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

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

Resolution Low / High (Å)	27.94 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.188, 84.563, 109.144, 90.00, 106.43, 90.00
R / Rfree (%)	21 / 24.8

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Protocadherin Gamma C5 EC1-3 (pdb code 4zpp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of Protocadherin Gamma C5 EC1-3, PDB code: 4zpp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 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:78.3 occ:1.00 O A:ASN209 2.4 73.5 1.0 O A:ASN245 2.5 87.1 1.0 OD1 A:ASN207 2.5 76.7 1.0 OD2 A:ASP241 2.5 88.4 1.0 OD1 A:ASP239 2.5 81.1 1.0 OD2 A:ASP239 2.5 97.6 1.0 CG A:ASP239 2.8 87.6 1.0 OD2 A:ASP295 2.9 0.7 1.0 CG A:ASP295 3.3 83.9 1.0 CG A:ASP241 3.5 85.3 1.0 C A:ASN245 3.6 95.0 1.0 C A:ASN209 3.6 78.7 1.0 CB A:ASP295 3.6 85.3 1.0 CG A:ASN207 3.7 91.6 1.0 CB A:ASP241 3.9 80.1 1.0 OD1 A:ASP295 4.2 80.3 1.0 CB A:ASP239 4.3 86.1 1.0 ND2 A:ASN207 4.3 0.4 1.0 CB A:ASN245 4.3 0.4 1.0 CA A:ASN245 4.3 1.0 1.0 CA A:ASN209 4.5 67.3 1.0 N A:ALA210 4.5 85.8 1.0 CA A:ALA210 4.6 77.2 1.0 N A:ASN209 4.6 70.8 1.0 OD1 A:ASP241 4.6 89.6 1.0 N A:GLY246 4.6 99.6 1.0 CD A:PRO211 4.7 81.1 1.0 CB A:ASN209 4.7 76.3 1.0 CA A:GLY246 4.8 0.0 1.0 CB A:ASN207 4.8 83.4 1.0 CA A:ASN207 4.9 81.5 1.0 C A:ALA210 4.9 76.4 1.0

Calcium binding site 2 out of 12 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:61.1 occ:1.00 OE2 A:GLU115 2.3 95.9 1.0 OE2 A:GLU174 2.4 73.9 1.0 OD1 A:ASP172 2.5 73.1 1.0 OD2 A:ASP208 2.6 0.8 1.0 OD1 A:ASP208 2.7 71.2 1.0 CD A:GLU115 3.0 90.3 1.0 CG A:ASP208 3.0 87.4 1.0 OE1 A:GLU115 3.4 67.0 1.0 CG A:ASP172 3.7 73.8 1.0 CD A:GLU174 3.7 79.7 1.0 CA A:CA403 4.0 64.6 1.0 CG A:GLU115 4.0 0.3 1.0 OD1 A:ASN209 4.0 78.9 1.0 CA A:ASP172 4.3 67.8 1.0 CB A:ASP172 4.4 71.1 1.0 CB A:ASP208 4.4 74.3 1.0 OE1 A:GLU174 4.4 74.8 1.0 N A:ARG173 4.5 67.1 1.0 OD2 A:ASP172 4.6 96.4 1.0 CG A:GLU174 4.6 79.1 1.0 C A:ASP172 4.7 68.1 1.0 N A:GLU174 4.8 79.5 1.0 CB A:GLU174 4.8 79.3 1.0

Calcium binding site 3 out of 12 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:64.6 occ:1.00 O A:VAL206 2.4 80.3 1.0 OE1 A:GLU174 2.4 74.8 1.0 OD1 A:ASP205 2.5 72.2 1.0 OD1 A:ASP241 2.7 89.6 1.0 OE1 A:GLU115 2.8 67.0 1.0 OE2 A:GLU174 2.9 73.9 1.0 OD1 A:ASP208 2.9 71.2 1.0 CD A:GLU174 2.9 79.7 1.0 C A:VAL206 3.5 80.3 1.0 N A:VAL206 3.5 86.4 1.0 CG A:ASP205 3.6 80.3 1.0 CG A:ASP241 3.7 85.3 1.0 CD A:GLU115 3.7 90.3 1.0 OE2 A:GLU115 3.8 95.9 1.0 CA A:CA402 4.0 61.1 1.0 CG A:ASP208 4.0 87.4 1.0 CA A:VAL206 4.1 77.9 1.0 OD2 A:ASP205 4.2 1.0 1.0 OD1 A:ASN209 4.2 78.9 1.0 N A:ASP208 4.3 85.0 1.0 CB A:ASP241 4.3 80.1 1.0 CG A:GLU174 4.4 79.1 1.0 CA A:ASP241 4.4 81.1 1.0 N A:ASN207 4.5 88.8 1.0 C A:ASP205 4.5 86.3 1.0 OD2 A:ASP241 4.6 88.4 1.0 NE A:ARG173 4.6 82.9 1.0 CA A:ASP205 4.6 79.5 1.0 OD2 A:ASP208 4.6 0.8 1.0 CB A:ASP205 4.7 73.1 1.0 CB A:VAL206 4.7 78.5 1.0 CB A:ARG173 4.8 67.3 1.0 CA A:ASN207 4.8 81.5 1.0 CB A:ASP208 5.0 74.3 1.0

Calcium binding site 4 out of 12 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:60.8 occ:1.00 O A:ASN136 2.3 51.0 1.0 OD1 A:ASN98 2.3 54.9 1.0 O A:ASN100 2.3 48.4 1.0 OD2 A:ASP130 2.5 71.9 1.0 OD2 A:ASP132 2.5 54.3 1.0 OD2 A:ASP187 2.6 51.0 1.0 OD1 A:ASP130 2.8 47.6 1.0 CG A:ASP130 3.0 56.8 1.0 CG A:ASN98 3.4 57.8 1.0 CG A:ASP132 3.5 59.3 1.0 C A:ASN136 3.5 71.4 1.0 C A:ASN100 3.5 48.2 1.0 CG A:ASP187 3.7 74.5 1.0 CB A:ASP132 3.8 60.1 1.0 CB A:ASP187 4.0 56.5 1.0 ND2 A:ASN98 4.0 56.5 1.0 N A:ASN100 4.2 49.9 1.0 CA A:ASN100 4.3 48.9 1.0 CA A:ASN136 4.3 55.1 1.0 CD A:ARG193 4.3 55.6 1.0 CB A:ASN136 4.4 55.0 1.0 N A:SER101 4.5 48.0 1.0 N A:THR137 4.5 75.5 1.0 CB A:ASP130 4.5 55.2 1.0 OD1 A:ASP132 4.5 65.6 1.0 CB A:ASN100 4.5 48.5 1.0 CA A:ASN98 4.6 59.9 1.0 CB A:ASN98 4.6 56.9 1.0 C A:ASN98 4.6 58.8 1.0 CA A:THR137 4.7 64.7 1.0 CA A:SER101 4.7 47.6 1.0 O A:ASN98 4.7 57.9 1.0 OD1 A:ASP187 4.8 90.3 1.0 CD A:PRO102 4.8 50.6 1.0 CG A:ARG193 4.9 53.7 1.0 N A:ASP99 5.0 59.9 1.0

Calcium binding site 5 out of 12 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:52.8 occ:1.00 O A:LEU97 2.4 78.0 1.0 OE2 A:GLU64 2.4 76.7 1.0 OE1 A:GLU64 2.5 84.4 1.0 OD1 A:ASP96 2.5 57.3 1.0 OD1 A:ASP99 2.6 52.4 1.0 OD1 A:ASP132 2.7 65.6 1.0 CD A:GLU64 2.7 75.4 1.0 OE1 A:GLU8 2.8 54.2 1.0 OE2 A:GLU8 3.2 56.0 1.0 CD A:GLU8 3.4 65.0 1.0 CG A:ASP132 3.5 59.3 1.0 C A:LEU97 3.6 80.5 1.0 CG A:ASP96 3.7 74.3 1.0 N A:LEU97 3.8 68.2 1.0 CG A:ASP99 3.8 57.6 1.0 CA A:CA406 3.9 63.5 1.0 ND2 A:ASN100 4.1 54.6 1.0 CA A:LEU97 4.2 59.4 1.0 OD2 A:ASP132 4.2 54.3 1.0 CG A:GLU64 4.2 60.2 1.0 NH1 A:ARG63 4.2 54.6 1.0 N A:ASP99 4.3 59.9 1.0 CB A:ASP132 4.3 60.1 1.0 OD2 A:ASP96 4.3 92.5 1.0 OD2 A:ASP99 4.4 61.7 1.0 CG A:ARG63 4.4 55.4 1.0 CA A:ASP132 4.4 60.9 1.0 C A:ASP96 4.6 74.6 1.0 CB A:LEU97 4.6 58.3 1.0 N A:ASN98 4.7 62.3 1.0 CA A:ASP96 4.7 68.4 1.0 CD A:ARG63 4.8 48.3 1.0 CB A:ASP96 4.8 71.0 1.0 CG A:GLU8 4.8 63.2 1.0 CA A:ASN98 4.9 59.9 1.0 CB A:ASP99 4.9 54.7 1.0

Calcium binding site 6 out of 12 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:63.5 occ:1.00 OE2 A:GLU8 2.2 56.0 1.0 OE2 A:GLU64 2.4 76.7 1.0 OD2 A:ASP99 2.5 61.7 1.0 OD1 A:ASP62 2.5 64.8 1.0 OE2 A:GLU9 2.5 54.7 1.0 OD1 A:ASP99 3.1 52.4 1.0 NH2 B:ARG193 3.1 68.2 1.0 CG A:ASP99 3.1 57.6 1.0 ND2 A:ASN100 3.4 54.6 1.0 CD A:GLU8 3.4 65.0 1.0 CG A:ASP62 3.6 54.3 1.0 CD A:GLU9 3.6 70.5 1.0 CD A:GLU64 3.6 75.4 1.0 OG B:SER101 3.9 48.6 1.0 CA A:CA405 3.9 52.8 1.0 CG A:GLU9 4.0 63.4 1.0 OE1 A:GLU8 4.2 54.2 1.0 CB A:GLU64 4.2 58.0 1.0 OD2 A:ASP62 4.2 57.1 1.0 CG A:GLU64 4.3 60.2 1.0 CZ B:ARG193 4.3 62.2 1.0 CG A:GLU8 4.4 63.2 1.0 CB A:ASP62 4.5 66.7 1.0 OE1 A:GLU64 4.6 84.4 1.0 CB A:ASP99 4.6 54.7 1.0 OE1 A:GLU9 4.6 75.4 1.0 O B:ASP99 4.6 57.0 1.0 CG A:ASN100 4.7 59.9 1.0 CA A:ASP62 4.7 48.1 1.0 N A:GLU64 4.7 60.8 1.0 NE B:ARG193 4.7 71.5 1.0 N A:ARG63 4.9 49.3 1.0

Calcium binding site 7 out of 12 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 7 of Crystal Structure of Protocadherin Gamma C5 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:0.8 occ:1.00 OD1 B:ASN207 2.4 0.6 1.0 O B:ASN209 2.5 0.2 1.0 O B:ASN245 2.5 0.1 1.0 OD2 B:ASP239 2.5 0.5 1.0 OD2 B:ASP241 2.6 0.1 1.0 OD1 B:ASP239 2.7 0.2 1.0 CG B:ASP239 2.9 0.3 1.0 OD2 B:ASP295 3.0 0.5 1.0 CG B:ASP295 3.5 0.8 1.0 CG B:ASP241 3.6 0.0 1.0 CG B:ASN207 3.6 0.5 1.0 C B:ASN245 3.7 0.4 1.0 C B:ASN209 3.7 0.0 1.0 CB B:ASP241 3.8 0.6 1.0 OD1 B:ASP295 3.9 0.8 1.0 ND2 B:ASN207 4.2 0.3 1.0 CA B:ASN245 4.3 0.1 1.0 CB B:ASN245 4.4 1.0 1.0 CB B:ASP239 4.4 0.6 1.0 CB B:ASP295 4.4 0.3 1.0 CG B:MET301 4.4 1.0 1.0 CB B:MET301 4.4 0.3 1.0 CA B:ASN209 4.6 0.3 1.0 N B:ASN209 4.6 0.6 1.0 N B:ALA210 4.6 0.2 1.0 CA B:ALA210 4.7 1.0 1.0 OD1 B:ASP241 4.7 0.9 1.0 CB B:ASN207 4.7 0.2 1.0 CD B:PRO211 4.7 0.1 1.0 N B:GLY246 4.7 0.6 1.0 CB B:ASN209 4.8 0.7 1.0 CA B:ASN207 4.9 0.2 1.0 CA B:GLY246 5.0 0.6 1.0

Calcium binding site 8 out of 12 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 8 of Crystal Structure of Protocadherin Gamma C5 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:88.2 occ:1.00 OE2 B:GLU115 2.3 0.8 1.0 OD1 B:ASP172 2.4 83.4 1.0 OD2 B:ASP208 2.5 0.1 1.0 OE2 B:GLU174 2.6 67.3 1.0 OD1 B:ASP208 2.7 1.0 1.0 CG B:ASP208 2.8 0.2 1.0 CD B:GLU115 3.0 88.7 1.0 CG B:ASP172 3.5 82.2 1.0 OE1 B:GLU115 3.7 71.0 1.0 CD B:GLU174 3.8 84.3 1.0 CG B:GLU115 3.8 72.4 1.0 OD1 B:ASN209 4.1 0.4 1.0 CB B:ASP208 4.2 0.1 1.0 CA B:CA403 4.2 74.6 1.0 CB B:ASP172 4.2 78.7 1.0 CA B:ASP172 4.2 67.8 1.0 OD2 B:ASP172 4.3 82.2 1.0 N B:ARG173 4.5 64.5 1.0 O B:HOH503 4.6 66.2 1.0 OE1 B:GLU174 4.6 71.9 1.0 CG B:GLU174 4.7 84.7 1.0 C B:ASP172 4.8 68.1 1.0 CB B:GLU174 4.8 83.3 1.0 N B:GLU174 4.9 87.4 1.0 O B:LEU171 5.0 85.8 1.0

Calcium binding site 9 out of 12 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 9 of Crystal Structure of Protocadherin Gamma C5 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:74.6 occ:1.00 O B:VAL206 2.4 83.8 1.0 OD1 B:ASP241 2.5 0.9 1.0 OD1 B:ASP205 2.5 66.0 1.0 OE1 B:GLU174 2.5 71.9 1.0 OD1 B:ASP208 2.6 1.0 1.0 OE1 B:GLU115 2.7 71.0 1.0 OE2 B:GLU174 2.9 67.3 1.0 CD B:GLU174 3.0 84.3 1.0 OE2 B:GLU115 3.4 0.8 1.0 CD B:GLU115 3.5 88.7 1.0 CG B:ASP241 3.5 0.0 1.0 C B:VAL206 3.5 79.7 1.0 N B:VAL206 3.6 88.5 1.0 CG B:ASP208 3.6 0.2 1.0 CG B:ASP205 3.7 96.0 1.0 N B:ASP208 4.1 0.0 1.0 OD1 B:ASN209 4.1 0.4 1.0 CA B:VAL206 4.2 87.9 1.0 CA B:CA402 4.2 88.2 1.0 OD2 B:ASP241 4.3 0.1 1.0 CB B:ASP241 4.3 0.6 1.0 OD2 B:ASP208 4.3 0.1 1.0 OD2 B:ASP205 4.4 0.5 1.0 CG B:GLU174 4.4 84.7 1.0 CA B:ASP241 4.5 0.3 1.0 N B:ASN207 4.5 0.4 1.0 C B:ASP205 4.6 88.9 1.0 CB B:ASP208 4.6 0.1 1.0 CA B:ASP205 4.6 82.2 1.0 NH1 B:ARG173 4.7 0.7 1.0 CB B:ASP205 4.8 90.8 1.0 CA B:ASN207 4.8 0.2 1.0 CB B:ARG173 4.8 59.2 1.0 CB B:VAL206 4.8 88.5 1.0 CA B:ASP208 4.9 0.1 1.0 CD B:ARG173 4.9 73.6 1.0 CG B:GLU115 4.9 72.4 1.0 C B:ASN207 5.0 0.2 1.0

Calcium binding site 10 out of 12 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 10 of Crystal Structure of Protocadherin Gamma C5 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:58.9 occ:1.00 O B:ASN136 2.3 47.9 1.0 O B:ASN100 2.4 44.4 1.0 OD2 B:ASP130 2.4 67.3 1.0 OD1 B:ASN98 2.4 72.4 1.0 OD2 B:ASP132 2.5 58.1 1.0 OD1 B:ASP130 2.7 64.5 1.0 OD2 B:ASP187 2.7 56.1 1.0 CG B:ASP130 2.9 76.3 1.0 C B:ASN136 3.5 54.0 1.0 CG B:ASP132 3.5 66.5 1.0 C B:ASN100 3.5 45.7 1.0 CG B:ASN98 3.6 75.5 1.0 CG B:ASP187 3.7 74.8 1.0 CB B:ASP132 3.7 78.0 1.0 CB B:ASP187 3.9 45.0 1.0 N B:ASN100 4.2 47.6 1.0 CA B:ASN100 4.2 53.7 1.0 ND2 B:ASN98 4.3 87.7 1.0 CB B:ASN100 4.3 47.3 1.0 CA B:ASN136 4.4 52.1 1.0 CB B:ASP130 4.4 74.8 1.0 N B:THR137 4.4 51.7 1.0 CD B:ARG193 4.4 70.1 1.0 CA B:THR137 4.4 56.4 1.0 CB B:ASN136 4.5 52.9 1.0 N B:SER101 4.6 49.6 1.0 OD1 B:ASP132 4.6 64.9 1.0 CA B:ASN98 4.7 60.9 1.0 C B:ASN98 4.8 58.9 1.0 CB B:ASN98 4.8 60.6 1.0 CD B:PRO102 4.8 47.4 1.0 CA B:SER101 4.8 47.5 1.0 OD1 B:ASP187 4.9 90.3 1.0 O B:ASN98 5.0 55.0 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