Calcium in PDB 4zps: Crystal Structure of Protocadherin Gamma A8 EC1-3

The structure of Crystal Structure of Protocadherin Gamma A8 EC1-3, PDB code: 4zps was solved by K.M.Goodman, S.Mannepalli, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.65 / 2.90
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.060, 78.120, 167.730, 90.00, 90.00, 90.00
R / Rfree (%)	26.4 / 28.7

The binding sites of Calcium atom in the Crystal Structure of Protocadherin Gamma A8 EC1-3 (pdb code 4zps). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Protocadherin Gamma A8 EC1-3, PDB code: 4zps:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Crystal Structure of Protocadherin Gamma A8 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 A8 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:66.2 occ:1.00 O A:ASN100 2.5 0.5 1.0 OD2 A:ASP187 2.5 0.0 1.0 OD1 A:ASN98 2.6 0.6 1.0 OD2 A:ASP132 2.9 0.3 1.0 O A:ASN136 3.0 0.4 1.0 C A:ASN100 3.0 0.2 1.0 CA A:ASN101 3.4 0.9 1.0 N A:ASN101 3.4 0.7 1.0 CG A:ASN98 3.5 0.3 1.0 CG A:ASP187 3.5 0.1 1.0 CG A:ASP132 3.9 0.7 1.0 ND2 A:ASN98 3.9 0.8 1.0 C A:ASN136 4.0 0.8 1.0 N A:ASN100 4.0 0.4 1.0 CA A:ASN100 4.1 0.3 1.0 CG A:ARG193 4.2 0.2 1.0 C A:ASN101 4.2 1.0 1.0 OD1 A:ASP187 4.2 0.3 1.0 CD A:PRO102 4.3 0.8 1.0 CB A:ASP187 4.3 0.6 1.0 CB A:ASP132 4.4 0.9 1.0 CB A:ARG193 4.4 0.6 1.0 CB A:ASN101 4.5 0.7 1.0 N A:PRO102 4.5 0.8 1.0 CA A:ASN136 4.6 0.2 1.0 CB A:ASN136 4.6 0.3 1.0 CB A:ASN98 4.7 0.6 1.0 CA A:ASN98 4.7 0.3 1.0 CB A:ASN100 4.8 0.1 1.0 N A:ASP99 4.9 0.0 1.0 OD1 A:ASP132 4.9 0.9 1.0 N A:SER137 4.9 0.6 1.0 O A:ASN101 4.9 0.9 1.0 C A:ASN98 5.0 0.6 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of Protocadherin Gamma A8 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 A8 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca804 b:21.6 occ:1.00 OE1 A:GLU174 2.4 26.5 1.0 OE2 A:GLU174 2.5 26.3 1.0 OD1 A:ASP205 2.5 48.6 1.0 O A:THR206 2.5 37.4 1.0 CD A:GLU174 2.7 26.3 1.0 OD1 A:ASP241 2.8 43.0 1.0 OE1 A:GLU115 2.9 49.2 1.0 OD1 A:ASP208 2.9 37.4 1.0 CG A:ASP205 3.2 46.0 1.0 OD2 A:ASP205 3.4 38.6 1.0 CG A:ASP241 3.7 33.7 1.0 C A:THR206 3.7 46.4 1.0 CD A:GLU115 3.7 52.4 1.0 N A:THR206 3.8 47.6 1.0 OE2 A:GLU115 3.9 59.8 1.0 CG A:ASP208 4.1 46.7 1.0 CG A:GLU174 4.1 33.3 1.0 CA A:ASP241 4.2 33.6 1.0 CB A:ASP241 4.2 32.7 1.0 CA A:CA806 4.2 40.0 1.0 NH1 A:ARG173 4.3 28.4 1.0 OD1 A:ASN209 4.3 60.1 1.0 CA A:THR206 4.3 47.3 1.0 CB A:ASP205 4.4 50.9 1.0 CG A:ARG173 4.4 35.6 1.0 OD2 A:ASP241 4.5 32.0 1.0 CA A:ASP205 4.5 28.7 1.0 N A:ASP208 4.5 35.9 1.0 OD2 A:ASP208 4.6 39.9 1.0 CG2 A:THR206 4.6 45.5 1.0 C A:ASP205 4.6 35.1 1.0 N A:ASN207 4.7 47.6 1.0 CD A:ARG173 4.8 36.7 1.0 N A:GLU242 4.9 35.9 1.0 CA A:ASN207 4.9 39.3 1.0

Calcium binding site 3 out of 7 in the Crystal Structure of Protocadherin Gamma A8 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 A8 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca805 b:22.7 occ:1.00 O A:ASN209 2.4 30.1 1.0 O A:ASN245 2.5 42.0 1.0 OD2 A:ASP239 2.5 39.6 1.0 OD2 A:ASP241 2.5 32.0 1.0 OD2 A:ASP294 2.6 33.4 1.0 OD1 A:ASP239 2.6 29.2 1.0 OD1 A:ASN207 2.7 44.8 1.0 CG A:ASP239 2.9 32.4 1.0 CG A:ASP241 3.5 33.7 1.0 CG A:ASP294 3.6 35.8 1.0 C A:ASN209 3.6 41.3 1.0 C A:ASN245 3.7 46.1 1.0 CG A:ASN207 3.7 40.7 1.0 CB A:ASP241 3.9 32.7 1.0 CB A:ASP294 3.9 32.2 1.0 ND2 A:ASN207 4.1 33.6 1.0 CB A:ASP239 4.4 29.2 1.0 CA A:ASN245 4.4 45.9 1.0 CA A:ASN209 4.5 38.7 1.0 CB A:ASN245 4.5 43.5 1.0 N A:ALA210 4.6 40.1 1.0 N A:ASN209 4.6 33.7 1.0 CB A:ASN209 4.6 36.0 1.0 OD1 A:ASP241 4.6 43.0 1.0 OD1 A:ASP294 4.6 43.9 1.0 N A:GLY246 4.7 47.0 1.0 CA A:ALA210 4.7 38.2 1.0 CD A:PRO211 4.7 34.4 1.0 CA A:GLY246 4.8 42.7 1.0 CD1 A:LEU298 4.8 39.2 1.0 CB A:ASN207 4.9 43.2 1.0 C A:ALA210 5.0 28.5 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of Protocadherin Gamma A8 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 A8 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca806 b:40.0 occ:1.00 OD1 A:ASP172 2.4 33.4 1.0 OD2 A:ASP208 2.5 39.9 1.0 OE2 A:GLU174 2.5 26.3 1.0 OE1 A:GLU115 3.0 49.2 1.0 OE2 A:GLU115 3.0 59.8 1.0 CD A:GLU115 3.2 52.4 1.0 CG A:ASP208 3.3 46.7 1.0 CG A:ASP172 3.4 40.7 1.0 OD1 A:ASP208 3.5 37.4 1.0 CD A:GLU174 3.7 26.3 1.0 OD2 A:ASP172 4.1 51.8 1.0 CB A:ASP172 4.2 33.3 1.0 CA A:CA804 4.2 21.6 1.0 OD1 A:ASN209 4.3 60.1 1.0 CA A:ASP172 4.3 28.6 1.0 CG A:GLU115 4.3 54.8 1.0 CG A:GLU174 4.4 33.3 1.0 CB A:GLU174 4.5 35.4 1.0 CB A:GLU115 4.6 50.5 1.0 OE1 A:GLU174 4.6 26.5 1.0 CB A:ASP208 4.8 38.5 1.0 N A:GLU174 4.9 30.5 1.0 N A:ARG173 4.9 29.6 1.0 C A:ASP172 4.9 31.3 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of Protocadherin Gamma A8 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 A8 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca807 b:60.6 occ:1.00 OE2 A:GLU8 2.4 0.6 1.0 OD2 A:ASP96 2.4 98.6 1.0 OE2 A:GLU64 2.5 0.1 1.0 O A:ILE97 2.6 0.0 1.0 CG A:ASP96 2.9 0.7 1.0 CD A:GLU64 3.1 0.7 1.0 CD A:GLU8 3.1 0.5 1.0 OD1 A:ASP132 3.1 0.9 1.0 OE1 A:GLU8 3.2 91.5 1.0 OE1 A:GLU64 3.2 0.4 1.0 OD1 A:ASP96 3.3 98.9 1.0 N A:ILE97 3.4 0.8 1.0 OD1 A:ASP99 3.4 0.1 1.0 CG A:ASP132 3.5 0.7 1.0 CA A:CA808 3.5 0.3 1.0 C A:ILE97 3.6 0.8 1.0 CB A:ASP132 3.9 0.9 1.0 CB A:ASP96 4.0 0.6 1.0 CA A:ASP96 4.0 90.5 1.0 C A:ASP96 4.1 91.2 1.0 CA A:ILE97 4.1 0.1 1.0 OD2 A:ASP132 4.1 0.3 1.0 CG A:GLU64 4.5 0.1 1.0 CA A:ASP132 4.5 1.0 1.0 CG A:GLU8 4.6 87.7 1.0 CG A:ASP99 4.6 0.5 1.0 N A:ASN98 4.8 0.1 1.0 CB A:ARG63 4.9 92.1 1.0 CB A:ILE97 5.0 0.5 1.0 N A:ASP99 5.0 0.0 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of Protocadherin Gamma A8 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 A8 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca808 b:0.3 occ:1.00 OD2 A:ASP99 2.4 1.0 1.0 OD1 A:ASP62 2.4 93.3 1.0 OE1 A:GLU64 2.4 0.4 1.0 OE2 A:GLU8 2.5 0.6 1.0 OD1 A:ASP99 2.5 0.1 1.0 CD A:GLU8 2.7 0.5 1.0 CG A:ASP99 2.7 0.5 1.0 OE1 A:GLU8 3.0 91.5 1.0 CG A:ASP62 3.2 0.0 1.0 OD2 A:ASP62 3.3 0.5 1.0 CA A:CA807 3.5 60.6 1.0 CG A:GLU8 3.5 87.7 1.0 CD A:GLU64 3.5 0.7 1.0 OE2 A:GLU64 4.0 0.1 1.0 CB A:ASP99 4.1 0.5 1.0 CB A:GLU8 4.4 93.2 1.0 O A:ILE97 4.4 0.0 1.0 CB A:ASP62 4.5 98.9 1.0 CB A:GLU9 4.6 89.3 1.0 CA A:ASP62 4.8 95.2 1.0 CG A:GLU64 4.8 0.1 1.0 N A:ARG63 4.9 97.5 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of Protocadherin Gamma A8 EC1-3


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 Protocadherin Gamma A8 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca809 b:73.2 occ:1.00 OD2 A:ASP310 2.5 65.6 1.0 OD1 A:ASP310 3.0 72.5 1.0 OD1 A:ASP279 3.0 57.0 1.0 CG A:ASP310 3.1 64.8 1.0 OD1 A:ASN312 3.1 0.8 1.0 OE2 A:GLU224 3.1 53.5 1.0 OE1 A:GLU224 3.4 57.3 1.0 CD A:GLU224 3.7 54.9 1.0 CG A:ASN312 4.1 0.4 1.0 CG A:ASP279 4.2 56.2 1.0 O A:ASN312 4.2 0.5 1.0 ND2 A:ASN312 4.3 0.2 1.0 CB A:ASP310 4.5 54.8 1.0 O A:HOH908 4.6 32.2 1.0 OD2 A:ASP279 4.6 56.4 1.0 O A:ASP279 5.0 38.9 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