Calcium in PDB 4zpo: Crystal Structure of Protocadherin Gamma C5 EC1-3

The structure of Crystal Structure of Protocadherin Gamma C5 EC1-3, PDB code: 4zpo was solved by H.N.Wolcott, K.M.Goodman, F.Bahna, S.Mannepalli, R.Rubinstein, B.Honig, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.06 / 2.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	108.637, 108.637, 96.614, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 24.7

The binding sites of Calcium atom in the Crystal Structure of Protocadherin Gamma C5 EC1-3 (pdb code 4zpo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Protocadherin Gamma C5 EC1-3, PDB code: 4zpo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Protocadherin Gamma C5 EC1-3


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 Protocadherin Gamma C5 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:75.5 occ:1.00 OD2 A:ASP295 2.4 91.1 1.0 O A:ASN209 2.4 85.8 1.0 OD2 A:ASP241 2.5 84.0 1.0 OD1 A:ASP239 2.5 0.1 1.0 O A:ASN245 2.5 78.8 1.0 OD2 A:ASP239 2.6 98.0 1.0 CG A:ASP239 2.9 96.9 1.0 OD1 A:ASN207 2.9 89.9 1.0 CG A:ASP241 3.3 82.1 1.0 CG A:ASP295 3.4 88.3 1.0 C A:ASN209 3.5 82.6 1.0 CB A:ASP241 3.6 80.9 1.0 CG A:ASN207 3.7 86.6 1.0 C A:ASN245 3.7 86.2 1.0 OD1 A:ASP295 3.8 93.5 1.0 ND2 A:ASN207 3.9 86.9 1.0 CA A:ASN209 4.2 79.7 1.0 CB A:ASN209 4.2 79.5 1.0 N A:ASN209 4.3 77.1 1.0 CB A:ASP239 4.4 90.9 1.0 OD1 A:ASP241 4.4 87.8 1.0 N A:ALA210 4.4 87.2 1.0 CA A:ASN245 4.5 86.7 1.0 CB A:ASP295 4.6 87.1 1.0 CA A:ALA210 4.6 81.4 1.0 CB A:ASN245 4.6 84.9 1.0 N A:GLY246 4.7 91.9 1.0 CG A:MET301 4.7 87.2 1.0 CD A:PRO211 4.7 71.7 1.0 CB A:MET301 4.8 79.9 1.0 CA A:GLY246 4.8 87.6 1.0 N A:ASP241 4.9 79.9 1.0 CA A:ASP241 4.9 85.1 1.0 CB A:ASN207 4.9 80.4 1.0 C A:ALA210 5.0 75.9 1.0 CA A:ASN207 5.0 80.0 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Protocadherin Gamma C5 EC1-3


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 Protocadherin Gamma C5 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:89.3 occ:1.00 OD2 A:ASP208 2.4 0.5 1.0 OD1 A:ASP172 2.5 86.9 1.0 OE2 A:GLU115 2.5 96.8 1.0 CG A:ASP208 3.0 76.3 1.0 CG A:ASP172 3.3 85.1 1.0 OD1 A:ASP208 3.3 78.5 1.0 CD A:GLU115 3.4 92.8 1.0 OE2 A:GLU174 3.6 69.8 1.0 CB A:ASP172 3.8 75.2 1.0 CA A:ASP172 3.8 71.4 1.0 CG A:GLU115 3.8 94.6 1.0 O A:LEU171 4.1 89.2 1.0 CB A:ASP208 4.1 76.5 1.0 OD2 A:ASP172 4.1 88.6 1.0 OE1 A:GLU115 4.3 89.2 1.0 N A:ARG173 4.7 69.4 1.0 C A:ASP172 4.7 69.3 1.0 CD A:GLU174 4.8 77.8 1.0 N A:ASP172 4.9 79.1 1.0 C A:LEU171 4.9 82.4 1.0 OD1 A:ASN209 4.9 81.8 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Protocadherin Gamma C5 EC1-3


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 Protocadherin Gamma C5 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:66.8 occ:1.00 OD1 A:ASP205 2.5 82.6 1.0 OD1 A:ASP208 2.5 78.5 1.0 O A:VAL206 2.5 87.5 1.0 OE1 A:GLU174 2.5 78.0 1.0 OD1 A:ASP241 2.7 87.8 1.0 OE1 A:GLU115 2.7 89.2 1.0 OE2 A:GLU174 3.1 69.8 1.0 CD A:GLU174 3.1 77.8 1.0 CD A:GLU115 3.5 92.8 1.0 CG A:ASP241 3.5 82.1 1.0 OE2 A:GLU115 3.5 96.8 1.0 CG A:ASP208 3.6 76.3 1.0 C A:VAL206 3.6 82.3 1.0 CG A:ASP205 3.6 85.6 1.0 N A:VAL206 3.8 82.0 1.0 N A:ASP208 4.1 80.9 1.0 CB A:ASP241 4.2 80.9 1.0 OD2 A:ASP241 4.2 84.0 1.0 OD2 A:ASP208 4.2 0.5 1.0 OD2 A:ASP205 4.2 91.8 1.0 CA A:VAL206 4.3 78.5 1.0 CA A:ASP241 4.4 85.1 1.0 OD1 A:ASN209 4.4 81.8 1.0 NH1 A:ARG173 4.5 91.3 1.0 N A:ASN207 4.6 94.5 1.0 CG A:GLU174 4.6 76.9 1.0 CB A:ASP208 4.6 76.5 1.0 CA A:ASP205 4.7 76.3 1.0 C A:ASP205 4.7 81.1 1.0 CA A:ASN207 4.8 80.0 1.0 CB A:ASP205 4.8 81.9 1.0 CB A:ARG173 4.8 73.8 1.0 CA A:ASP208 4.8 79.3 1.0 CG A:GLU115 4.9 94.6 1.0 CD A:ARG173 4.9 74.7 1.0 C A:ASN207 4.9 86.4 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Protocadherin Gamma C5 EC1-3


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 Protocadherin Gamma C5 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:63.9 occ:1.00 O A:ASN100 2.4 52.8 1.0 OD1 A:ASN98 2.5 75.2 1.0 O A:ASN136 2.5 57.4 1.0 OD2 A:ASP130 2.6 87.0 1.0 OD2 A:ASP132 2.6 58.3 1.0 OD1 A:ASP130 2.7 79.9 1.0 CG A:ASP130 3.0 80.3 1.0 OD2 A:ASP187 3.0 72.9 1.0 CG A:ASP132 3.5 57.6 1.0 C A:ASN100 3.5 64.5 1.0 CG A:ASN98 3.6 70.7 1.0 CG A:ASP187 3.7 72.4 1.0 C A:ASN136 3.7 62.2 1.0 CB A:ASP132 3.7 58.8 1.0 CB A:ASP187 4.0 68.3 1.0 N A:ASN100 4.2 72.3 1.0 CA A:ASN100 4.2 68.8 1.0 CB A:ASN100 4.3 69.6 1.0 ND2 A:ASN98 4.3 72.0 1.0 CB A:ASP130 4.5 74.4 1.0 CB A:ASN136 4.5 71.9 1.0 CA A:ASN136 4.5 66.8 1.0 OD1 A:ASP187 4.5 74.0 1.0 CD A:ARG193 4.5 73.8 1.0 N A:SER101 4.6 62.8 1.0 OD1 A:ASP132 4.6 58.3 1.0 N A:THR137 4.6 66.8 1.0 CA A:THR137 4.7 65.4 1.0 CA A:ASN98 4.7 62.5 1.0 CB A:ASN98 4.8 63.3 1.0 C A:ASN98 4.8 62.9 1.0 CA A:SER101 4.8 65.0 1.0 CD A:PRO102 4.9 50.2 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Protocadherin Gamma C5 EC1-3


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 Protocadherin Gamma C5 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:56.5 occ:1.00 O A:LEU97 2.4 71.9 1.0 OE2 A:GLU64 2.5 62.5 1.0 OE1 A:GLU64 2.6 62.2 1.0 OD1 A:ASP132 2.6 58.3 1.0 OD1 A:ASP96 2.6 51.8 1.0 OE1 A:GLU8 2.7 58.5 1.0 OD1 A:ASP99 2.8 68.8 1.0 CD A:GLU64 2.8 64.3 1.0 OE2 A:GLU8 3.4 56.0 1.0 CD A:GLU8 3.4 61.4 1.0 C A:LEU97 3.5 67.2 1.0 CG A:ASP132 3.5 57.6 1.0 N A:LEU97 3.7 67.2 1.0 CG A:ASP96 3.8 64.7 1.0 ND2 A:ASN100 3.9 80.5 1.0 CG A:ASP99 4.0 72.0 1.0 CA A:CA406 4.0 67.7 1.0 CA A:LEU97 4.1 62.8 1.0 OD2 A:ASP132 4.2 58.3 1.0 CG A:GLU64 4.3 60.0 1.0 NE A:ARG63 4.3 69.8 1.0 CB A:ASP132 4.4 58.8 1.0 CB A:LEU97 4.4 61.3 1.0 N A:ASP99 4.4 56.8 1.0 OD2 A:ASP99 4.5 59.2 1.0 OD2 A:ASP96 4.5 68.6 1.0 CA A:ASP132 4.6 65.2 1.0 N A:ASN98 4.6 75.1 1.0 C A:ASP96 4.6 66.0 1.0 CA A:ASP96 4.8 65.5 1.0 CG A:GLU8 4.9 68.8 1.0 CB A:ASP96 4.9 69.5 1.0 CB A:ARG63 4.9 63.5 1.0 NH1 A:ARG63 4.9 70.4 1.0 CA A:ASN98 5.0 62.5 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Protocadherin Gamma C5 EC1-3


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 Protocadherin Gamma C5 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:67.7 occ:1.00 OD1 A:ASP62 2.4 76.9 1.0 OE2 A:GLU8 2.4 56.0 1.0 OD2 A:ASP99 2.6 59.2 1.0 OE2 A:GLU64 2.6 62.5 1.0 OE2 A:GLU9 2.7 53.9 1.0 CG A:ASP99 3.4 72.0 1.0 OD1 A:ASP99 3.4 68.8 1.0 ND2 A:ASN100 3.5 80.5 1.0 CG A:ASP62 3.6 74.4 1.0 CD A:GLU8 3.6 61.4 1.0 CD A:GLU9 3.8 58.3 1.0 CD A:GLU64 3.8 64.3 1.0 CA A:CA405 4.0 56.5 1.0 OD2 A:ASP62 4.1 76.8 1.0 OE1 A:GLU8 4.2 58.5 1.0 CG A:GLU9 4.3 58.9 1.0 CG A:GLU64 4.5 60.0 1.0 CB A:GLU64 4.6 64.0 1.0 CG A:ASN100 4.7 74.5 1.0 CG A:GLU8 4.7 68.8 1.0 CB A:ASP62 4.7 70.0 1.0 CB A:ASP99 4.8 73.8 1.0 OE1 A:GLU64 4.8 62.2 1.0 OE1 A:GLU9 4.8 58.0 1.0 CA A:ASP62 4.8 66.7 1.0 N A:GLU64 4.8 61.7 1.0 N A:ARG63 4.8 66.9 1.0

R.Rubinstein, C.A.Thu, K.M.Goodman, H.N.Wolcott, F.Bahna, S.Mannepalli, G.Ahlsen, M.Chevee, A.Halim, H.Clausen, T.Maniatis, L.Shapiro, B.Honig. Molecular Logic of Neuronal Self-Recognition Through Protocadherin Domain Interactions. Cell V. 163 629 2015.
ISSN: ISSN 1097-4172
PubMed: 26478182
DOI: 10.1016/J.CELL.2015.09.026