Calcium in PDB 4zpl: Crystal Structure of Protocadherin Beta 1 EC1-3

The structure of Crystal Structure of Protocadherin Beta 1 EC1-3, PDB code: 4zpl was solved by K.M.Goodman, F.Bahna, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.70 / 3.30
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.990, 106.520, 149.350, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 27.8

The binding sites of Calcium atom in the Crystal Structure of Protocadherin Beta 1 EC1-3 (pdb code 4zpl). 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 Beta 1 EC1-3, PDB code: 4zpl:
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 Beta 1 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 Beta 1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca413 b:46.7 occ:1.00 OD1 A:ASP100 2.5 97.1 1.0 OE1 A:GLU65 2.5 55.9 1.0 OD1 A:ASP97 2.5 54.7 1.0 OE1 A:GLU9 2.5 0.2 1.0 OE2 A:GLU65 2.7 54.4 1.0 O A:ILE98 2.8 70.1 1.0 CD A:GLU65 2.9 55.7 1.0 OE2 A:GLU9 2.9 85.4 1.0 OD1 A:ASP133 3.1 78.0 1.0 CD A:GLU9 3.1 96.3 1.0 CG A:ASP100 3.5 94.5 1.0 CG A:ASP97 3.7 74.1 1.0 N A:ILE98 3.8 67.7 1.0 OD2 A:ASP100 3.8 86.5 1.0 C A:ILE98 3.9 74.4 1.0 CG A:ASP133 3.9 80.2 1.0 CA A:CA414 3.9 58.6 1.0 CG1 A:ILE98 4.1 57.7 1.0 CG A:GLU65 4.4 57.3 1.0 OD2 A:ASP97 4.4 77.5 1.0 CA A:ILE98 4.4 65.0 1.0 N A:ASP100 4.4 69.3 1.0 NE A:ARG64 4.5 86.0 1.0 CG A:GLU9 4.6 90.9 1.0 CB A:ASP133 4.6 76.4 1.0 OD2 A:ASP133 4.6 77.4 1.0 C A:ASP97 4.8 61.0 1.0 CA A:ASP97 4.8 68.5 1.0 CB A:ARG64 4.8 53.8 1.0 CA A:ASP133 4.8 66.1 1.0 CB A:ASP97 4.8 71.1 1.0 CB A:ASP100 4.9 97.4 1.0 CB A:ILE98 4.9 58.1 1.0 N A:ASN99 4.9 85.1 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Protocadherin Beta 1 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 Beta 1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca414 b:58.6 occ:1.00 OD1 A:ASP63 2.4 67.8 1.0 OD2 A:ASP100 2.4 86.5 1.0 OE2 A:GLU9 2.5 85.4 1.0 OE2 A:GLU65 2.5 54.4 1.0 OE2 A:GLU10 3.0 70.6 1.0 CG A:ASP100 3.4 94.5 1.0 CG A:ASP63 3.6 71.9 1.0 CD A:GLU65 3.7 55.7 1.0 OD1 A:ASP100 3.7 97.1 1.0 CD A:GLU9 3.7 96.3 1.0 OD1 A:ASN101 3.9 67.7 1.0 CA A:CA413 3.9 46.7 1.0 CD A:GLU10 4.0 81.9 1.0 OD2 A:ASP63 4.3 80.2 1.0 CG A:GLU65 4.4 57.3 1.0 CB A:GLU65 4.5 70.1 1.0 OE1 A:GLU9 4.5 0.2 1.0 OE1 A:GLU65 4.6 55.9 1.0 N A:GLU65 4.6 79.4 1.0 CB A:ASP100 4.6 97.4 1.0 CG A:GLU9 4.6 90.9 1.0 N A:ARG64 4.6 78.4 1.0 CB A:ASP63 4.7 79.0 1.0 OE1 A:GLU10 4.7 80.8 1.0 CA A:ASP63 4.7 83.4 1.0 CG A:ASN101 4.8 78.0 1.0 CG A:GLU10 4.9 86.9 1.0 C A:ASP63 5.0 80.9 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Protocadherin Beta 1 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 Beta 1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca415 b:63.6 occ:1.00 O A:ASN137 2.4 97.0 1.0 O A:ASN101 2.4 65.0 1.0 OD2 A:ASP131 2.5 67.7 1.0 OD1 A:ASN99 2.5 83.2 1.0 OD2 A:ASP133 2.7 77.4 1.0 OD2 A:ASP188 2.9 67.8 1.0 OD1 A:ASP131 3.0 59.2 1.0 CG A:ASP131 3.1 66.0 1.0 CG A:ASN99 3.4 77.8 1.0 CG A:ASP188 3.6 73.3 1.0 C A:ASN137 3.6 87.6 1.0 C A:ASN101 3.6 72.4 1.0 CG A:ASP133 3.7 80.2 1.0 ND2 A:ASN99 3.7 78.7 1.0 CB A:ASP188 3.8 76.4 1.0 CB A:ASP133 4.1 76.4 1.0 CA A:ASN137 4.4 74.2 1.0 CA A:ALA102 4.5 65.0 1.0 N A:ALA102 4.5 66.2 1.0 OD1 A:ASP188 4.6 85.8 1.0 N A:GLY138 4.6 88.8 1.0 CB A:ASN99 4.6 78.4 1.0 CD A:PRO103 4.6 60.6 1.0 CB A:ASP131 4.6 78.5 1.0 CA A:ASN101 4.6 74.5 1.0 N A:ASN101 4.6 73.7 1.0 CA A:GLY138 4.7 86.6 1.0 CB A:ASN137 4.7 86.1 1.0 CA A:ASN99 4.7 79.6 1.0 OD1 A:ASP133 4.8 78.0 1.0 CB A:LYS194 4.8 79.1 1.0 CB A:ASN101 5.0 77.7 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Protocadherin Beta 1 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 Beta 1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca416 b:65.5 occ:1.00 OE1 A:GLU116 2.4 0.7 1.0 OD1 A:ASP209 2.5 83.6 1.0 OE2 A:GLU175 2.5 74.8 1.0 O A:VAL207 2.5 94.0 1.0 OD1 A:ASP242 3.0 0.3 1.0 OD2 A:ASP206 3.2 74.3 1.0 CD A:GLU116 3.3 0.9 1.0 CG A:ASP209 3.4 83.7 1.0 N A:VAL207 3.4 99.7 1.0 OE2 A:GLU116 3.5 0.7 1.0 CD A:GLU175 3.5 91.2 1.0 C A:VAL207 3.6 95.4 1.0 CG A:ASP206 3.6 85.8 1.0 CG A:ASP242 3.7 0.9 1.0 OD2 A:ASP209 3.8 81.8 1.0 OE1 A:GLU175 3.8 82.6 1.0 OD1 A:ASP206 3.9 74.7 1.0 CA A:VAL207 4.0 92.5 1.0 N A:ASP209 4.3 73.6 1.0 C A:ASP206 4.3 0.3 1.0 CA A:ASP206 4.3 0.4 1.0 OD2 A:ASP242 4.4 0.0 1.0 CA A:CA417 4.4 72.8 1.0 CB A:ASP242 4.4 0.1 1.0 NH1 A:ARG174 4.5 93.8 1.0 CB A:ASP206 4.6 96.2 1.0 CB A:VAL207 4.6 90.1 1.0 CB A:ASP209 4.7 84.3 1.0 N A:ASN208 4.7 0.9 1.0 CD A:ARG174 4.7 85.7 1.0 CG A:GLU116 4.7 0.6 1.0 CB A:ARG174 4.8 78.2 1.0 CA A:ASP242 4.8 0.4 1.0 CG A:GLU175 4.8 0.1 1.0 CA A:ASP209 4.9 68.3 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Protocadherin Beta 1 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 Beta 1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca417 b:72.8 occ:1.00 OD2 A:ASP209 2.4 81.8 1.0 OD1 A:ASP173 2.4 90.9 1.0 OE1 A:GLU175 2.5 82.6 1.0 OE2 A:GLU116 2.5 0.7 1.0 CG A:ASP209 3.1 83.7 1.0 OD1 A:ASP209 3.4 83.6 1.0 CD A:GLU175 3.5 91.2 1.0 CG A:ASP173 3.6 99.5 1.0 CD A:GLU116 3.7 0.9 1.0 OE2 A:GLU175 4.0 74.8 1.0 OD2 A:ASP173 4.2 0.4 1.0 OE1 A:GLU116 4.3 0.7 1.0 CB A:ASP209 4.3 84.3 1.0 CA A:CA416 4.4 65.5 1.0 O A:ASP209 4.5 66.3 1.0 CG A:GLU175 4.6 0.1 1.0 CE1 A:HIS210 4.6 73.2 1.0 CG A:GLU116 4.7 0.6 1.0 NE2 A:HIS210 4.8 74.2 1.0 CB A:ASP173 4.8 0.7 1.0 CA A:ASP173 4.9 0.3 1.0 ND1 A:HIS210 5.0 69.6 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Protocadherin Beta 1 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 Beta 1 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca418 b:76.2 occ:1.00 O A:HIS210 2.4 61.3 1.0 OD2 A:ASP295 2.4 86.3 1.0 OD2 A:ASP240 2.5 0.3 1.0 OD1 A:ASN208 2.6 0.1 1.0 OD2 A:ASP242 2.8 0.0 1.0 OD1 A:ASP240 2.8 0.2 1.0 CG A:ASP240 3.0 0.7 1.0 O A:ASN246 3.2 84.6 1.0 CG A:ASP295 3.3 84.2 1.0 CG A:ASN208 3.4 0.6 1.0 C A:HIS210 3.5 68.5 1.0 ND2 A:ASN208 3.8 0.3 1.0 CG A:ASP242 3.8 0.9 1.0 OD1 A:ASP295 3.9 95.8 1.0 CB A:ASP295 4.2 81.8 1.0 C A:ASN246 4.2 91.8 1.0 CA A:HIS210 4.2 67.6 1.0 N A:HIS210 4.3 65.1 1.0 CB A:ASP242 4.3 0.1 1.0 CB A:HIS210 4.4 70.4 1.0 CB A:ASP240 4.5 0.7 1.0 N A:VAL211 4.5 80.2 1.0 CB A:ASN208 4.6 0.3 1.0 CA A:ASN208 4.6 95.1 1.0 CA A:VAL211 4.7 79.0 1.0 CD A:PRO212 4.7 59.0 1.0 CD1 A:LEU299 4.7 80.4 1.0 CB A:ASN246 4.8 90.2 1.0 C A:ASN208 4.8 79.3 1.0 OD1 A:ASP242 4.9 0.3 1.0 N A:PRO212 4.9 74.7 1.0 C A:VAL211 4.9 75.7 1.0 CA A:ASN246 5.0 100.0 1.0 CG A:PRO212 5.0 59.7 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