Calcium in PDB 6vg1: Xenopus Protocadherin 8.1 EC1-6

The structure of Xenopus Protocadherin 8.1 EC1-6, PDB code: 6vg1 was solved by O.J.Harrison, B.Brasch, L.S.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.27 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	146.645, 42.393, 167.471, 90.00, 110.60, 90.00
R / Rfree (%)	25.3 / 29.7

The structure of Xenopus Protocadherin 8.1 EC1-6 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Calcium atom in the Xenopus Protocadherin 8.1 EC1-6 (pdb code 6vg1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 30 binding sites of Calcium where determined in the Xenopus Protocadherin 8.1 EC1-6, PDB code: 6vg1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 30 in the Xenopus Protocadherin 8.1 EC1-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xenopus Protocadherin 8.1 EC1-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:56.2 occ:1.00 O A:ILE96 2.0 47.8 1.0 OE2 A:GLU61 2.1 50.5 1.0 OD1 A:ASP95 2.4 62.0 1.0 OD1 A:ASP98 2.4 97.0 1.0 OE2 A:GLU9 2.4 50.7 1.0 OD1 A:ASP131 2.4 49.4 1.0 CD A:GLU61 2.7 51.0 1.0 OE1 A:GLU61 2.8 52.9 1.0 HG22 A:ILE96 3.0 65.5 1.0 H A:ILE96 3.1 93.9 1.0 H A:ASP98 3.1 79.5 1.0 C A:ILE96 3.2 51.0 1.0 CG A:ASP131 3.4 82.7 1.0 CG A:ASP98 3.5 69.5 1.0 CG A:ASP95 3.5 48.2 1.0 CD A:GLU9 3.6 66.5 1.0 N A:ILE96 3.6 77.7 1.0 HD22 A:ASN99 3.7 63.9 1.0 HA A:ASP131 3.7 49.9 1.0 HB3 A:ASP131 3.9 49.9 1.0 CG2 A:ILE96 3.9 54.0 1.0 N A:ASP98 4.0 65.7 1.0 CA A:ILE96 4.0 70.7 1.0 HE A:ARG60 4.0 72.3 1.0 HA A:ASN97 4.0 84.2 1.0 CA A:CA707 4.0 58.1 1.0 OD2 A:ASP98 4.0 91.5 1.0 OD2 A:ASP95 4.1 56.4 1.0 OE1 A:GLU9 4.1 66.1 1.0 CB A:ASP131 4.1 44.5 1.0 HG23 A:ILE96 4.1 65.5 1.0 CG A:GLU61 4.1 61.1 1.0 HH21 A:ARG60 4.2 56.5 1.0 N A:ASN97 4.2 66.8 1.0 OD2 A:ASP131 4.2 44.1 1.0 HG2 A:GLU61 4.3 74.0 1.0 HA A:ASP95 4.3 96.7 1.0 CA A:ASP131 4.4 44.4 1.0 HG3 A:GLU61 4.4 74.0 1.0 ND2 A:ASN99 4.4 52.7 1.0 HB3 A:ARG60 4.5 74.5 1.0 HD22 A:ASN135 4.5 90.9 1.0 CA A:ASN97 4.5 69.6 1.0 HG21 A:ILE96 4.5 65.5 1.0 CB A:ILE96 4.6 53.8 1.0 HB2 A:ASN99 4.6 56.7 1.0 C A:ASP95 4.6 76.1 1.0 H A:ASN99 4.6 60.4 1.0 CB A:ASP98 4.7 99.3 1.0 CB A:ASP95 4.7 54.4 1.0 HD21 A:ASN99 4.7 63.9 1.0 HG2 A:GLU9 4.7 1.0 1.0 C A:ASN97 4.8 50.9 1.0 CA A:ASP98 4.8 49.7 1.0 CG A:GLU9 4.8 85.2 1.0 NE A:ARG60 4.8 59.7 1.0 CA A:ASP95 4.8 80.0 1.0 HA A:ILE96 4.8 85.6 1.0 H A:GLU61 4.9 82.6 1.0 N A:ASN99 4.9 49.8 1.0 NH2 A:ARG60 5.0 50.0 1.0 HB A:ILE96 5.0 65.3 1.0 HB2 A:ASP131 5.0 49.9 1.0

Calcium binding site 2 out of 30 in the Xenopus Protocadherin 8.1 EC1-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xenopus Protocadherin 8.1 EC1-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:58.1 occ:1.00 OD2 A:ASP98 2.2 91.5 1.0 OE1 A:GLU61 2.3 52.9 1.0 OD1 A:ASP59 2.4 69.0 1.0 OE1 A:GLU9 2.4 66.1 1.0 OE2 A:GLU10 2.5 80.0 1.0 O A:HOH842 2.9 48.6 1.0 CG A:ASP98 3.1 69.5 1.0 CD A:GLU9 3.1 66.5 1.0 HG3 A:GLU10 3.2 79.3 1.0 OD1 A:ASP98 3.3 97.0 1.0 CD A:GLU10 3.4 70.1 1.0 CG A:ASP59 3.4 63.6 1.0 OE2 A:GLU9 3.5 50.7 1.0 CD A:GLU61 3.5 51.0 1.0 HG2 A:GLU10 3.5 79.3 1.0 H A:GLU61 3.6 82.6 1.0 CG A:GLU10 3.6 65.5 1.0 HA A:ASP59 3.7 62.7 1.0 HB2 A:GLU61 3.7 58.6 1.0 H A:ARG60 3.8 98.0 1.0 HG22 A:ILE96 4.0 65.5 1.0 CA A:CA706 4.0 56.2 1.0 OD2 A:ASP59 4.1 86.1 1.0 HD21 A:ASN99 4.1 63.9 1.0 HG3 A:GLU9 4.2 1.0 1.0 OE2 A:GLU61 4.2 50.5 1.0 CG A:GLU9 4.3 85.2 1.0 N A:ARG60 4.3 81.1 1.0 CA A:ASP59 4.4 52.3 1.0 HG21 A:ILE96 4.4 65.5 1.0 CB A:ASP59 4.4 60.3 1.0 N A:GLU61 4.4 68.2 1.0 HD22 A:ASN99 4.5 63.9 1.0 CB A:ASP98 4.5 99.3 1.0 CB A:GLU61 4.5 51.7 1.0 HB2 A:GLU9 4.5 61.8 1.0 CG A:GLU61 4.6 61.1 1.0 OE1 A:GLU10 4.6 66.0 1.0 ND2 A:ASN99 4.6 52.7 1.0 HB2 A:ASP98 4.6 0.9 1.0 CG2 A:ILE96 4.6 54.0 1.0 C A:ASP59 4.7 76.2 1.0 HB2 A:ASP59 4.7 73.0 1.0 HB3 A:ARG60 4.7 74.5 1.0 HG23 A:ILE96 4.9 65.5 1.0 HB3 A:ASP98 4.9 0.9 1.0 HG2 A:GLU61 4.9 74.0 1.0 HG2 A:GLU9 5.0 1.0 1.0

Calcium binding site 3 out of 30 in the Xenopus Protocadherin 8.1 EC1-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Xenopus Protocadherin 8.1 EC1-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca708 b:56.0 occ:1.00 OD2 A:ASP129 2.2 70.6 1.0 OD2 A:ASP131 2.3 44.1 1.0 O A:ASN135 2.3 45.6 1.0 OD1 A:ASN97 2.4 80.6 1.0 O A:ASN99 2.4 42.5 1.0 OD2 A:ASP186 2.5 54.6 1.0 OD1 A:ASP129 2.7 49.4 1.0 CG A:ASP129 2.8 47.5 1.0 HB2 A:ASP131 3.0 49.9 1.0 HB3 A:ASN135 3.2 73.8 1.0 CG A:ASP131 3.3 82.7 1.0 C A:ASN135 3.5 43.2 1.0 CG A:ASP186 3.6 49.5 1.0 CG A:ASN97 3.6 59.3 1.0 C A:ASN99 3.6 42.4 1.0 CB A:ASP131 3.7 44.5 1.0 HB3 A:ASP186 3.8 78.0 1.0 HA A:SER100 3.8 69.2 1.0 HA A:ASN135 3.9 71.5 1.0 H A:ASN99 3.9 60.4 1.0 HD3 A:ARG192 3.9 75.4 1.0 HD3 A:PRO101 4.0 43.2 1.0 HB2 A:ASP186 4.0 78.0 1.0 HA A:ASN97 4.0 84.2 1.0 CB A:ASP186 4.0 64.4 1.0 CB A:ASN135 4.0 60.9 1.0 CA A:ASN135 4.0 59.0 1.0 HD21 A:ASN97 4.1 90.6 1.0 H A:ASP131 4.1 53.4 1.0 HB3 A:ASP131 4.2 49.9 1.0 CB A:ASP129 4.3 39.9 1.0 ND2 A:ASN97 4.3 74.9 1.0 HB2 A:ARG192 4.3 55.0 1.0 HB2 A:ASN99 4.3 56.7 1.0 HA A:SER136 4.3 61.1 1.0 OD1 A:ASP131 4.4 49.4 1.0 N A:SER100 4.5 41.5 1.0 CA A:ASN99 4.5 43.4 1.0 CA A:SER100 4.5 57.1 1.0 N A:ASN99 4.6 49.8 1.0 HB3 A:ASP129 4.6 44.4 1.0 OD1 A:ASP186 4.6 66.9 1.0 N A:SER136 4.6 64.9 1.0 HB2 A:ASP129 4.6 44.4 1.0 HB2 A:ASN135 4.6 73.8 1.0 CA A:ASN97 4.7 69.6 1.0 CB A:ASN97 4.7 46.5 1.0 CB A:ASN99 4.8 46.7 1.0 N A:ASP131 4.8 44.0 1.0 HB3 A:ASN99 4.8 56.7 1.0 CA A:ASP131 4.9 44.4 1.0 CD A:PRO101 4.9 38.9 1.0 CD A:ARG192 4.9 62.3 1.0 C A:ASN97 4.9 50.9 1.0 CA A:SER136 4.9 50.3 1.0 O A:ASN97 5.0 54.4 1.0 CG A:ASN135 5.0 62.8 1.0 HE A:ARG192 5.0 92.4 1.0

Calcium binding site 4 out of 30 in the Xenopus Protocadherin 8.1 EC1-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Xenopus Protocadherin 8.1 EC1-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca709 b:21.7 occ:1.00 OE2 A:GLU173 2.3 27.4 1.0 OE2 A:GLU114 2.4 27.6 1.0 OD1 A:ASP204 2.4 34.9 1.0 OD1 A:ASP207 2.4 16.4 1.0 O A:PHE205 2.4 46.5 1.0 OD2 A:ASP240 2.4 39.0 1.0 CD A:GLU173 2.9 51.7 1.0 OE1 A:GLU173 3.0 68.3 1.0 CG A:ASP204 3.3 16.0 1.0 H A:ASP207 3.3 38.3 1.0 H A:PHE205 3.3 35.2 1.0 CD A:GLU114 3.3 44.3 1.0 CG A:ASP207 3.5 52.3 1.0 CA A:CA711 3.5 34.0 1.0 CG A:ASP240 3.6 36.2 1.0 C A:PHE205 3.6 60.5 1.0 OD2 A:ASP204 3.6 55.4 1.0 OE1 A:GLU114 3.6 74.2 1.0 HA A:ASP240 3.7 21.9 1.0 HE A:ARG172 3.8 31.2 1.0 OD2 A:ASP207 3.9 80.5 1.0 N A:PHE205 3.9 28.8 1.0 HB3 A:ARG172 4.0 24.4 1.0 N A:ASP207 4.2 31.3 1.0 HA A:ASN206 4.2 15.9 1.0 HB3 A:ASP240 4.2 29.4 1.0 OD1 A:ASN208 4.2 61.8 1.0 HA A:ASP204 4.2 52.9 1.0 CB A:ASP240 4.3 23.9 1.0 CG A:GLU173 4.3 33.0 1.0 CA A:PHE205 4.4 25.1 1.0 HB3 A:PHE205 4.4 24.9 1.0 CA A:ASP240 4.4 17.6 1.0 HG2 A:GLU173 4.5 40.4 1.0 HH21 A:ARG172 4.5 35.1 1.0 CB A:ASP204 4.5 16.6 1.0 OD1 A:ASP240 4.5 24.7 1.0 N A:ASN206 4.6 32.3 1.0 HG3 A:GLU173 4.7 40.4 1.0 CG A:GLU114 4.7 55.1 1.0 NE A:ARG172 4.7 25.5 1.0 HG2 A:GLU114 4.7 66.8 1.0 HB2 A:ASN208 4.7 34.2 1.0 CA A:ASP204 4.7 43.5 1.0 CB A:ASP207 4.8 35.4 1.0 H A:ASN208 4.8 52.0 1.0 C A:ASP204 4.8 17.5 1.0 CA A:ASN206 4.8 16.1 1.0 H A:GLU241 4.8 36.0 1.0 H A:GLU173 4.8 43.2 1.0 HB2 A:ASP204 4.9 16.4 1.0 H A:ARG172 4.9 20.8 1.0 CB A:ARG172 4.9 19.8 1.0 CA A:ASP207 4.9 16.8 1.0 CB A:PHE205 5.0 20.1 1.0

Calcium binding site 5 out of 30 in the Xenopus Protocadherin 8.1 EC1-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Xenopus Protocadherin 8.1 EC1-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca710 b:23.7 occ:1.00 O A:ASN208 2.3 13.6 1.0 OD2 A:ASP294 2.4 18.4 1.0 OD1 A:ASP240 2.4 24.7 1.0 O A:ASN244 2.4 20.3 1.0 OD1 A:ASP238 2.4 45.0 1.0 OD1 A:ASN206 2.4 30.4 1.0 OD2 A:ASP238 2.4 30.2 1.0 CG A:ASP238 2.7 32.9 1.0 HB2 A:ASP240 3.1 29.4 1.0 HD12 A:LEU300 3.4 51.1 1.0 CG A:ASP240 3.4 36.2 1.0 HB3 A:ASP294 3.4 39.1 1.0 CG A:ASP294 3.4 16.0 1.0 C A:ASN208 3.5 28.0 1.0 C A:ASN244 3.6 42.5 1.0 CG A:ASN206 3.6 41.7 1.0 HB3 A:ASN244 3.7 51.2 1.0 HA2 A:GLY245 3.7 51.4 1.0 CB A:ASP240 3.7 23.9 1.0 HB2 A:ASP294 3.7 39.1 1.0 HD3 A:PRO210 3.7 11.4 1.0 CB A:ASP294 3.7 32.0 1.0 H A:ASN208 3.9 52.0 1.0 HD21 A:ASN206 3.9 67.7 1.0 HA A:SER209 3.9 12.6 1.0 HB2 A:LEU300 4.1 64.5 1.0 HB2 A:ASN208 4.1 34.2 1.0 ND2 A:ASN206 4.2 55.9 1.0 H A:ASP240 4.2 22.4 1.0 CB A:ASP238 4.2 26.6 1.0 HB3 A:ASP240 4.2 29.4 1.0 CD1 A:LEU300 4.4 42.0 1.0 HA A:ASN206 4.4 15.9 1.0 HA A:ASN244 4.4 34.4 1.0 CA A:ASN244 4.4 28.1 1.0 CA A:ASN208 4.5 16.6 1.0 N A:SER209 4.5 13.8 1.0 HB3 A:ASP238 4.5 32.6 1.0 CB A:ASN244 4.5 42.1 1.0 N A:GLY245 4.5 15.8 1.0 CA A:SER209 4.5 13.4 1.0 CA A:GLY245 4.5 42.3 1.0 N A:ASN208 4.5 42.7 1.0 OD1 A:ASP294 4.5 51.4 1.0 OD2 A:ASP240 4.5 39.0 1.0 HB2 A:ASP238 4.5 32.6 1.0 CD A:PRO210 4.6 12.4 1.0 CB A:ASN208 4.6 27.9 1.0 C A:SER209 4.7 12.7 1.0 HD13 A:LEU300 4.7 51.1 1.0 HB3 A:ASN208 4.7 34.2 1.0 HD2 A:PRO239 4.7 57.5 1.0 N A:PRO210 4.7 25.6 1.0 CB A:ASN206 4.8 25.3 1.0 HD11 A:LEU300 4.9 51.1 1.0 N A:ASP240 4.9 18.1 1.0 HB2 A:ASN244 4.9 51.2 1.0 CB A:LEU300 4.9 53.2 1.0 CA A:ASP240 4.9 17.6 1.0 HG A:LEU300 5.0 73.5 1.0 CA A:ASN206 5.0 16.1 1.0

Calcium binding site 6 out of 30 in the Xenopus Protocadherin 8.1 EC1-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Xenopus Protocadherin 8.1 EC1-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca711 b:34.0 occ:1.00 OD2 A:ASP207 2.2 80.5 1.0 O A:HOH814 2.3 36.6 1.0 OE1 A:GLU114 2.3 74.2 1.0 OE1 A:GLU173 2.3 68.3 1.0 OD1 A:ASP171 2.5 23.6 1.0 O A:HOH836 2.6 37.3 1.0 CG A:ASP207 3.0 52.3 1.0 OD1 A:ASP207 3.1 16.4 1.0 CD A:GLU114 3.2 44.3 1.0 CD A:GLU173 3.4 51.7 1.0 CG A:ASP171 3.5 59.6 1.0 HA A:ASP171 3.5 31.1 1.0 CA A:CA709 3.5 21.7 1.0 OE2 A:GLU114 3.6 27.6 1.0 H A:GLU173 3.6 43.2 1.0 H A:ARG172 3.7 20.8 1.0 OD1 A:ASN208 3.8 61.8 1.0 HB2 A:GLU173 3.9 44.4 1.0 OE2 A:GLU173 4.1 27.4 1.0 N A:ARG172 4.2 17.4 1.0 O A:HOH873 4.3 31.1 1.0 CA A:ASP171 4.3 25.3 1.0 OD2 A:ASP171 4.3 44.3 1.0 CG A:GLU173 4.3 33.0 1.0 HG2 A:GLU173 4.3 40.4 1.0 CB A:ASP207 4.4 35.4 1.0 HG3 A:GLU114 4.4 66.8 1.0 CB A:ASP171 4.4 28.0 1.0 CG A:GLU114 4.4 55.1 1.0 N A:GLU173 4.4 35.5 1.0 HB2 A:ASP207 4.5 43.1 1.0 CB A:GLU173 4.6 36.4 1.0 C A:ASP171 4.6 26.5 1.0 HB2 A:ASP171 4.6 34.3 1.0 HB2 A:GLU114 4.8 34.7 1.0 HB3 A:ARG172 4.8 24.4 1.0 HB3 A:ASP207 4.9 43.1 1.0 CG A:ASN208 4.9 47.4 1.0 H A:ASP207 4.9 38.3 1.0

Calcium binding site 7 out of 30 in the Xenopus Protocadherin 8.1 EC1-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Xenopus Protocadherin 8.1 EC1-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca712 b:33.9 occ:1.00 OD2 A:ASP315 2.1 19.6 1.0 OD1 A:ASP279 2.2 36.8 1.0 O A:HOH846 2.3 38.4 1.0 OE1 A:GLU281 2.4 61.3 1.0 O A:HOH847 2.4 43.3 1.0 OE1 A:GLU223 2.4 27.2 1.0 CG A:ASP315 3.1 9.5 1.0 CG A:ASP279 3.3 9.3 1.0 CD A:GLU223 3.3 9.1 1.0 OD1 A:ASP315 3.4 53.5 1.0 H A:GLU281 3.6 12.3 1.0 HA A:ASP279 3.6 7.4 1.0 CD A:GLU281 3.6 14.4 1.0 OE2 A:GLU223 3.7 9.1 1.0 HD21 A:ASN316 3.8 30.4 1.0 H A:PHE280 3.8 19.5 1.0 HB2 A:GLU281 3.8 8.2 1.0 OD2 A:ASP279 3.9 39.7 1.0 CA A:CA713 4.1 18.1 1.0 CB A:ASP279 4.2 9.2 1.0 CA A:ASP279 4.2 9.1 1.0 N A:PHE280 4.2 15.7 1.0 HB2 A:ASP279 4.3 7.6 1.0 O A:HOH835 4.4 36.0 1.0 OE2 A:GLU281 4.4 24.1 1.0 CB A:ASP315 4.4 22.5 1.0 ND2 A:ASN316 4.4 24.8 1.0 N A:GLU281 4.4 9.7 1.0 HB2 A:ASP315 4.4 27.7 1.0 HD22 A:ASN316 4.4 30.4 1.0 C A:ASP279 4.5 11.9 1.0 HG3 A:GLU223 4.5 10.7 1.0 HB3 A:PHE280 4.5 37.4 1.0 CG A:GLU223 4.5 9.0 1.0 CG A:GLU281 4.5 12.7 1.0 CB A:GLU281 4.6 9.8 1.0 HB2 A:GLU223 4.6 8.5 1.0 HG2 A:GLU281 4.7 15.9 1.0 HB3 A:ASP315 4.8 27.7 1.0 O A:HOH871 4.8 30.7 1.0

Calcium binding site 8 out of 30 in the Xenopus Protocadherin 8.1 EC1-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Xenopus Protocadherin 8.1 EC1-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca713 b:18.1 occ:1.00 OE2 A:GLU281 2.1 24.1 1.0 OD1 A:ASP312 2.2 16.8 1.0 OD1 A:ASP315 2.2 53.5 1.0 O A:VAL313 2.3 26.7 1.0 OE2 A:GLU223 2.3 9.1 1.0 OD1 A:ASP354 2.3 33.8 1.0 CD A:GLU281 2.8 14.4 1.0 H A:VAL313 2.9 35.2 1.0 OE1 A:GLU281 3.0 61.3 1.0 H A:ASP315 3.2 31.5 1.0 CG A:ASP315 3.3 9.5 1.0 CG A:ASP312 3.3 36.1 1.0 CG A:ASP354 3.4 28.7 1.0 C A:VAL313 3.4 9.3 1.0 CD A:GLU223 3.4 9.1 1.0 HD22 A:ASN316 3.5 30.4 1.0 N A:VAL313 3.5 28.8 1.0 HA A:ASP354 3.6 31.7 1.0 HB3 A:ASP354 3.7 8.8 1.0 HB3 A:PHE280 3.7 37.4 1.0 OD2 A:ASP315 3.8 19.6 1.0 OE1 A:GLU223 3.9 27.2 1.0 CB A:ASP354 3.9 10.0 1.0 HA A:ASP312 4.0 12.9 1.0 OD2 A:ASP312 4.0 45.8 1.0 N A:ASP315 4.0 25.7 1.0 CA A:VAL313 4.1 9.2 1.0 CA A:CA712 4.1 33.9 1.0 CG A:GLU281 4.2 12.7 1.0 ND2 A:ASN316 4.2 24.8 1.0 HA A:ASN314 4.3 8.1 1.0 CA A:ASP354 4.3 25.8 1.0 HD2 A:PHE280 4.3 34.6 1.0 HD21 A:ASN316 4.3 30.4 1.0 HB A:VAL313 4.3 7.5 1.0 OD2 A:ASP354 4.3 18.6 1.0 C A:ASP312 4.4 9.1 1.0 HG2 A:GLU281 4.4 15.9 1.0 CB A:ASP312 4.4 19.8 1.0 CB A:ASP315 4.5 22.5 1.0 CA A:ASP312 4.5 10.2 1.0 HG3 A:GLU281 4.5 15.9 1.0 N A:ASN314 4.5 9.4 1.0 O A:HOH827 4.6 24.8 1.0 H A:GLU281 4.7 12.3 1.0 HB3 A:ASP315 4.7 27.7 1.0 CB A:PHE280 4.7 30.6 1.0 HG2 A:GLU223 4.7 10.7 1.0 CG A:GLU223 4.7 9.0 1.0 CA A:ASP315 4.7 15.0 1.0 CB A:VAL313 4.8 9.2 1.0 HB2 A:ASP312 4.8 24.4 1.0 CA A:ASN314 4.8 9.6 1.0 H A:SER355 4.8 10.5 1.0 H A:ASN316 4.9 15.0 1.0 CD2 A:PHE280 4.9 28.3 1.0 HB2 A:ASP354 4.9 8.8 1.0 HA A:VAL313 4.9 7.5 1.0 C A:ASN314 4.9 9.7 1.0

Calcium binding site 9 out of 30 in the Xenopus Protocadherin 8.1 EC1-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Xenopus Protocadherin 8.1 EC1-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca714 b:30.0 occ:1.00 O A:ASN358 2.3 32.1 1.0 OD1 A:ASN314 2.3 30.0 1.0 OD1 A:ASP352 2.3 32.4 1.0 OD2 A:ASP352 2.4 26.2 1.0 OD2 A:ASP405 2.4 31.6 1.0 O A:ASN316 2.5 33.1 1.0 OD2 A:ASP354 2.5 18.6 1.0 CG A:ASP352 2.7 39.0 1.0 HB2 A:ASP354 3.3 8.8 1.0 CG A:ASN314 3.4 24.7 1.0 C A:ASN358 3.4 10.4 1.0 CG A:ASP405 3.5 19.3 1.0 CG A:ASP354 3.5 28.7 1.0 C A:ASN316 3.6 10.3 1.0 HB3 A:ASP405 3.6 9.4 1.0 HB3 A:ASN358 3.7 8.4 1.0 HB2 A:ASP405 3.7 9.4 1.0 H A:ASN316 3.7 15.0 1.0 HD21 A:ASN314 3.7 60.1 1.0 HA2 A:GLY359 3.7 17.1 1.0 HD2 A:PHE411 3.8 23.0 1.0 CB A:ASP405 3.9 10.7 1.0 CB A:ASP354 4.0 10.0 1.0 HB2 A:ASN316 4.0 23.4 1.0 HA A:ALA317 4.0 9.3 1.0 ND2 A:ASN314 4.0 49.5 1.0 HA A:ASN314 4.1 8.1 1.0 H A:ASP354 4.1 20.6 1.0 HA A:ASN358 4.1 8.8 1.0 CB A:ASP352 4.2 25.6 1.0 HB2 A:PHE411 4.2 36.5 1.0 HD3 A:PRO318 4.2 9.7 1.0 CA A:ASN358 4.3 10.2 1.0 N A:GLY359 4.4 22.1 1.0 N A:ASN316 4.4 12.0 1.0 CA A:ASN316 4.4 10.1 1.0 CB A:ASN358 4.4 9.9 1.0 HB3 A:ASP352 4.4 31.4 1.0 CA A:GLY359 4.5 13.7 1.0 N A:ALA317 4.5 10.5 1.0 HB2 A:ASP352 4.5 31.4 1.0 HB3 A:ASP354 4.5 8.8 1.0 CB A:ASN316 4.6 19.0 1.0 CD2 A:PHE411 4.6 18.6 1.0 CA A:ALA317 4.6 10.7 1.0 OD1 A:ASP405 4.6 14.4 1.0 OD1 A:ASP354 4.6 33.8 1.0 CB A:ASN314 4.7 9.7 1.0 HB3 A:ASN316 4.7 23.4 1.0 CA A:ASN314 4.8 9.6 1.0 HD22 A:ASN314 4.9 60.1 1.0 N A:ASP354 4.9 16.6 1.0 HB2 A:ASN358 4.9 8.4 1.0 C A:ALA317 5.0 10.8 1.0

Calcium binding site 10 out of 30 in the Xenopus Protocadherin 8.1 EC1-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Xenopus Protocadherin 8.1 EC1-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca715 b:44.4 occ:1.00 OD1 A:ASP426 2.2 80.6 1.0 OE1 A:GLU337 2.4 56.6 1.0 OD1 A:ASP390 2.4 52.0 1.0 OE2 A:GLU392 2.6 33.2 1.0 CG A:ASP426 2.9 44.6 1.0 CG A:ASP390 3.2 51.8 1.0 HA A:ASP390 3.3 26.0 1.0 HB2 A:ASP426 3.3 67.9 1.0 CD A:GLU337 3.5 56.7 1.0 OD2 A:ASP426 3.6 68.2 1.0 CB A:ASP426 3.6 56.0 1.0 OD2 A:ASP390 3.8 60.2 1.0 CD A:GLU392 3.8 54.4 1.0 HB3 A:ASP426 3.9 67.9 1.0 H A:ARG391 4.0 37.5 1.0 H A:GLU392 4.0 80.3 1.0 CA A:ASP390 4.0 23.6 1.0 CB A:ASP390 4.1 67.9 1.0 OE2 A:GLU337 4.1 63.6 1.0 HB2 A:GLU392 4.1 56.2 1.0 O A:HOH824 4.2 33.7 1.0 HB2 A:GLU337 4.2 47.2 1.0 HD21 A:ASN427 4.2 0.1 1.0 HB2 A:ASP390 4.3 82.1 1.0 N A:ARG391 4.4 30.7 1.0 C A:ASP390 4.6 33.9 1.0 CG A:GLU337 4.6 49.3 1.0 OD1 A:ASN427 4.6 0.7 1.0 OE1 A:GLU392 4.6 58.0 1.0 HG3 A:GLU337 4.6 59.8 1.0 CA A:CA716 4.7 52.0 1.0 ND2 A:ASN427 4.8 84.5 1.0 CG A:GLU392 4.8 47.1 1.0 N A:GLU392 4.8 66.3 1.0 O A:LEU389 4.9 75.1 1.0 CB A:GLU337 4.9 38.8 1.0 CB A:GLU392 4.9 46.3 1.0 HG2 A:GLU392 4.9 57.2 1.0 HB3 A:ASP390 4.9 82.1 1.0 HB3 A:ARG391 5.0 46.9 1.0

O.J.Harrison, J.Brasch, P.S.Katsamba, G.Ahlsen, A.J.Noble, H.Dan, R.V.Sampogna, C.S.Potter, B.Carragher, B.Honig, L.Shapiro. Family-Wide Structural and Biophysical Analysis of Binding Interactions Among Non-Clustered Delta-Protocadherins. Cell Rep V. 30 2655 2020.
ISSN: ESSN 2211-1247
PubMed: 32101743
DOI: 10.1016/J.CELREP.2020.02.003