Calcium in PDB 7jgz: Protocadherin GAMMAC4 EC1-4 Crystal Structure

The structure of Protocadherin GAMMAC4 EC1-4 Crystal Structure, PDB code: 7jgz was solved by K.M.Goodman, 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)	38.50 / 3.51
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.22, 115.68, 194.48, 90, 90, 90
R / Rfree (%)	22.3 / 27.1

The binding sites of Calcium atom in the Protocadherin GAMMAC4 EC1-4 Crystal Structure (pdb code 7jgz). 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 GAMMAC4 EC1-4 Crystal Structure, PDB code: 7jgz:
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 GAMMAC4 EC1-4 Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Protocadherin GAMMAC4 EC1-4 Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:61.3 occ:1.00 OD1 A:ASP62 2.5 127.7 1.0 OE2 A:GLU9 2.6 122.3 1.0 OE1 A:GLU64 2.6 112.3 1.0 OD2 A:ASP99 2.8 99.0 1.0 CG A:ASP62 3.3 124.0 1.0 OE1 A:GLU8 3.4 105.2 1.0 NE2 A:HIS100 3.4 87.3 1.0 CG A:ASP99 3.6 98.8 1.0 CD A:GLU9 3.6 125.2 1.0 OD1 A:ASP99 3.8 95.0 1.0 CD A:GLU64 3.8 111.2 1.0 OD2 A:ASP62 3.9 124.7 1.0 CD2 A:HIS100 4.0 83.1 1.0 CD A:GLU8 4.2 109.8 1.0 CG A:GLU9 4.2 124.6 1.0 CA A:CA504 4.3 79.8 1.0 CB A:ASP62 4.4 114.7 1.0 CB A:GLU64 4.4 96.6 1.0 OE2 A:GLU8 4.5 108.6 1.0 CG A:GLU64 4.5 104.8 1.0 CE1 A:HIS100 4.5 86.1 1.0 OE1 A:GLU9 4.6 127.9 1.0 CA A:ASP62 4.7 102.4 1.0 OE2 A:GLU64 4.7 114.2 1.0 N A:GLU64 4.9 105.1 1.0 CB A:ASP99 5.0 101.6 1.0

Calcium binding site 2 out of 9 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Protocadherin GAMMAC4 EC1-4 Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:79.8 occ:1.00 OE2 A:GLU8 2.3 108.6 1.0 OE2 A:GLU64 2.3 114.2 1.0 OD1 A:ASP99 2.4 95.0 1.0 OD1 A:ASP132 2.5 107.2 1.0 O A:VAL97 2.5 129.0 1.0 OD1 A:ASP96 2.6 84.6 1.0 OE1 A:GLU64 2.8 112.3 1.0 CD A:GLU64 2.8 111.2 1.0 CD A:GLU8 3.3 109.8 1.0 CG A:ASP132 3.4 106.3 1.0 CG A:ASP99 3.5 98.8 1.0 CG A:ASP96 3.6 94.0 1.0 C A:VAL97 3.7 127.6 1.0 OE1 A:GLU8 3.8 105.2 1.0 CD2 A:HIS100 4.0 83.1 1.0 OD2 A:ASP132 4.0 104.2 1.0 N A:VAL97 4.0 107.6 1.0 OD2 A:ASP99 4.0 99.0 1.0 N A:ASP99 4.1 99.3 1.0 CG A:GLU64 4.1 104.8 1.0 OD2 A:ASP96 4.2 91.7 1.0 CA A:CA503 4.3 61.3 1.0 CG2 A:VAL97 4.4 95.8 1.0 CB A:ASP132 4.4 104.7 1.0 CA A:VAL97 4.4 113.9 1.0 CG A:GLU8 4.5 113.8 1.0 CA A:ASP132 4.6 102.5 1.0 N A:ASN98 4.7 119.9 1.0 CB A:ASP99 4.7 101.6 1.0 CB A:ASP96 4.8 102.7 1.0 NE2 A:HIS100 4.8 87.3 1.0 CA A:ASP99 4.8 95.1 1.0 C A:ASP96 4.8 107.3 1.0 CA A:ASP96 4.9 106.2 1.0 CA A:ASN98 4.9 109.2 1.0 N A:HIS100 5.0 85.9 1.0 CG A:HIS100 5.0 78.6 1.0

Calcium binding site 3 out of 9 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Protocadherin GAMMAC4 EC1-4 Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:63.3 occ:1.00 O A:HIS100 2.3 85.4 1.0 OD2 A:ASP130 2.4 77.9 1.0 OD1 A:ASN98 2.5 108.9 1.0 OD1 A:ASP130 2.5 83.3 1.0 O A:ASN136 2.5 72.7 1.0 OD2 A:ASP132 2.7 104.2 1.0 CG A:ASP130 2.8 77.7 1.0 OD2 A:ASP187 2.9 109.2 1.0 C A:HIS100 3.5 87.2 1.0 CG A:ASP132 3.6 106.3 1.0 CG A:ASP187 3.6 105.8 1.0 CG A:ASN98 3.7 109.7 1.0 C A:ASN136 3.7 73.6 1.0 CB A:ASP187 3.8 99.1 1.0 CB A:ASP132 3.9 104.7 1.0 CB A:HIS100 4.3 74.6 1.0 CA A:HIS100 4.3 82.8 1.0 CB A:ASP130 4.3 73.6 1.0 ND2 A:ASN98 4.4 108.3 1.0 N A:HIS100 4.4 85.9 1.0 CB A:ASN136 4.5 81.7 1.0 CA A:ASN136 4.5 78.6 1.0 N A:ALA101 4.5 88.7 1.0 OD1 A:ASP187 4.5 109.5 1.0 OD1 A:ASP132 4.6 107.2 1.0 N A:SER137 4.7 76.3 1.0 CA A:ALA101 4.7 82.9 1.0 CA A:ASN98 4.8 109.2 1.0 CD A:PRO102 4.8 81.6 1.0 CA A:SER137 4.8 83.7 1.0 CB A:ASN98 4.8 110.4 1.0 C A:ASN98 5.0 104.6 1.0 C A:ALA101 5.0 80.2 1.0

Calcium binding site 4 out of 9 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Protocadherin GAMMAC4 EC1-4 Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:65.9 occ:1.00 OD2 A:ASP208 2.1 94.6 1.0 OD1 A:ASP172 2.8 64.4 1.0 CG A:ASP208 3.0 85.8 1.0 OE1 A:GLU174 3.1 75.7 1.0 OE2 A:GLU115 3.1 69.5 1.0 CG A:ASP172 3.4 67.0 1.0 OD1 A:ASP208 3.5 87.1 1.0 CD A:GLU115 3.6 68.8 1.0 OD2 A:ASP172 3.7 70.2 1.0 OE1 A:GLU115 4.0 71.3 1.0 ND2 A:ASN209 4.0 74.8 1.0 CB A:ASP208 4.1 82.9 1.0 CD A:GLU174 4.3 79.0 1.0 CB A:ASP172 4.3 67.5 1.0 CG A:GLU115 4.4 65.1 1.0 CA A:CA507 4.5 46.0 1.0 CA A:ASP172 4.6 67.9 1.0 CB A:GLU174 4.9 74.3 1.0 CG A:GLU174 5.0 81.4 1.0 CG A:ASN209 5.0 71.3 1.0

Calcium binding site 5 out of 9 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Protocadherin GAMMAC4 EC1-4 Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:46.0 occ:1.00 OE2 A:GLU174 2.3 78.4 1.0 OD1 A:ASP208 2.3 87.1 1.0 OD1 A:ASP205 2.4 63.7 1.0 OE1 A:GLU174 2.5 75.7 1.0 O A:VAL206 2.5 83.9 1.0 CD A:GLU174 2.7 79.0 1.0 OD1 A:ASP241 2.7 90.3 1.0 OE1 A:GLU115 2.7 71.3 1.0 CG A:ASP241 3.3 89.1 1.0 CG A:ASP208 3.4 85.8 1.0 CG A:ASP205 3.5 76.8 1.0 CD A:GLU115 3.6 68.8 1.0 ND2 A:ASN209 3.6 74.8 1.0 OE2 A:GLU115 3.7 69.5 1.0 C A:VAL206 3.8 83.2 1.0 OD2 A:ASP241 3.8 88.2 1.0 OD2 A:ASP208 3.9 94.6 1.0 CG A:GLU174 4.0 81.4 1.0 OD2 A:ASP205 4.1 80.2 1.0 N A:ASP208 4.1 69.5 1.0 CB A:ASP241 4.1 88.8 1.0 N A:VAL206 4.1 61.7 1.0 CA A:ASP241 4.4 83.0 1.0 NE A:ARG173 4.5 70.8 1.0 CA A:CA506 4.5 65.9 1.0 CA A:VAL206 4.6 63.7 1.0 CB A:ASP205 4.6 76.3 1.0 NH2 A:ARG173 4.6 77.1 1.0 CB A:ASP208 4.7 82.9 1.0 N A:ASN207 4.7 61.6 1.0 CA A:ASN207 4.8 56.8 1.0 CA A:ASP205 4.8 60.7 1.0 CA A:ASP208 4.8 75.3 1.0 CG A:ASN209 4.9 71.3 1.0 N A:ASN209 4.9 63.4 1.0 C A:ASP205 4.9 62.0 1.0 C A:ASN207 5.0 60.0 1.0

Calcium binding site 6 out of 9 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Protocadherin GAMMAC4 EC1-4 Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:32.8 occ:1.00 OD1 A:ASP239 2.3 59.5 1.0 O A:ASN209 2.3 63.4 1.0 O A:SER245 2.4 45.4 1.0 ND2 A:ASN207 2.5 60.5 1.0 OD2 A:ASP239 2.6 57.1 1.0 OD2 A:ASP241 2.6 88.2 1.0 CG A:ASP239 2.8 57.0 1.0 OD2 A:ASP295 2.9 48.1 1.0 CG A:ASP241 3.2 89.1 1.0 CB A:ASP241 3.5 88.8 1.0 C A:ASN209 3.5 66.7 1.0 C A:SER245 3.6 52.3 1.0 CG A:ASP295 3.7 49.2 1.0 CG A:ASN207 3.7 61.4 1.0 CB A:ASP295 3.8 51.2 1.0 OD1 A:ASP241 4.2 90.3 1.0 CA A:ASN209 4.2 64.3 1.0 OD1 A:ASN207 4.3 63.2 1.0 CB A:ASN209 4.3 65.8 1.0 CB A:ASP239 4.3 54.7 1.0 N A:ASN209 4.3 63.4 1.0 N A:GLY246 4.5 62.7 1.0 CA A:SER245 4.5 54.4 1.0 N A:ASP241 4.5 71.5 1.0 N A:ALA210 4.5 72.0 1.0 CA A:GLY246 4.6 70.2 1.0 CA A:ASP241 4.6 83.0 1.0 CB A:SER245 4.7 57.5 1.0 OD1 A:ASP295 4.7 50.1 1.0 CA A:ALA210 4.7 73.5 1.0 CB A:ASN207 4.8 59.4 1.0 CA A:ASN207 4.9 56.8 1.0 C A:ALA210 4.9 72.8 1.0

Calcium binding site 7 out of 9 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Protocadherin GAMMAC4 EC1-4 Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca509 b:42.7 occ:1.00 OD1 A:ASP280 2.4 81.7 1.0 OE1 A:GLU282 2.7 76.0 1.0 OD2 A:ASP316 2.8 76.4 1.0 ND2 A:ASN317 3.2 74.4 1.0 OE1 A:GLU224 3.3 72.4 1.0 CG A:ASP280 3.3 79.9 1.0 CG A:ASP316 3.4 77.2 1.0 OD1 A:ASP316 3.4 77.1 1.0 CD A:GLU282 3.6 80.5 1.0 OD2 A:ASP280 3.7 86.5 1.0 CA A:CA510 3.9 70.9 1.0 CG A:ASN317 4.1 72.5 1.0 OD1 A:ASN317 4.2 79.3 1.0 CD A:GLU224 4.2 72.8 1.0 CG A:GLU282 4.3 87.0 1.0 CB A:ASP280 4.4 75.6 1.0 CB A:GLU282 4.4 87.9 1.0 OE2 A:GLU282 4.4 85.1 1.0 OE2 A:GLU224 4.5 76.3 1.0 CA A:ASP280 4.5 77.5 1.0 CB A:ASP316 4.7 72.7 1.0 N A:GLU282 4.8 76.1 1.0 N A:PHE281 4.9 78.1 1.0

Calcium binding site 8 out of 9 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Protocadherin GAMMAC4 EC1-4 Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca510 b:70.9 occ:1.00 OE2 A:GLU282 2.2 85.1 1.0 OE2 A:GLU224 2.3 76.3 1.0 OD1 A:ASP316 2.3 77.1 1.0 OD1 A:ASP349 2.4 81.9 1.0 O A:VAL314 2.5 75.5 1.0 OD1 A:ASP313 2.6 76.4 1.0 OE1 A:GLU282 2.7 76.0 1.0 CD A:GLU282 2.8 80.5 1.0 CD A:GLU224 3.2 72.8 1.0 CG A:ASP316 3.4 77.2 1.0 CG A:ASP349 3.5 85.7 1.0 OE1 A:GLU224 3.6 72.4 1.0 C A:VAL314 3.7 76.3 1.0 OD2 A:ASP316 3.8 76.4 1.0 ND2 A:ASN317 3.8 74.4 1.0 CG A:ASP313 3.9 79.3 1.0 N A:VAL314 3.9 68.7 1.0 CA A:CA509 3.9 42.7 1.0 N A:ASP316 4.2 64.1 1.0 CG A:GLU282 4.2 87.0 1.0 CB A:ASP349 4.3 91.4 1.0 OD2 A:ASP349 4.3 82.3 1.0 CA A:VAL314 4.4 69.7 1.0 CG A:GLU224 4.5 69.3 1.0 CA A:ASP349 4.5 91.7 1.0 CB A:ASP316 4.6 72.7 1.0 OD2 A:ASP313 4.6 79.0 1.0 CB A:PHE281 4.7 82.0 1.0 N A:ASN315 4.8 66.2 1.0 CA A:ASP313 4.8 82.2 1.0 C A:ASP313 4.8 76.7 1.0 CB A:ASP313 4.8 85.6 1.0 CA A:ASP316 4.9 64.8 1.0 CA A:ASN315 4.9 64.7 1.0

Calcium binding site 9 out of 9 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Protocadherin GAMMAC4 EC1-4 Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca511 b:47.2 occ:1.00 O A:ASN317 2.3 85.2 1.0 OD1 A:ASN315 2.3 79.3 1.0 O A:ASN353 2.4 72.6 1.0 OD2 A:ASP347 2.5 100.8 1.0 OD2 A:ASP349 2.5 82.3 1.0 OD2 A:ASP400 2.6 103.0 1.0 OD1 A:ASP347 2.9 102.5 1.0 CG A:ASP347 3.0 99.8 1.0 CG A:ASN315 3.5 78.0 1.0 CG A:ASP400 3.5 104.4 1.0 CG A:ASP349 3.5 85.7 1.0 C A:ASN317 3.5 82.7 1.0 C A:ASN353 3.6 86.8 1.0 CB A:ASP400 3.8 102.0 1.0 CB A:ASP349 3.8 91.4 1.0 ND2 A:ASN315 4.0 75.0 1.0 CD1 A:LEU406 4.3 57.2 1.0 CA A:ASN353 4.3 103.5 1.0 N A:ASN317 4.4 65.9 1.0 CA A:ASN317 4.4 70.6 1.0 N A:ALA318 4.5 85.5 1.0 CB A:ASN353 4.5 105.0 1.0 CB A:ASP347 4.5 99.6 1.0 OD1 A:ASP400 4.5 107.5 1.0 N A:GLY354 4.6 95.2 1.0 CA A:ALA318 4.6 88.3 1.0 OD1 A:ASP349 4.6 81.9 1.0 CA A:GLY354 4.6 105.1 1.0 CB A:ASN317 4.7 64.7 1.0 CB A:ASN315 4.7 72.9 1.0 CA A:ASN315 4.8 64.7 1.0 N A:ASP349 5.0 93.0 1.0 C A:ALA318 5.0 89.7 1.0

K.M.Goodman, P.S.Katsamba, R.Rubinstein, G.Ahlsen, F.Bahna, S.Mannepalli, L.Shapiro, B.Honig. How Clustered Protocadherin Binding Specificity Is Tuned For Neuronal Self/Non-Self-Recognition To Be Published.