Calcium in PDB 5dzw: Protocadherin Alpha 4 Extracellular Cadherin Domains 1-4

The structure of Protocadherin Alpha 4 Extracellular Cadherin Domains 1-4, PDB code: 5dzw 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)	29.57 / 2.43
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.480, 56.310, 173.670, 90.00, 99.05, 90.00
R / Rfree (%)	26.6 / 29.3

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

Calcium binding site 1 out of 9 in the Protocadherin Alpha 4 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 Alpha 4 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:19.8 occ:1.00 OD2 A:ASP96 2.4 41.7 1.0 OE2 A:GLU8 2.4 47.7 1.0 OE2 A:GLU64 2.4 29.8 1.0 O A:ILE97 2.6 23.0 1.0 OD1 A:ASP99 3.0 59.2 1.0 CD A:GLU64 3.0 30.5 1.0 OD1 A:ASP132 3.2 59.3 1.0 CG A:ASP132 3.2 64.2 1.0 OD2 A:ASP132 3.4 64.2 1.0 CA A:CA506 3.4 40.6 1.0 OE1 A:GLU64 3.4 38.1 1.0 CG A:ASP96 3.5 39.0 1.0 CD A:GLU8 3.5 47.4 1.0 C A:ILE97 3.6 37.5 1.0 N A:ILE97 3.8 41.8 1.0 CG A:GLU64 4.0 33.9 1.0 OE1 A:GLU8 4.0 46.4 1.0 CB A:ASP132 4.0 59.4 1.0 OD1 A:ASP96 4.1 38.5 1.0 CG A:ASP99 4.1 66.1 1.0 CA A:ILE97 4.2 44.5 1.0 NH2 A:ARG63 4.4 51.3 1.0 CA A:ASP132 4.4 59.3 1.0 N A:ASP99 4.4 65.7 1.0 N A:ASN98 4.6 71.3 1.0 C A:ASP96 4.7 37.3 1.0 CB A:ASP96 4.7 36.7 1.0 CA A:ASP96 4.7 35.8 1.0 OD2 A:ASP99 4.7 64.3 1.0 CG A:GLU8 4.8 45.1 1.0 CA A:ASN98 4.9 69.8 1.0 CB A:ILE97 4.9 52.8 1.0 CD A:ARG63 4.9 38.9 1.0 ND2 A:ASN100 5.0 59.1 1.0

Calcium binding site 2 out of 9 in the Protocadherin Alpha 4 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 Alpha 4 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:40.6 occ:1.00 OE2 A:GLU64 2.5 29.8 1.0 OE1 A:GLU64 2.5 38.1 1.0 OD2 A:ASP99 2.5 64.3 1.0 OE1 A:GLU8 2.6 46.4 1.0 OD1 A:ASP99 2.7 59.2 1.0 CD A:GLU64 2.8 30.5 1.0 CG A:ASP99 2.9 66.1 1.0 OE2 A:GLU9 3.1 36.6 1.0 OE2 A:GLU8 3.1 47.7 1.0 CD A:GLU8 3.1 47.4 1.0 OD1 A:ASP62 3.2 40.9 1.0 CA A:CA505 3.4 19.8 1.0 CG A:GLU9 3.8 29.1 1.0 CD A:GLU9 3.9 33.4 1.0 CG A:ASP62 4.1 40.0 1.0 CG A:GLU64 4.3 33.9 1.0 CB A:ASP99 4.5 67.3 1.0 ND2 A:ASN100 4.5 59.1 1.0 CG A:GLU8 4.5 45.1 1.0 N A:ARG63 4.5 20.7 1.0 O A:ILE97 4.5 23.0 1.0 OD2 A:ASP62 4.6 38.5 1.0 N A:GLU64 4.8 33.6 1.0 CB A:GLU64 4.9 34.5 1.0 CA A:ASP62 5.0 38.4 1.0 CG A:ASN100 5.0 59.2 1.0

Calcium binding site 3 out of 9 in the Protocadherin Alpha 4 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 Alpha 4 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:42.0 occ:1.00 O A:ASN100 2.5 61.7 1.0 OD1 A:ASN98 2.5 83.7 1.0 OD2 A:ASP130 2.5 64.5 1.0 O A:ASN136 2.7 59.6 1.0 OD2 A:ASP132 3.0 64.2 1.0 OD1 A:ASP130 3.1 59.4 1.0 CG A:ASP130 3.2 63.9 1.0 CG A:ASP132 3.2 64.2 1.0 CB A:ASP132 3.4 59.4 1.0 OD2 A:ASP187 3.6 59.7 1.0 CG A:ASN98 3.7 80.5 1.0 C A:ASN100 3.7 62.0 1.0 C A:ASN136 3.7 64.3 1.0 OD1 A:ASP132 4.0 59.3 1.0 CB A:ASN136 4.1 76.7 1.0 CG A:ASP187 4.4 61.9 1.0 CB A:ASP187 4.4 66.0 1.0 CA A:ASN136 4.4 71.0 1.0 ND2 A:ASN98 4.4 83.1 1.0 N A:ASN100 4.4 60.9 1.0 CA A:ASN100 4.5 61.7 1.0 CB A:ASN100 4.6 62.7 1.0 CA A:ASP132 4.6 59.3 1.0 N A:ASP132 4.6 63.9 1.0 CB A:ASP130 4.6 59.5 1.0 CA A:ASN98 4.7 69.8 1.0 N A:ALA137 4.7 62.9 1.0 N A:PRO101 4.7 61.9 1.0 CB A:ASN98 4.7 75.5 1.0 CA A:ALA137 4.9 62.5 1.0 CA A:PRO101 4.9 59.4 1.0

Calcium binding site 4 out of 9 in the Protocadherin Alpha 4 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 Alpha 4 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:21.4 occ:1.00 O A:ALA206 2.4 63.7 1.0 OD1 A:ASP205 2.5 79.4 1.0 OE2 A:GLU174 2.5 63.6 1.0 OD1 A:ASP241 2.6 47.2 1.0 OD1 A:ASP208 2.8 55.3 1.0 CA A:CA509 3.0 44.3 1.0 OE1 A:GLU115 3.1 63.3 1.0 CG A:ASP241 3.2 47.1 1.0 OE1 A:GLU174 3.2 63.7 1.0 CD A:GLU174 3.2 63.6 1.0 C A:ALA206 3.5 68.2 1.0 N A:ALA206 3.6 63.2 1.0 OD2 A:ASP241 3.6 47.1 1.0 CG A:ASP205 3.7 79.2 1.0 CD A:GLU115 4.0 67.6 1.0 CG A:ASP208 4.0 62.9 1.0 CB A:ASP241 4.1 47.1 1.0 OE2 A:GLU115 4.1 63.5 1.0 CA A:ALA206 4.1 69.6 1.0 CD A:ARG173 4.3 72.9 1.0 CA A:ASP241 4.3 51.7 1.0 C A:ASP205 4.4 69.3 1.0 N A:ASP208 4.4 62.0 1.0 OD2 A:ASP205 4.4 83.4 1.0 CA A:ASP205 4.5 71.5 1.0 OD2 A:ASP208 4.6 66.0 1.0 N A:ASN207 4.6 56.7 1.0 CB A:ASP205 4.7 75.7 1.0 CB A:ALA206 4.7 63.4 1.0 CG A:GLU174 4.7 73.8 1.0 CB A:ARG173 4.8 62.9 1.0 CA A:ASN207 4.9 60.6 1.0 N A:ASP241 5.0 56.1 1.0

Calcium binding site 5 out of 9 in the Protocadherin Alpha 4 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 Alpha 4 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca509 b:44.3 occ:1.00 OE1 A:GLU174 2.4 63.7 1.0 OE2 A:GLU115 2.4 63.5 1.0 OD1 A:ASP208 2.6 55.3 1.0 OD2 A:ASP208 2.7 66.0 1.0 CG A:ASP208 2.9 62.9 1.0 CA A:CA508 3.0 21.4 1.0 OD1 A:ASP172 3.0 63.7 1.0 CD A:GLU115 3.3 67.6 1.0 CD A:GLU174 3.3 63.6 1.0 OD1 A:ASN209 3.3 56.6 1.0 OE1 A:GLU115 3.4 63.3 1.0 OE2 A:GLU174 3.7 63.6 1.0 CG A:ASN209 3.9 58.8 1.0 CG A:ASP172 4.0 76.1 1.0 OD1 A:ASP241 4.1 47.2 1.0 CB A:ASP208 4.4 64.5 1.0 ND2 A:ASN209 4.4 58.4 1.0 CG A:GLU174 4.5 73.8 1.0 OD2 A:ASP172 4.6 63.6 1.0 O A:ALA206 4.6 63.7 1.0 CG A:GLU115 4.7 70.6 1.0 C A:ASP208 4.7 61.0 1.0 N A:ARG173 4.8 63.0 1.0 CB A:ASN209 4.8 61.0 1.0 N A:GLU174 4.9 74.1 1.0 CB A:GLU174 4.9 72.7 1.0 N A:ASN209 4.9 62.8 1.0 CA A:ASP208 4.9 63.1 1.0 N A:ASP208 4.9 62.0 1.0 O A:ASP208 5.0 57.5 1.0

Calcium binding site 6 out of 9 in the Protocadherin Alpha 4 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 Alpha 4 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca510 b:34.5 occ:1.00 OD2 A:ASP239 2.4 92.9 1.0 O A:ASN209 2.4 61.3 1.0 O A:ASN245 2.6 46.5 1.0 OD1 A:ASN207 2.7 85.5 1.0 OD2 A:ASP295 2.8 45.9 1.0 OD2 A:ASP241 2.9 47.1 1.0 CG A:ASP239 3.3 90.8 1.0 OD1 A:ASP239 3.4 95.0 1.0 CG A:ASP241 3.4 47.1 1.0 CB A:ASP241 3.6 47.1 1.0 C A:ASN209 3.7 62.4 1.0 CG A:ASP295 3.7 45.8 1.0 C A:ASN245 3.7 51.1 1.0 CG A:ASN207 3.9 80.0 1.0 CB A:ASP295 4.1 53.0 1.0 OD1 A:ASP241 4.4 47.2 1.0 CB A:ASN245 4.4 55.8 1.0 CA A:ASN245 4.4 54.9 1.0 N A:ASN209 4.4 62.8 1.0 CA A:ASN209 4.5 63.4 1.0 ND2 A:ASN207 4.6 83.1 1.0 N A:ALA210 4.6 63.6 1.0 CB A:ASP239 4.7 81.8 1.0 CB A:ASN209 4.7 61.0 1.0 OD1 A:ASP295 4.7 45.8 1.0 CA A:ALA210 4.8 68.2 1.0 CA A:ASP241 4.8 51.7 1.0 N A:GLY246 4.8 49.5 1.0 CA A:ASN207 4.8 60.6 1.0 N A:ASP241 4.8 56.1 1.0 CD A:PRO211 4.9 57.9 1.0 CB A:ASN207 4.9 68.9 1.0 CD1 A:LEU301 5.0 62.0 1.0 C A:ASN207 5.0 57.4 1.0

Calcium binding site 7 out of 9 in the Protocadherin Alpha 4 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 Alpha 4 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca511 b:35.7 occ:1.00 OE1 A:GLU282 2.4 37.2 1.0 OE2 A:GLU224 2.5 56.6 1.0 OD1 A:ASP316 2.6 37.1 1.0 OD2 A:ASP316 2.7 42.1 1.0 CA A:CA512 2.8 32.2 1.0 ND2 A:ASN317 2.9 33.4 1.0 CG A:ASP316 3.0 37.4 1.0 OD1 A:ASP280 3.0 42.2 1.0 CD A:GLU224 3.3 56.4 1.0 OE1 A:GLU224 3.4 54.2 1.0 CD A:GLU282 3.6 40.9 1.0 OD1 A:ASP349 3.9 29.1 1.0 CG A:ASN317 4.1 29.2 1.0 CG A:ASP280 4.1 42.5 1.0 CG A:GLU282 4.3 42.2 1.0 CB A:GLU282 4.4 45.9 1.0 OE2 A:GLU282 4.5 37.1 1.0 CB A:ASP316 4.5 32.3 1.0 OD1 A:ASN317 4.5 24.3 1.0 N A:GLU282 4.6 41.2 1.0 OD2 A:ASP280 4.7 43.8 1.0 O A:ILE314 4.7 37.1 1.0 CG A:GLU224 4.8 58.2 1.0 N A:PHE281 4.8 38.0 1.0 C A:ASP316 5.0 28.2 1.0

Calcium binding site 8 out of 9 in the Protocadherin Alpha 4 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 Alpha 4 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca512 b:32.2 occ:1.00 OD1 A:ASP313 2.5 37.2 1.0 OE1 A:GLU282 2.6 37.2 1.0 OD1 A:ASP316 2.6 37.1 1.0 O A:ILE314 2.7 37.1 1.0 OD1 A:ASP349 2.8 29.1 1.0 CA A:CA511 2.8 35.7 1.0 OE1 A:GLU224 2.9 54.2 1.0 CD A:GLU282 3.3 40.9 1.0 CG A:ASP313 3.3 41.6 1.0 OE2 A:GLU282 3.4 37.1 1.0 CG A:ASP349 3.5 28.5 1.0 CG A:ASP316 3.7 37.4 1.0 ND2 A:ASN317 3.8 33.4 1.0 CD A:GLU224 3.8 56.4 1.0 OD2 A:ASP313 3.8 37.2 1.0 N A:ILE314 3.8 44.1 1.0 C A:ILE314 3.8 49.0 1.0 OE2 A:GLU224 3.9 56.6 1.0 CB A:ASP349 4.2 24.9 1.0 OD2 A:ASP349 4.2 30.9 1.0 OD2 A:ASP316 4.3 42.1 1.0 CB A:ASP313 4.4 37.6 1.0 CA A:ASP349 4.4 25.6 1.0 CB A:PHE281 4.4 42.0 1.0 CA A:ILE314 4.4 47.2 1.0 CA A:ASP313 4.5 43.8 1.0 N A:ASP316 4.5 18.4 1.0 C A:ASP313 4.6 44.7 1.0 CG1 A:ILE314 4.7 47.3 1.0 CG A:GLU282 4.7 42.2 1.0 CD1 A:PHE281 4.8 41.9 1.0 N A:ASN315 4.9 21.6 1.0 CB A:ASP316 4.9 32.3 1.0 CG A:PHE281 5.0 43.2 1.0

Calcium binding site 9 out of 9 in the Protocadherin Alpha 4 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 Alpha 4 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca513 b:15.8 occ:1.00 O A:ASN317 2.5 30.3 1.0 OD1 A:ASN315 2.5 40.6 1.0 O A:ASN353 2.5 8.2 1.0 OD2 A:ASP349 2.6 30.9 1.0 OD1 A:ASP347 2.6 45.5 1.0 OD2 A:ASP400 2.8 38.2 1.0 OD2 A:ASP347 2.8 32.9 1.0 CG A:ASP347 3.0 38.9 1.0 CG A:ASP349 3.3 28.5 1.0 CB A:ASP349 3.6 24.9 1.0 C A:ASN317 3.6 30.5 1.0 CG A:ASP400 3.7 35.1 1.0 C A:ASN353 3.7 13.7 1.0 CG A:ASN315 3.7 40.5 1.0 N A:ASN317 4.0 36.3 1.0 CB A:ASP400 4.1 33.8 1.0 CA A:ASN317 4.1 31.8 1.0 CB A:ASN317 4.2 30.4 1.0 OD1 A:ASP349 4.3 29.1 1.0 ND2 A:ASN315 4.5 43.4 1.0 CA A:GLY354 4.5 23.8 1.0 CB A:ASP347 4.6 37.0 1.0 N A:GLY354 4.6 18.1 1.0 N A:ASP349 4.6 36.2 1.0 CA A:ASN353 4.7 21.9 1.0 OD1 A:ASP400 4.7 33.6 1.0 CA A:ASP349 4.7 25.6 1.0 N A:VAL318 4.8 33.3 1.0 CA A:ASN315 4.8 23.5 1.0 CD A:PRO319 4.8 33.6 1.0 CB A:ASN315 4.8 34.5 1.0 CB A:ASN353 4.8 25.6 1.0 N A:ASP316 4.9 18.4 1.0 C A:ASN315 5.0 19.6 1.0 CD1 A:LEU406 5.0 25.3 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