Calcium in PDB 5dzy: Protocadherin Beta 8 Extracellular Cadherin Domains 1-4

The structure of Protocadherin Beta 8 Extracellular Cadherin Domains 1-4, PDB code: 5dzy was solved by K.M.Goodman, F.Bahna, S.Mannepalli, B.Honig, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.99 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.140, 137.070, 326.190, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 28.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 54;

Binding sites:

The binding sites of Calcium atom in the Protocadherin Beta 8 Extracellular Cadherin Domains 1-4 (pdb code 5dzy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 54 binding sites of Calcium where determined in the Protocadherin Beta 8 Extracellular Cadherin Domains 1-4, PDB code: 5dzy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 54 in the Protocadherin Beta 8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Protocadherin Beta 8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:92.8 occ:1.00 OE2 A:GLU65 2.4 0.4 1.0 OD1 A:ASP100 2.5 0.1 1.0 OD1 A:ASP97 2.6 0.1 1.0 O A:ILE98 2.6 0.8 1.0 OD1 A:ASP133 2.8 0.9 1.0 OE1 A:GLU9 2.8 0.2 1.0 CD A:GLU65 3.1 0.2 1.0 OE1 A:GLU65 3.2 0.1 1.0 CG A:ASP97 3.3 0.7 1.0 OD2 A:ASP97 3.5 1.0 1.0 CG A:ASP100 3.7 0.8 1.0 CG A:ASP133 3.7 0.9 1.0 CD A:GLU9 3.7 0.3 1.0 C A:ILE98 3.8 0.6 1.0 OE2 A:GLU9 3.9 0.9 1.0 N A:ILE98 4.0 97.5 1.0 CD2 A:HIS101 4.0 0.9 1.0 CA A:CA509 4.1 1.0 1.0 OD2 A:ASP100 4.1 0.1 1.0 N A:ASP100 4.3 0.4 1.0 CB A:ASP133 4.4 0.4 1.0 CA A:ASP133 4.4 0.2 1.0 CG A:GLU65 4.4 0.9 1.0 CA A:ILE98 4.5 96.9 1.0 CG1 A:ILE98 4.5 0.8 1.0 CB A:ASP97 4.6 0.1 1.0 OD2 A:ASP133 4.6 0.3 1.0 NH1 A:ARG64 4.7 0.3 1.0 C A:ASP97 4.8 0.0 1.0 N A:ASN99 4.8 0.9 1.0 NE2 A:HIS101 4.8 0.1 1.0 CA A:ASP97 4.8 0.9 1.0 CB A:ASP100 4.9 0.0 1.0 CG A:HIS101 5.0 0.6 1.0 CA A:ASN99 5.0 0.3 1.0

Calcium binding site 2 out of 54 in the Protocadherin Beta 8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Protocadherin Beta 8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca509 b:1.0 occ:1.00 OD2 A:ASP100 2.2 0.1 1.0 OD1 A:ASP63 2.5 0.0 1.0 OE1 A:GLU65 2.7 0.1 1.0 CG A:ASP100 2.9 0.8 1.0 OE2 A:GLU9 2.9 0.9 1.0 NE2 A:HIS101 3.0 0.1 1.0 OD1 A:ASP100 3.1 0.1 1.0 CD2 A:HIS101 3.2 0.9 1.0 CG A:ASP63 3.5 0.0 1.0 OE2 A:GLU10 3.6 0.7 1.0 CD A:GLU65 3.8 0.2 1.0 CD A:GLU9 3.9 0.3 1.0 OD2 A:ASP63 4.0 0.5 1.0 CA A:CA508 4.1 92.8 1.0 CE1 A:HIS101 4.2 0.7 1.0 CB A:ASP100 4.2 0.0 1.0 OE1 A:GLU9 4.2 0.2 1.0 CG A:GLU10 4.4 0.0 1.0 CD A:GLU10 4.5 0.2 1.0 OE2 A:GLU65 4.5 0.4 1.0 CG A:HIS101 4.5 0.6 1.0 O A:ASP100 4.6 0.8 1.0 CG A:GLU65 4.7 0.9 1.0 CB A:ASP63 4.8 1.0 1.0 C A:ASP100 4.9 0.4 1.0 ND1 A:HIS101 4.9 0.3 1.0 CB A:GLU65 5.0 0.1 1.0

Calcium binding site 3 out of 54 in the Protocadherin Beta 8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Protocadherin Beta 8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca510 b:0.7 occ:1.00 OD2 A:ASP131 2.2 0.6 1.0 OD2 A:ASP188 2.3 0.6 1.0 OD2 A:ASP133 2.3 0.3 1.0 O A:HIS101 2.5 0.8 1.0 OD1 A:ASN99 2.5 0.8 1.0 O A:ASN137 2.7 0.8 1.0 CG A:ASP131 2.9 0.2 1.0 OD1 A:ASP131 2.9 0.7 1.0 CG A:ASP133 3.5 0.9 1.0 CG A:ASP188 3.5 0.3 1.0 C A:HIS101 3.6 0.4 1.0 CG A:ASN99 3.6 0.3 1.0 C A:ASN137 3.9 1.0 1.0 CB A:ASP133 4.2 0.4 1.0 ND2 A:ASN99 4.3 0.4 1.0 CA A:HIS101 4.3 0.3 1.0 CB A:HIS101 4.3 0.1 1.0 OD1 A:ASP188 4.3 0.1 1.0 CB A:ASP131 4.4 0.9 1.0 N A:HIS101 4.4 0.6 1.0 OD1 A:ASP133 4.4 0.9 1.0 CB A:ASP188 4.4 0.1 1.0 CD A:PRO103 4.5 0.1 1.0 N A:PHE102 4.7 0.5 1.0 CA A:ALA138 4.7 0.6 1.0 CB A:LYS194 4.7 0.5 1.0 N A:ALA138 4.8 0.1 1.0 CB A:ASN99 4.8 0.1 1.0 CG A:PRO103 4.8 0.1 1.0 CA A:ASN137 4.8 0.1 1.0 CA A:ASN99 4.9 0.3 1.0 CA A:PHE102 4.9 0.5 1.0 N A:PRO103 4.9 0.4 1.0

Calcium binding site 4 out of 54 in the Protocadherin Beta 8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Protocadherin Beta 8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca511 b:83.4 occ:1.00 OE2 A:GLU116 2.2 91.0 1.0 OD2 A:ASP209 2.3 64.9 1.0 OD1 A:ASP173 2.5 96.7 1.0 OE1 A:GLU175 2.5 79.6 1.0 CG A:ASP209 3.0 82.8 1.0 OD1 A:ASP209 3.1 86.5 1.0 CD A:GLU116 3.3 99.3 1.0 CD A:GLU175 3.4 80.9 1.0 ND2 A:ASN210 3.4 97.5 1.0 CG A:ASP173 3.5 98.0 1.0 CA A:CA512 3.8 53.2 1.0 OE1 A:GLU116 3.9 95.0 1.0 OD2 A:ASP173 3.9 98.8 1.0 CG A:GLU175 4.1 0.6 1.0 OE2 A:GLU175 4.2 70.0 1.0 CB A:GLU175 4.4 96.3 1.0 CB A:ASP209 4.4 88.2 1.0 CG A:ASN210 4.5 74.2 1.0 CG A:GLU116 4.5 100.0 1.0 CB A:ASP173 4.6 0.6 1.0 OD1 A:ASN210 4.8 68.0 1.0 CA A:ASP173 4.9 0.9 1.0 N A:GLU175 4.9 88.7 1.0

Calcium binding site 5 out of 54 in the Protocadherin Beta 8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Protocadherin Beta 8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca512 b:53.2 occ:1.00 OE2 A:GLU175 2.3 70.0 1.0 O A:ILE207 2.4 83.3 1.0 OE1 A:GLU116 2.4 95.0 1.0 OD1 A:ASP209 2.4 86.5 1.0 OD1 A:ASP242 2.5 91.9 1.0 CD A:GLU175 2.9 80.9 1.0 OE1 A:GLU175 2.9 79.6 1.0 OD1 A:ASP206 3.0 64.7 1.0 CD A:GLU116 3.3 99.3 1.0 OE2 A:GLU116 3.4 91.0 1.0 CG A:ASP209 3.4 82.8 1.0 CG A:ASP242 3.5 76.7 1.0 C A:ILE207 3.6 85.2 1.0 ND2 A:ASN210 3.7 97.5 1.0 CA A:CA511 3.8 83.4 1.0 OD2 A:ASP209 3.8 64.9 1.0 N A:ILE207 3.9 70.2 1.0 OD2 A:ASP242 4.1 85.0 1.0 N A:ASP209 4.2 64.4 1.0 CG A:ASP206 4.2 92.5 1.0 CA A:ILE207 4.3 79.6 1.0 CG A:GLU175 4.3 0.6 1.0 CB A:ASP242 4.5 56.1 1.0 N A:ASN208 4.6 82.0 1.0 CB A:ASP209 4.6 88.2 1.0 NE A:ARG174 4.7 90.1 1.0 CG A:GLU116 4.7 100.0 1.0 CA A:ASN208 4.8 76.0 1.0 CA A:ASP242 4.8 58.0 1.0 NH1 A:ARG174 4.8 70.2 1.0 C A:ASP206 4.9 70.8 1.0 CB A:ILE207 4.9 69.5 1.0 CA A:ASP209 4.9 70.2 1.0 OD2 A:ASP206 4.9 99.2 1.0 CG A:ASN210 5.0 74.2 1.0 CA A:ASP206 5.0 83.5 1.0 CB A:ARG174 5.0 65.7 1.0

Calcium binding site 6 out of 54 in the Protocadherin Beta 8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Protocadherin Beta 8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca513 b:75.3 occ:1.00 OD2 A:ASP240 2.1 81.2 1.0 OD1 A:ASN208 2.4 86.0 1.0 O A:ASN210 2.6 59.3 1.0 O A:HIS246 2.6 57.5 1.0 OD2 A:ASP294 2.9 78.1 1.0 CG A:ASP240 2.9 86.6 1.0 OD1 A:ASP240 2.9 83.5 1.0 OD2 A:ASP242 3.0 85.0 1.0 CG A:ASN208 3.2 88.0 1.0 ND2 A:ASN208 3.7 90.1 1.0 C A:ASN210 3.7 72.7 1.0 C A:HIS246 3.8 71.7 1.0 CG A:ASP294 3.8 85.3 1.0 CG A:ASP242 3.9 76.7 1.0 CB A:ASP242 4.0 56.1 1.0 CB A:ASP294 4.0 87.4 1.0 CB A:ASP240 4.3 84.4 1.0 CB A:ASN208 4.4 84.2 1.0 CA A:GLY247 4.5 87.5 1.0 CD A:PRO212 4.6 40.9 1.0 CA A:ASN210 4.6 71.1 1.0 N A:GLY247 4.6 83.0 1.0 N A:ASN210 4.6 61.5 1.0 N A:ALA211 4.7 77.1 1.0 CA A:ASN208 4.7 76.0 1.0 CB A:ASN210 4.8 62.5 1.0 CA A:ALA211 4.8 59.2 1.0 CA A:HIS246 4.8 71.0 1.0 CD1 A:LEU298 4.9 78.2 1.0 N A:PRO212 4.9 46.7 1.0 N A:ASP242 4.9 65.4 1.0 OD1 A:ASP294 5.0 89.0 1.0 OD1 A:ASP242 5.0 91.9 1.0 CB A:HIS246 5.0 69.0 1.0

Calcium binding site 7 out of 54 in the Protocadherin Beta 8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Protocadherin Beta 8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca514 b:52.4 occ:1.00 OE2 A:GLU225 2.2 0.8 1.0 OD2 A:ASP313 2.4 81.3 1.0 OE1 A:GLU281 2.5 68.5 1.0 OD1 A:ASP279 2.5 0.2 1.0 OD1 A:ASP313 2.7 77.3 1.0 CG A:ASP313 2.9 79.2 1.0 CD A:GLU225 3.2 0.0 1.0 CG A:ASP279 3.4 0.3 1.0 OD1 A:ASN314 3.4 0.2 1.0 CA A:CA515 3.5 54.1 1.0 CD A:GLU281 3.6 69.5 1.0 OE1 A:GLU225 3.6 0.6 1.0 OD2 A:ASP279 3.8 0.8 1.0 CG A:ASN314 4.3 82.8 1.0 OE2 A:GLU281 4.3 69.6 1.0 CB A:ASP313 4.4 80.3 1.0 CG A:GLU281 4.5 97.2 1.0 CB A:ASP279 4.5 92.5 1.0 CG A:GLU225 4.5 0.9 1.0 ND2 A:ASN314 4.7 78.3 1.0 CB A:GLU281 4.7 69.4 1.0 CA A:ASP279 4.7 85.4 1.0 N A:PHE280 4.8 60.8 1.0 O A:VAL311 4.9 88.7 1.0 N A:GLU281 4.9 97.0 1.0 OD1 A:ASP345 5.0 0.8 1.0

Calcium binding site 8 out of 54 in the Protocadherin Beta 8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Protocadherin Beta 8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca515 b:54.1 occ:1.00 OE2 A:GLU281 2.2 69.6 1.0 O A:VAL311 2.5 88.7 1.0 OD1 A:ASP313 2.6 77.3 1.0 OD1 A:ASP310 2.7 68.7 1.0 CD A:GLU281 2.7 69.5 1.0 OE1 A:GLU281 2.7 68.5 1.0 OD1 A:ASP345 2.8 0.8 1.0 OE1 A:GLU225 3.1 0.6 1.0 CA A:CA514 3.5 52.4 1.0 C A:VAL311 3.6 86.4 1.0 CG A:ASP313 3.7 79.2 1.0 CG A:ASP345 3.7 0.1 1.0 N A:VAL311 3.8 83.0 1.0 CG A:ASP310 3.9 94.0 1.0 CD A:GLU225 3.9 0.0 1.0 OE2 A:GLU225 4.0 0.8 1.0 OD1 A:ASN314 4.0 0.2 1.0 CG A:GLU281 4.1 97.2 1.0 N A:ASP313 4.1 81.3 1.0 OD2 A:ASP313 4.3 81.3 1.0 CA A:VAL311 4.3 85.0 1.0 OD2 A:ASP345 4.4 0.1 1.0 CB A:ASP345 4.5 0.3 1.0 N A:ASN312 4.5 0.9 1.0 OD2 A:ASP310 4.6 96.7 1.0 CA A:ASN312 4.7 99.4 1.0 CB A:PHE280 4.7 61.5 1.0 CA A:ASP345 4.7 0.1 1.0 C A:ASP310 4.8 75.1 1.0 CB A:ASP313 4.8 80.3 1.0 CA A:ASP310 4.9 73.4 1.0 CA A:ASP313 4.9 90.4 1.0 C A:ASN312 5.0 85.0 1.0 CB A:VAL311 5.0 68.7 1.0 CG A:ASN314 5.0 82.8 1.0 CB A:ASP310 5.0 88.0 1.0

Calcium binding site 9 out of 54 in the Protocadherin Beta 8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Protocadherin Beta 8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca516 b:62.4 occ:1.00 OD2 A:ASP345 2.5 0.1 1.0 O A:ASN349 2.5 79.4 1.0 O A:ASN314 2.6 83.0 1.0 OD1 A:ASN312 2.8 0.3 1.0 OD2 A:ASP343 2.8 0.2 1.0 OD2 A:ASP396 3.0 0.6 1.0 OD1 A:ASP343 3.2 84.0 1.0 CG A:ASP343 3.4 88.5 1.0 CG A:ASP345 3.5 0.1 1.0 C A:ASN349 3.6 90.1 1.0 C A:ASN314 3.8 89.7 1.0 CG A:ASP396 3.9 0.0 1.0 CG A:ASN312 3.9 0.8 1.0 CB A:ASP345 3.9 0.3 1.0 CB A:ASP396 4.0 99.0 1.0 CA A:ASN349 4.3 98.7 1.0 ND2 A:ASN312 4.5 0.9 1.0 CB A:ASN349 4.5 0.1 1.0 CA A:ASN314 4.5 86.1 1.0 CB A:ASN314 4.6 79.5 1.0 OD1 A:ASP345 4.6 0.8 1.0 N A:ASN314 4.6 75.3 1.0 N A:GLY350 4.7 0.9 1.0 CD1 A:LEU402 4.7 77.8 1.0 N A:ALA315 4.8 84.6 1.0 CD A:PRO316 4.8 85.5 1.0 CB A:ASP343 4.9 95.4 1.0 CA A:ALA315 4.9 88.2 1.0 CA A:GLY350 4.9 0.6 1.0

Calcium binding site 10 out of 54 in the Protocadherin Beta 8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Protocadherin Beta 8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca514 b:58.1 occ:1.00 OD2 B:ASP100 2.3 0.5 1.0 OE2 B:GLU9 2.4 82.4 1.0 OE1 B:GLU65 2.5 79.2 1.0 OD1 B:ASP63 2.6 0.6 1.0 OE2 B:GLU10 2.9 0.2 1.0 CG B:ASP100 3.2 0.3 1.0 CD B:GLU9 3.3 90.6 1.0 OD1 B:ASP100 3.4 0.8 1.0 OE1 B:GLU9 3.6 95.4 1.0 CG B:ASP63 3.6 0.1 1.0 CE1 B:HIS101 3.6 95.6 1.0 CD B:GLU65 3.6 82.2 1.0 CA B:CA515 3.9 60.2 1.0 CD B:GLU10 3.9 1.0 1.0 OD2 B:ASP63 4.1 0.9 1.0 CG B:GLU10 4.1 91.2 1.0 ND1 B:HIS101 4.2 80.1 1.0 OE2 B:GLU65 4.3 71.4 1.0 NE2 B:HIS101 4.5 75.5 1.0 CG B:GLU9 4.5 99.4 1.0 CB B:ASP100 4.6 0.0 1.0 CG B:GLU65 4.6 0.8 1.0 CB B:ASP63 4.6 0.7 1.0 CB B:GLU65 4.8 0.8 1.0 CA B:ASP63 4.8 97.5 1.0 N B:ARG64 4.8 80.0 1.0 N B:GLU65 4.9 91.0 1.0

K.M.Goodman, R.Rubinstein, C.A.Thu, F.Bahna, S.Mannepalli, G.Ahlsen, C.Rittenhouse, T.Maniatis, B.Honig, L.Shapiro. Structural Basis of Diverse Homophilic Recognition By Clustered Alpha- and Beta-Protocadherins. Neuron V. 90 709 2016.
ISSN: ISSN 0896-6273
PubMed: 27161523
DOI: 10.1016/J.NEURON.2016.04.004