CG A:ASP1118 3.2 84.3 1.0 CA A:ASP1075 3.4 64.3 1.0 CB A:ASP1075 3.5 65.4 1.0 CD A:GLU1026 3.5 70.2 1.0 OD1 A:ASP1075 3.7 65.0 1.0 O A:LEU1074 3.7 70.0 1.0 OE1 A:GLU1077 3.8 60.5 1.0 OD1 A:ASP1118 3.9 81.4 1.0 CB A:ASP1118 4.1 88.6 1.0 CG A:GLU1026 4.2 71.1 1.0 N A:TYR1076 4.3 61.9 1.0 OE2 A:GLU1026 4.3 69.6 1.0 C A:ASP1075 4.4 62.3 1.0 N A:ASP1075 4.4 63.6 1.0 C A:LEU1074 4.5 66.3 1.0 CB A:GLU1026 4.6 69.8 1.0 CD2 A:LEU1027 4.6 88.0 1.0 CA A:CA2002 4.8 80.7 1.0 CD A:GLU1077 5.0 62.9 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of Mouse Protocadherin-15 EC9-10


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 Protocadherin-15 EC9-10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2001 b:74.6 occ:1.00 OD2 B:ASP933 2.2 93.7 1.0 OD1 B:ASN899 2.3 0.5 1.0 O B:ALA939 2.3 99.0 1.0 O B:TYR901 2.3 1.0 1.0 OD1 B:ASP931 2.6 99.6 1.0 OD2 B:ASP989 2.7 95.0 1.0 OD2 B:ASP931 3.0 95.7 1.0 CG B:ASP931 3.1 96.8 1.0 CG B:ASP933 3.3 93.0 1.0 C B:ALA939 3.4 96.7 1.0 CG B:ASN899 3.4 0.1 1.0 C B:TYR901 3.5 0.4 1.0 CG B:ASP989 3.8 95.1 1.0 CB B:ASP933 3.9 90.3 1.0 ND2 B:ASN899 3.9 0.0 1.0 N B:TYR901 4.1 0.1 1.0 CA B:ALA939 4.1 97.3 1.0 CB B:ASP989 4.2 94.6 1.0 CA B:TYR901 4.2 0.1 1.0 OD1 B:ASP933 4.3 93.5 1.0 CB B:ALA939 4.3 99.4 1.0 N B:SER940 4.3 95.0 1.0 CB B:TYR901 4.5 0.6 1.0 CB B:ASP931 4.5 94.4 1.0 N B:PRO902 4.5 0.3 1.0 CA B:SER940 4.5 92.8 1.0 CA B:PRO902 4.6 0.3 1.0 CB B:ASN899 4.7 0.0 1.0 SD B:MET995 4.7 0.3 1.0 OD1 B:ASP989 4.8 93.9 1.0 N B:ASP933 4.8 86.9 1.0 N B:ASP900 4.9 0.9 1.0 C B:PRO902 4.9 0.9 1.0 CA B:ASN899 4.9 0.3 1.0 CA B:ASP933 5.0 88.8 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of Mouse Protocadherin-15 EC9-10


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 Protocadherin-15 EC9-10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:69.2 occ:1.00 OE2 B:GLU1077 2.0 71.5 1.0 OD1 B:ASP1118 2.2 76.3 1.0 OD1 B:ASP1115 2.4 73.8 1.0 OE2 B:GLU1026 2.5 65.3 1.0 O B:GLU1116 2.7 75.0 1.0 CD B:GLU1077 2.8 74.2 1.0 OE1 B:GLU1077 3.0 76.6 1.0 O B:HOH2103 3.2 34.8 1.0 CG B:ASP1118 3.4 76.2 1.0 CA B:CA2003 3.5 60.0 1.0 CG B:ASP1115 3.5 74.7 1.0 CD B:GLU1026 3.5 66.5 1.0 OE1 B:GLU1026 3.8 65.3 1.0 C B:GLU1116 3.9 75.7 1.0 OD2 B:ASP1115 3.9 73.7 1.0 OD2 B:ASP1118 4.0 78.7 1.0 N B:ASP1118 4.1 73.9 1.0 N B:GLU1116 4.2 73.4 1.0 CG B:GLU1077 4.2 72.6 1.0 O B:ASP1118 4.4 75.0 1.0 CB B:ASP1118 4.6 76.0 1.0 C B:ASP1118 4.6 76.5 1.0 CA B:ASP1118 4.7 75.8 1.0 CA B:GLU1116 4.7 75.8 1.0 CB B:ASP1115 4.8 74.6 1.0 CB B:TYR1076 4.8 69.1 1.0 N B:ASN1117 4.9 75.4 1.0 CG B:GLU1026 4.9 66.3 1.0 CA B:ASP1115 4.9 73.8 1.0 C B:ASP1115 5.0 73.8 1.0 CA B:ASN1117 5.0 74.3 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of Mouse Protocadherin-15 EC9-10


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 Protocadherin-15 EC9-10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:60.0 occ:1.00 OE1 B:GLU1077 2.2 76.6 1.0 OD1 B:ASP1075 2.4 87.1 1.0 OE1 B:GLU1026 2.4 65.3 1.0 OD2 B:ASP1118 2.4 78.7 1.0 CG B:ASP1118 3.1 76.2 1.0 OD1 B:ASP1118 3.2 76.3 1.0 CD B:GLU1026 3.2 66.5 1.0 CD B:GLU1077 3.4 74.2 1.0 CA B:CA2002 3.5 69.2 1.0 CG B:ASP1075 3.5 79.5 1.0 OE2 B:GLU1026 3.5 65.3 1.0 O B:HOH2110 3.6 37.2 1.0 OE2 B:GLU1077 3.9 71.5 1.0 OD2 B:ASP1075 4.2 78.7 1.0 O B:HIS1119 4.3 76.6 1.0 N B:TYR1076 4.5 67.5 1.0 CG B:GLU1026 4.5 66.3 1.0 CB B:ASP1075 4.5 76.2 1.0 CA B:ASP1075 4.5 72.6 1.0 CB B:ASP1118 4.5 76.0 1.0 CG B:GLU1077 4.6 72.6 1.0 N B:GLU1077 4.7 70.0 1.0 CB B:GLU1077 4.8 70.8 1.0 C B:ASP1075 4.9 68.9 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of Mouse Protocadherin-15 EC9-10


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 Protocadherin-15 EC9-10 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2001 b:99.0 occ:1.00 O C:ALA939 2.2 0.3 1.0 OD2 C:ASP989 2.3 98.7 1.0 O C:TYR901 2.3 0.7 1.0 OD1 C:ASN899 2.4 0.7 1.0 OD2 C:ASP933 2.7 0.6 1.0 OD1 C:ASP931 2.7 99.4 1.0 OD2 C:ASP931 2.8 0.1 1.0 CG C:ASP931 3.1 99.3 1.0 CG C:ASP989 3.3 99.3 1.0 C C:ALA939 3.4 0.9 1.0 CG C:ASN899 3.4 0.1 1.0 C C:TYR901 3.5 1.0 1.0 CB C:ASP989 3.7 98.7 1.0 CG C:ASP933 3.8 0.8 1.0 ND2 C:ASN899 3.8 0.7 1.0 CA C:ALA939 4.2 0.8 1.0 CB C:ASP933 4.3 0.9 1.0 N C:TYR901 4.3 0.7 1.0 N C:SER940 4.4 0.9 1.0 OD1 C:ASP989 4.4 0.4 1.0 CA C:TYR901 4.4 0.7 1.0 CA C:PRO902 4.4 0.8 1.0 CB C:ALA939 4.5 0.1 1.0 N C:PRO902 4.5 0.7 1.0 CB C:ASP931 4.5 0.3 1.0 CA C:SER940 4.6 100.0 1.0 SD C:MET995 4.6 91.7 1.0 OD1 C:ASP933 4.7 0.7 1.0 C C:PRO902 4.7 0.7 1.0 CB C:TYR901 4.8 0.5 1.0 CB C:ASN899 4.8 0.9 1.0 CB C:MET995 4.8 91.8 1.0 CD C:PRO903 5.0 0.8 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of Mouse Protocadherin-15 EC9-10


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 Protocadherin-15 EC9-10 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2002 b:54.4 occ:1.00 OE2 C:GLU1077 2.1 64.2 1.0 OD1 C:ASP1118 2.1 69.7 1.0 OE2 C:GLU1026 2.3 65.7 1.0 OE1 C:GLU1077 2.5 61.9 1.0 CD C:GLU1077 2.6 64.9 1.0 OD1 C:ASP1115 2.7 56.4 1.0 CG C:ASP1118 3.0 72.0 1.0 O C:GLU1116 3.0 85.0 1.0 CD C:GLU1026 3.1 66.2 1.0 OE1 C:GLU1026 3.2 67.0 1.0 OD2 C:ASP1118 3.3 71.8 1.0 CA C:CA2003 3.8 53.8 1.0 CB C:HIS1119 3.9 75.9 1.0 CG C:ASP1115 3.9 62.2 1.0 N C:ASP1118 4.0 75.5 1.0 CG C:GLU1077 4.1 67.9 1.0 N C:HIS1119 4.1 72.8 1.0 C C:GLU1116 4.1 80.1 1.0 CB C:ASP1118 4.3 73.9 1.0 N C:GLU1116 4.3 74.9 1.0 CA C:ASP1118 4.4 74.8 1.0 OD2 C:ASP1115 4.4 64.4 1.0 C C:ASP1118 4.4 73.5 1.0 OD1 C:ASP1075 4.5 62.7 1.0 CG C:GLU1026 4.5 63.5 1.0 CA C:HIS1119 4.6 75.3 1.0 CB C:TYR1076 4.6 65.3 1.0 CA C:GLU1116 4.9 78.1 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of Mouse Protocadherin-15 EC9-10


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 Protocadherin-15 EC9-10 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2003 b:53.8 occ:1.00 OD1 C:ASP1075 2.1 62.7 1.0 OD2 C:ASP1118 2.2 71.8 1.0 OE1 C:GLU1077 2.6 61.9 1.0 CG C:ASP1075 3.0 63.4 1.0 OE1 C:GLU1026 3.2 67.0 1.0 CG C:ASP1118 3.3 72.0 1.0 OD2 C:ASP1075 3.5 63.0 1.0 CA C:CA2002 3.8 54.4 1.0 CD C:GLU1077 3.8 64.9 1.0 OD1 C:ASP1118 3.8 69.7 1.0 CB C:ASP1075 4.1 62.7 1.0 CD C:GLU1026 4.2 66.2 1.0 CB C:HIS1119 4.4 75.9 1.0 CA C:ASP1075 4.5 61.5 1.0 CB C:ASP1118 4.5 73.9 1.0 CG C:HIS1119 4.5 78.8 1.0 OE2 C:GLU1077 4.6 64.2 1.0 OE2 C:GLU1026 4.6 65.7 1.0 CD2 C:HIS1119 4.7 80.3 1.0 CG C:GLU1077 4.8 67.9 1.0 CB C:GLU1077 4.8 69.3 1.0 N C:TYR1076 4.9 61.7 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of Mouse Protocadherin-15 EC9-10


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 Protocadherin-15 EC9-10 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2001 b:93.5 occ:1.00 O D:ALA939 2.2 0.7 1.0 OD2 D:ASP989 2.3 96.0 1.0 O D:TYR901 2.3 100.0 1.0 OD1 D:ASN899 2.6 0.8 1.0 OD2 D:ASP931 2.6 95.3 1.0 OD1 D:ASP931 2.6 0.1 1.0 OD2 D:ASP933 2.7 0.7 1.0 CG D:ASP931 2.9 97.1 1.0 CG D:ASP989 3.3 97.3 1.0 C D:ALA939 3.3 0.9 1.0 C D:TYR901 3.5 99.3 1.0 CG D:ASN899 3.6 0.1 1.0 CB D:ASP989 3.7 95.8 1.0 CG D:ASP933 3.8 0.6 1.0 ND2 D:ASN899 4.0 0.6 1.0 CA D:ALA939 4.2 0.5 1.0 N D:SER940 4.3 0.9 1.0 CB D:ASP931 4.3 96.7 1.0 CB D:ASP933 4.3 0.0 1.0 OD1 D:ASP989 4.4 97.9 1.0 CA D:PRO902 4.4 0.0 1.0 N D:TYR901 4.4 0.7 1.0 CA D:SER940 4.5 0.7 1.0 CA D:TYR901 4.5 99.8 1.0 N D:PRO902 4.5 99.8 1.0 CB D:ALA939 4.5 0.7 1.0 C D:PRO902 4.6 0.1 1.0 CB D:TYR901 4.8 97.9 1.0 SD D:MET995 4.8 99.4 1.0 OD1 D:ASP933 4.8 0.1 1.0 CD D:PRO903 4.9 98.7 1.0 CB D:MET995 4.9 95.4 1.0 CB D:ASN899 5.0 0.9 1.0 N D:PRO903 5.0 99.3 1.0

R.Araya-Secchi, B.L.Neel, M.Sotomayor. An Elastic Element in the Protocadherin-15 Tip Link of the Inner Ear. Nat Commun V. 7 13458 2016.
ISSN: ESSN 2041-1723
PubMed: 27857071
DOI: 10.1038/NCOMMS13458