Calcium in PDB 5iu9: Crystal Structure of Zebrafish Protocadherin-19 EC1-4

The structure of Crystal Structure of Zebrafish Protocadherin-19 EC1-4, PDB code: 5iu9 was solved by S.R.Cooper, J.D.Jontes, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.390, 59.776, 165.925, 90.00, 94.39, 90.00
R / Rfree (%)	24.6 / 30.5

The structure of Crystal Structure of Zebrafish Protocadherin-19 EC1-4 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4 (pdb code 5iu9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4, PDB code: 5iu9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4


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 Zebrafish Protocadherin-19 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:67.4 occ:1.00 OE1 A:GLU11 2.3 92.5 1.0 OD1 A:ASP65 2.7 0.8 1.0 OD2 A:ASP101 2.8 89.7 1.0 OD2 A:ASP67 2.8 99.4 1.0 OE1 A:GLU10 2.9 94.3 1.0 OE2 A:GLU10 3.3 94.9 1.0 CD A:GLU10 3.4 94.1 1.0 CD A:GLU11 3.5 94.3 1.0 CG A:ASP65 3.5 0.4 1.0 CG A:ASP67 3.7 99.0 1.0 CG A:ASP101 3.7 92.6 1.0 OD1 A:ASN102 3.8 0.7 1.0 CA A:ASP65 3.8 98.4 1.0 OD1 A:ASP101 3.9 92.0 1.0 CB A:ASP67 4.0 0.3 1.0 CB A:ASP65 4.2 0.8 1.0 OE2 A:GLU11 4.2 94.7 1.0 OD2 A:ASP65 4.3 0.5 1.0 O A:ILE64 4.3 98.9 1.0 N A:ASP67 4.3 98.9 1.0 CG A:ASN102 4.3 0.3 1.0 ND2 A:ASN102 4.4 0.6 1.0 N A:ARG66 4.4 96.5 1.0 C A:ASP65 4.4 97.0 1.0 CA A:CA1002 4.4 99.0 1.0 CG A:GLU11 4.5 95.4 1.0 OD1 A:ASP67 4.6 97.2 1.0 CA A:ASP67 4.8 0.3 1.0 CB A:GLU11 4.8 94.8 1.0 CG A:GLU10 4.9 93.5 1.0 N A:ASP65 4.9 97.4 1.0

Calcium binding site 2 out of 18 in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4


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 Zebrafish Protocadherin-19 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:99.0 occ:1.00 OD1 A:ASP98 2.2 97.4 1.0 OE2 A:GLU10 2.2 94.9 1.0 OD1 A:ASP134 2.3 0.4 1.0 O A:VAL99 2.5 0.5 1.0 OD1 A:ASP67 2.5 97.2 1.0 OD1 A:ASP101 2.6 92.0 1.0 OD2 A:ASP67 2.6 99.4 1.0 CG A:ASP67 2.9 99.0 1.0 CD A:GLU10 3.2 94.1 1.0 CG A:ASP98 3.3 99.7 1.0 CG A:ASP134 3.4 1.0 1.0 N A:VAL99 3.5 0.0 1.0 C A:VAL99 3.5 0.8 1.0 CG A:ASP101 3.6 92.6 1.0 OE1 A:GLU10 3.9 94.3 1.0 OD2 A:ASP101 4.0 89.7 1.0 OD2 A:ASP98 4.0 0.4 1.0 CA A:VAL99 4.0 0.9 1.0 OD2 A:ASP134 4.1 0.9 1.0 CG A:GLU10 4.1 93.5 1.0 C A:ASP98 4.3 99.9 1.0 N A:ASP101 4.4 0.3 1.0 CA A:ASP98 4.4 98.4 1.0 CB A:ASP67 4.4 0.3 1.0 CA A:CA1001 4.4 67.4 1.0 CB A:ASP134 4.4 0.7 1.0 CB A:ASP98 4.4 99.6 1.0 CB A:VAL99 4.5 0.8 1.0 CA A:ASP134 4.6 0.3 1.0 N A:ASN100 4.7 0.1 1.0 CB A:ASP101 4.8 95.8 1.0 N A:ASP67 4.8 98.9 1.0 N A:ASN102 5.0 0.0 1.0

Calcium binding site 3 out of 18 in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4


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 Zebrafish Protocadherin-19 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:65.5 occ:1.00 OD2 A:ASP134 2.5 0.9 1.0 OD2 A:ASP189 2.5 100.0 1.0 O A:ASN102 2.6 95.3 1.0 OD1 A:ASP132 2.6 0.6 1.0 OD1 A:ASP189 3.0 98.4 1.0 O A:ASN138 3.1 0.1 1.0 OD1 A:ASN100 3.1 0.9 1.0 CG A:ASP189 3.1 99.7 1.0 OD2 A:ASP132 3.2 0.2 1.0 CG A:ASP132 3.3 0.5 1.0 CG A:ASP134 3.5 1.0 1.0 C A:ASN102 3.5 98.1 1.0 CB A:ASP134 3.8 0.7 1.0 CG A:ASN100 3.8 0.5 1.0 O A:ASN100 3.9 0.6 1.0 CA A:ALA103 4.0 96.8 1.0 N A:ALA103 4.1 98.9 1.0 C A:ASN100 4.1 0.6 1.0 CA A:ASN100 4.2 0.2 1.0 C A:ASN138 4.3 0.8 1.0 ND2 A:ASN100 4.4 0.4 1.0 N A:ASN102 4.4 0.0 1.0 CA A:ASN102 4.5 0.1 1.0 CB A:ASP189 4.6 0.7 1.0 OD1 A:ASP134 4.6 0.4 1.0 CB A:ASN100 4.6 0.9 1.0 CB A:ASP132 4.7 98.7 1.0 N A:ASP101 4.8 0.3 1.0 CD A:PRO104 4.8 92.1 1.0 C A:ALA103 4.8 93.0 1.0 CB A:ASN138 4.9 0.3 1.0

Calcium binding site 4 out of 18 in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4


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 Zebrafish Protocadherin-19 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:57.5 occ:1.00 OD2 A:ASP210 2.2 74.6 1.0 OE1 A:GLU117 2.4 72.0 1.0 OE1 A:GLU176 2.6 70.8 1.0 CG A:ASP210 3.0 72.6 1.0 O A:HOH1105 3.2 38.6 1.0 OD1 A:ASP210 3.3 72.8 1.0 OD1 A:ASP174 3.4 76.8 1.0 CD A:GLU117 3.4 70.1 1.0 CG A:ASP174 3.7 78.5 1.0 OD1 A:ASN118 3.7 84.0 1.0 CD A:GLU176 3.8 72.1 1.0 CA A:ASP174 3.9 75.7 1.0 N A:ARG175 3.9 72.6 1.0 OE2 A:GLU117 4.1 68.7 1.0 OD2 A:ASP174 4.2 80.5 1.0 CB A:ASP210 4.2 70.8 1.0 CB A:ASP174 4.2 78.0 1.0 CG A:GLU117 4.3 69.4 1.0 ND2 A:ASN118 4.4 84.8 1.0 CA A:CA1005 4.4 66.3 1.0 CG A:ASN118 4.4 82.2 1.0 C A:ASP174 4.4 74.8 1.0 OE2 A:GLU176 4.5 68.7 1.0 N A:GLU176 4.6 74.8 1.0 O A:LEU173 4.7 77.5 1.0 CG A:GLU176 4.8 76.4 1.0 CB A:GLU176 4.9 79.0 1.0 OD1 A:ASN211 4.9 66.2 1.0

Calcium binding site 5 out of 18 in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4


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 Zebrafish Protocadherin-19 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:66.3 occ:1.00 OE2 A:GLU176 2.2 68.7 1.0 OD1 A:ASP207 2.2 65.7 1.0 OD1 A:ASP243 2.3 63.0 1.0 OD1 A:ASP210 2.4 72.8 1.0 OE2 A:GLU117 2.4 68.7 1.0 O A:SER208 2.6 64.1 1.0 CD A:GLU176 3.0 72.1 1.0 OE1 A:GLU176 3.1 70.8 1.0 CD A:GLU117 3.3 70.1 1.0 CG A:ASP207 3.4 65.3 1.0 CG A:ASP243 3.5 61.7 1.0 OE1 A:GLU117 3.5 72.0 1.0 CG A:ASP210 3.6 72.6 1.0 C A:SER208 3.8 64.0 1.0 N A:SER208 4.0 64.8 1.0 OD2 A:ASP207 4.0 65.2 1.0 OD1 A:ASN211 4.0 66.2 1.0 N A:ASP210 4.1 66.5 1.0 CB A:ASP243 4.2 61.3 1.0 CA A:ASP243 4.2 61.5 1.0 OD2 A:ASP210 4.3 74.6 1.0 NH1 A:ARG175 4.4 74.3 1.0 CA A:CA1004 4.4 57.5 1.0 CA A:ASP207 4.4 64.8 1.0 OD2 A:ASP243 4.4 61.0 1.0 CB A:ASP207 4.5 65.1 1.0 CG A:GLU176 4.5 76.4 1.0 CA A:SER208 4.5 64.3 1.0 CB A:ARG175 4.5 71.3 1.0 CD A:ARG175 4.5 70.4 1.0 C A:ASP207 4.6 64.6 1.0 CB A:ASP210 4.6 70.8 1.0 CG A:GLU117 4.7 69.4 1.0 N A:ASN209 4.8 63.5 1.0 CA A:ASP210 4.9 69.3 1.0 CA A:ASN209 4.9 64.2 1.0

Calcium binding site 6 out of 18 in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4


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 Zebrafish Protocadherin-19 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:38.3 occ:1.00 OD2 A:ASP241 2.3 66.0 1.0 O A:ASN211 2.5 62.7 1.0 O A:ASN247 2.5 49.4 1.0 OD1 A:ASN209 2.6 67.6 1.0 OD1 A:ASP241 2.6 68.4 1.0 OD2 A:ASP243 2.7 61.0 1.0 CG A:ASP241 2.8 66.7 1.0 CG A:ASP297 3.3 57.7 1.0 OD1 A:ASP297 3.3 55.8 1.0 C A:ASN211 3.5 61.8 1.0 CB A:ASP297 3.6 58.2 1.0 CG A:ASP243 3.6 61.7 1.0 C A:ASN247 3.7 50.9 1.0 OD2 A:ASP297 3.7 58.8 1.0 CG A:ASN209 3.8 66.0 1.0 CB A:ASP243 3.8 61.3 1.0 CA A:ASN212 4.1 59.3 1.0 CB A:ASP241 4.2 66.2 1.0 N A:ASN212 4.2 60.9 1.0 CA A:GLY248 4.4 51.9 1.0 ND2 A:ASN209 4.4 66.5 1.0 CA A:ASN211 4.4 62.6 1.0 N A:ASN211 4.5 62.5 1.0 N A:GLY248 4.5 51.9 1.0 CD A:PRO213 4.6 54.8 1.0 O A:ASN209 4.6 64.7 1.0 CB A:ASN211 4.7 63.0 1.0 C A:ASN209 4.7 65.1 1.0 CA A:ASN247 4.7 52.3 1.0 OD1 A:ASP243 4.7 63.0 1.0 C A:ASN212 4.8 57.7 1.0 CA A:ASN209 4.9 64.2 1.0 CB A:ASN209 4.9 64.4 1.0 N A:PRO213 5.0 55.4 1.0 OD1 A:ASN212 5.0 62.5 1.0

Calcium binding site 7 out of 18 in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4


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 Zebrafish Protocadherin-19 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1007 b:53.9 occ:1.00 OD2 A:ASP318 2.4 66.8 1.0 OE1 A:GLU284 2.8 84.3 1.0 OD1 A:ASP282 2.9 69.9 1.0 OE1 A:GLU226 3.0 61.1 1.0 OD1 A:ASP318 3.0 66.0 1.0 CG A:ASP318 3.1 67.2 1.0 OD1 A:ASN319 3.2 76.9 1.0 OD2 A:ASP282 3.4 70.5 1.0 CG A:ASP282 3.5 70.2 1.0 OE2 A:GLU226 3.7 61.1 1.0 CD A:GLU226 3.7 61.0 1.0 CD A:GLU284 3.7 85.2 1.0 CB A:GLU284 3.9 85.2 1.0 CG A:ASN319 4.0 77.5 1.0 CG A:GLU284 4.1 86.1 1.0 CA A:CA1008 4.1 49.0 1.0 ND2 A:ASN319 4.2 79.4 1.0 ND2 A:ASN227 4.3 63.1 1.0 CB A:ASP318 4.5 68.9 1.0 N A:GLU284 4.6 79.2 1.0 O A:ASP318 4.7 69.8 1.0 OE2 A:GLU284 4.8 85.8 1.0 OD1 A:ASP354 4.8 76.6 1.0 CA A:GLU284 4.8 82.4 1.0 CB A:ASP282 4.9 70.4 1.0

Calcium binding site 8 out of 18 in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4


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 Zebrafish Protocadherin-19 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1008 b:49.0 occ:1.00 OE2 A:GLU226 2.2 61.1 1.0 O A:ILE316 2.3 70.3 1.0 OD1 A:ASP318 2.3 66.0 1.0 OD1 A:ASP315 2.4 60.2 1.0 OD1 A:ASP354 2.5 76.6 1.0 OE1 A:GLU284 2.9 84.3 1.0 OE2 A:GLU284 3.0 85.8 1.0 CD A:GLU284 3.2 85.2 1.0 CD A:GLU226 3.3 61.0 1.0 CG A:ASP318 3.4 67.2 1.0 C A:ILE316 3.5 70.0 1.0 CG A:ASP354 3.5 76.1 1.0 CG A:ASP315 3.6 61.6 1.0 N A:ILE316 3.7 64.8 1.0 N A:ASP318 3.9 70.4 1.0 OE1 A:GLU226 4.1 61.1 1.0 OD2 A:ASP318 4.1 66.8 1.0 CA A:CA1007 4.1 53.9 1.0 CB A:ASP354 4.2 76.4 1.0 CA A:ILE316 4.2 68.7 1.0 OD1 A:ASN319 4.2 76.9 1.0 CG A:GLU226 4.3 60.5 1.0 CA A:ASP315 4.3 60.8 1.0 OD2 A:ASP354 4.3 75.5 1.0 C A:ASP315 4.4 62.6 1.0 CB A:ASP318 4.4 68.9 1.0 OD2 A:ASP315 4.4 62.9 1.0 N A:ASN317 4.5 71.7 1.0 CB A:ASP315 4.5 61.7 1.0 CG A:GLU284 4.6 86.1 1.0 CA A:ASP354 4.6 77.1 1.0 CG1 A:ILE316 4.6 71.2 1.0 CA A:ASP318 4.6 69.9 1.0 CB A:HIS283 4.7 70.5 1.0 CA A:ASN317 4.7 72.0 1.0 C A:ASN317 4.8 72.0 1.0

Calcium binding site 9 out of 18 in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4


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 Zebrafish Protocadherin-19 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1009 b:47.3 occ:1.00 O A:ASN319 2.4 70.8 1.0 OD2 A:ASP352 2.5 74.9 1.0 OD2 A:ASP354 2.5 75.5 1.0 OD2 A:ASP404 2.6 66.0 1.0 OD1 A:ASN317 2.6 74.5 1.0 OD1 A:ASP352 2.6 75.9 1.0 O A:ASN358 2.9 77.4 1.0 CG A:ASP352 2.9 76.2 1.0 CG A:ASP354 3.4 76.1 1.0 CG A:ASP404 3.5 65.6 1.0 C A:ASN319 3.5 72.4 1.0 CB A:ASP354 3.8 76.4 1.0 CG A:ASN317 3.8 75.1 1.0 O A:ALA320 4.0 72.9 1.0 C A:ASN358 4.0 78.0 1.0 CB A:ASP404 4.0 66.2 1.0 CA A:GLY359 4.2 79.8 1.0 C A:ALA320 4.3 71.9 1.0 CA A:ASN319 4.4 74.8 1.0 ND2 A:ASN317 4.4 77.3 1.0 OD1 A:ASP404 4.4 65.1 1.0 CB A:ASP352 4.4 78.0 1.0 N A:ASN319 4.4 74.8 1.0 CB A:ASN319 4.5 76.1 1.0 N A:ALA320 4.5 72.0 1.0 N A:GLY359 4.5 78.6 1.0 OD1 A:ASP354 4.6 76.6 1.0 CA A:ALA320 4.6 71.6 1.0 N A:ASP354 4.6 78.1 1.0 CD1 A:LEU410 4.7 73.6 1.0 N A:PRO321 4.8 72.2 1.0 CA A:ASP354 4.8 77.1 1.0 CB A:ASN317 5.0 74.0 1.0 CA A:ASN317 5.0 72.0 1.0

Calcium binding site 10 out of 18 in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4


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 Zebrafish Protocadherin-19 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:48.0 occ:1.00 OE1 B:GLU10 2.2 70.0 1.0 OD1 B:ASP65 2.3 78.8 1.0 OE1 B:GLU11 2.8 81.3 1.0 CD B:GLU10 3.0 69.5 1.0 CG B:ASP65 3.1 82.0 1.0 OE2 B:GLU10 3.1 69.2 1.0 OD2 B:ASP101 3.2 71.4 1.0 OD1 B:ASP101 3.3 70.8 1.0 OD2 B:ASP67 3.4 67.0 1.0 CA B:ASP65 3.6 77.6 1.0 CG B:ASP101 3.6 71.3 1.0 CG B:ASP67 3.7 69.6 1.0 OD2 B:ASP65 3.7 85.5 1.0 N B:ARG66 3.9 73.6 1.0 CB B:ASP65 3.9 81.5 1.0 CA B:CA1002 3.9 60.2 1.0 N B:ASP67 4.0 75.1 1.0 C B:ASP65 4.0 76.1 1.0 CB B:ASP67 4.0 74.9 1.0 CD B:GLU11 4.1 81.7 1.0 OD1 B:ASP67 4.3 66.0 1.0 O B:ILE64 4.3 77.5 1.0 ND2 B:ASN102 4.4 78.5 1.0 CG B:GLU10 4.5 68.9 1.0 CA B:ASP67 4.6 77.1 1.0 N B:ASP65 4.8 78.6 1.0 OE2 B:GLU11 4.8 83.7 1.0 CA B:ARG66 4.9 73.3 1.0 O B:ASP65 4.9 77.2 1.0 C B:ARG66 4.9 74.7 1.0 CG B:GLU11 5.0 79.7 1.0

S.R.Cooper, J.D.Jontes, M.Sotomayor. Structural Determinants of Adhesion By Protocadherin-19 and Implications For Its Role in Epilepsy. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27787195
DOI: 10.7554/ELIFE.18529