Calcium in PDB 7rgf: Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface

The structure of Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface, PDB code: 7rgf 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)	38.16 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.944, 103.948, 200.592, 90, 90, 90
R / Rfree (%)	19.6 / 24.1

The structure of Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface (pdb code 7rgf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface, PDB code: 7rgf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


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 Disrupted Trans Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:76.3 occ:1.00 OE1 A:GLU64 2.3 87.3 1.0 OD2 A:ASP99 2.4 84.3 1.0 OD1 A:ASP62 2.5 90.3 1.0 OE2 A:GLU9 2.6 93.8 1.0 OE1 A:GLU8 2.6 70.3 1.0 O A:HOH646 2.7 65.8 1.0 CG A:ASP99 3.4 82.8 1.0 CD A:GLU8 3.5 67.2 1.0 CG A:ASP62 3.5 88.7 1.0 CD A:GLU64 3.6 78.6 1.0 CD A:GLU9 3.6 89.1 1.0 OD1 A:ASP99 3.8 87.1 1.0 CG A:GLU9 3.9 79.2 1.0 OE2 A:GLU8 3.9 69.6 1.0 N A:ARG63 4.3 65.5 1.0 CA A:ASP62 4.3 75.3 1.0 OD2 A:ASP62 4.3 91.3 1.0 OE2 A:GLU64 4.3 78.6 1.0 CA A:CA506 4.4 60.2 1.0 CB A:ASP62 4.4 81.1 1.0 N A:GLU64 4.5 60.1 1.0 CE1 A:HIS100 4.5 77.6 1.0 CG A:GLU64 4.5 75.4 1.0 CB A:GLU64 4.5 69.8 1.0 OE1 A:GLU9 4.7 92.9 1.0 C A:ASP62 4.7 72.7 1.0 CG A:GLU8 4.7 63.9 1.0 CB A:ASP99 4.7 77.7 1.0 ND1 A:HIS100 5.0 75.9 1.0

Calcium binding site 2 out of 18 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


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 Disrupted Trans Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:60.2 occ:1.00 OD1 A:ASP99 2.3 87.1 1.0 OD1 A:ASP96 2.3 62.7 1.0 OE2 A:GLU8 2.4 69.6 1.0 OE2 A:GLU64 2.4 78.6 1.0 O A:VAL97 2.4 64.3 1.0 OD1 A:ASP132 2.5 66.3 1.0 CD A:GLU64 3.1 78.6 1.0 CG A:ASP132 3.2 65.0 1.0 OE1 A:GLU64 3.2 87.3 1.0 CG A:ASP96 3.3 65.2 1.0 CG A:ASP99 3.4 82.8 1.0 CD A:GLU8 3.5 67.2 1.0 C A:VAL97 3.6 67.8 1.0 N A:VAL97 3.8 57.0 1.0 OD2 A:ASP132 3.8 75.4 1.0 OD2 A:ASP99 3.8 84.3 1.0 OD2 A:ASP96 3.9 71.7 1.0 OE1 A:GLU8 4.0 70.3 1.0 CB A:ASP132 4.0 64.4 1.0 N A:ASP99 4.0 70.2 1.0 ND1 A:HIS100 4.1 75.9 1.0 CA A:ASP132 4.3 67.8 1.0 CA A:VAL97 4.3 62.1 1.0 CG2 A:VAL97 4.3 64.2 1.0 CA A:CA505 4.4 76.3 1.0 CB A:ASP96 4.5 58.7 1.0 NE A:ARG63 4.5 66.7 1.0 CG A:GLU64 4.5 75.4 1.0 CB A:ASP99 4.6 77.7 1.0 N A:ASN98 4.6 69.2 1.0 C A:ASP96 4.6 60.7 1.0 CA A:ASP96 4.6 55.2 1.0 CG A:GLU8 4.7 63.9 1.0 CA A:ASP99 4.7 73.5 1.0 CE1 A:HIS100 4.8 77.6 1.0 NH2 A:ARG63 4.8 75.8 1.0 CA A:ASN98 4.8 65.1 1.0 N A:ASP132 4.9 68.4 1.0 C A:ASN98 5.0 70.8 1.0 CB A:VAL97 5.0 61.8 1.0

Calcium binding site 3 out of 18 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


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 Disrupted Trans Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:52.6 occ:1.00 O A:ASN136 2.3 61.6 1.0 O A:HIS100 2.4 63.7 1.0 OD1 A:ASN98 2.4 63.2 1.0 OD1 A:ASP130 2.6 67.9 1.0 OD2 A:ASP130 2.6 65.9 1.0 OD2 A:ASP132 2.7 75.4 1.0 OD2 A:ASP187 2.9 68.8 1.0 CG A:ASP130 2.9 68.1 1.0 CG A:ASP132 3.5 65.0 1.0 C A:HIS100 3.5 69.6 1.0 C A:ASN136 3.5 61.8 1.0 CG A:ASN98 3.6 63.5 1.0 CG A:ASP187 3.6 69.5 1.0 CB A:ASP132 3.7 64.4 1.0 CB A:ASP187 3.9 71.2 1.0 CA A:HIS100 4.2 70.7 1.0 CB A:HIS100 4.2 67.5 1.0 CB A:ASN136 4.2 63.4 1.0 N A:HIS100 4.3 72.0 1.0 CA A:ASN136 4.3 62.5 1.0 ND2 A:ASN98 4.3 63.4 1.0 CB A:ASP130 4.5 61.1 1.0 N A:SER137 4.5 61.8 1.0 N A:ALA101 4.5 68.8 1.0 OD1 A:ASP132 4.5 66.3 1.0 CA A:SER137 4.6 62.6 1.0 OD1 A:ASP187 4.6 66.9 1.0 CA A:ASN98 4.7 65.1 1.0 CA A:ALA101 4.7 71.8 1.0 CB A:ASN98 4.7 64.4 1.0 CD A:PRO102 4.8 62.7 1.0 C A:ASN98 4.9 70.8 1.0 N A:ASP132 4.9 68.4 1.0 CA A:ASP132 4.9 67.8 1.0

Calcium binding site 4 out of 18 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


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 Disrupted Trans Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:77.5 occ:1.00 OD2 A:ASP208 2.4 69.0 1.0 OE2 A:GLU115 2.4 75.6 1.0 O A:HOH649 2.5 68.2 1.0 OD1 A:ASP172 2.5 83.1 1.0 O A:HOH639 2.6 72.2 1.0 OE1 A:GLU174 2.6 77.1 1.0 CD A:GLU115 3.0 71.1 1.0 CG A:ASP208 3.3 65.8 1.0 CG A:ASP172 3.4 84.2 1.0 OE1 A:GLU115 3.6 68.6 1.0 OD1 A:ASP208 3.6 63.9 1.0 CD A:GLU174 3.8 79.1 1.0 CG A:GLU115 3.8 68.4 1.0 CA A:CA509 4.0 69.2 1.0 OD2 A:ASP172 4.1 88.7 1.0 CA A:ASP172 4.2 73.3 1.0 ND2 A:ASN209 4.3 68.9 1.0 CB A:ASP172 4.3 78.3 1.0 N A:ARG173 4.4 73.1 1.0 N A:GLU174 4.5 80.3 1.0 OE2 A:GLU174 4.6 78.2 1.0 CB A:GLU174 4.6 84.2 1.0 C A:ASP172 4.6 74.5 1.0 CG A:GLU174 4.6 83.3 1.0 CB A:ASP208 4.7 64.6 1.0

Calcium binding site 5 out of 18 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


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 Disrupted Trans Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca509 b:69.2 occ:1.00 OD1 A:ASP205 2.4 73.2 1.0 OD1 A:ASP208 2.4 63.9 1.0 O A:VAL206 2.4 69.3 1.0 OE2 A:GLU174 2.4 78.2 1.0 OE1 A:GLU174 2.6 77.1 1.0 OD1 A:ASP241 2.8 69.8 1.0 OE1 A:GLU115 2.8 68.6 1.0 CD A:GLU174 2.8 79.1 1.0 CG A:ASP208 3.4 65.8 1.0 CG A:ASP241 3.4 63.2 1.0 CG A:ASP205 3.4 77.2 1.0 CD A:GLU115 3.5 71.1 1.0 OE2 A:GLU115 3.5 75.6 1.0 C A:VAL206 3.6 68.6 1.0 OD2 A:ASP208 3.8 69.0 1.0 ND2 A:ASN209 3.9 68.9 1.0 N A:VAL206 3.9 66.1 1.0 OD2 A:ASP205 4.0 78.9 1.0 OD2 A:ASP241 4.0 63.8 1.0 CA A:CA508 4.0 77.5 1.0 N A:ASP208 4.1 61.8 1.0 CB A:ASP241 4.2 57.4 1.0 CG A:GLU174 4.2 83.3 1.0 CA A:VAL206 4.4 65.1 1.0 CA A:ASP241 4.5 61.2 1.0 NE A:ARG173 4.5 86.0 1.0 CB A:ASP205 4.6 71.2 1.0 NH2 A:ARG173 4.6 82.1 1.0 CB A:ASP208 4.6 64.6 1.0 N A:ASN207 4.7 62.0 1.0 CA A:ASP205 4.7 68.3 1.0 C A:ASP205 4.7 66.4 1.0 CA A:ASN207 4.8 62.8 1.0 CA A:ASP208 4.9 61.0 1.0

Calcium binding site 6 out of 18 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


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 Disrupted Trans Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca510 b:51.1 occ:1.00 O A:ASN209 2.3 51.5 1.0 O A:SER245 2.3 51.8 1.0 OD1 A:ASN207 2.5 67.5 1.0 OD1 A:ASP239 2.6 55.5 1.0 OD2 A:ASP239 2.6 54.3 1.0 OD2 A:ASP295 2.6 64.8 1.0 OD2 A:ASP241 2.7 63.8 1.0 CG A:ASP239 2.9 56.0 1.0 CG A:ASP241 3.4 63.2 1.0 C A:ASN209 3.5 62.5 1.0 C A:SER245 3.5 57.1 1.0 CG A:ASN207 3.6 71.2 1.0 CG A:ASP295 3.6 65.2 1.0 CB A:ASP241 3.7 57.4 1.0 CB A:ASP295 3.9 57.9 1.0 ND2 A:ASN207 4.2 51.2 1.0 CA A:ASN209 4.2 61.2 1.0 N A:ASN209 4.2 64.5 1.0 CA A:SER245 4.3 60.6 1.0 CB A:ASN209 4.3 63.1 1.0 CB A:SER245 4.3 68.4 1.0 OD1 A:ASP241 4.4 69.8 1.0 CB A:ASP239 4.4 52.3 1.0 N A:ALA210 4.5 59.1 1.0 N A:GLY246 4.5 59.7 1.0 OD1 A:ASP295 4.6 65.8 1.0 CA A:GLY246 4.6 50.0 1.0 CA A:ALA210 4.7 59.7 1.0 CB A:ASN207 4.7 55.5 1.0 CG A:MET301 4.7 72.8 1.0 CA A:ASN207 4.8 62.8 1.0 N A:ASP241 4.8 57.3 1.0 CB A:MET301 4.9 65.8 1.0 CA A:ASP241 4.9 61.2 1.0 C A:ASN207 5.0 65.0 1.0 C A:ALA210 5.0 58.5 1.0

Calcium binding site 7 out of 18 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


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 Disrupted Trans Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca511 b:66.4 occ:1.00 OD2 A:ASP316 2.4 70.2 1.0 OE2 A:GLU282 2.4 70.1 1.0 OD1 A:ASP280 2.4 91.1 1.0 O A:HOH645 2.5 60.3 1.0 OE1 A:GLU224 2.6 64.4 1.0 O A:HOH648 2.7 69.5 1.0 CG A:ASP316 3.3 72.0 1.0 CG A:ASP280 3.4 83.4 1.0 OD1 A:ASP316 3.5 78.7 1.0 CD A:GLU224 3.6 63.1 1.0 CD A:GLU282 3.6 72.0 1.0 CA A:CA512 3.9 60.7 1.0 OE2 A:GLU224 4.1 75.5 1.0 CA A:ASP280 4.1 55.7 1.0 OD2 A:ASP280 4.2 91.2 1.0 CB A:ASP280 4.3 63.8 1.0 ND2 A:ASN317 4.3 75.7 1.0 N A:PHE281 4.3 62.2 1.0 OE1 A:GLU282 4.4 73.1 1.0 CG A:GLU282 4.6 77.2 1.0 C A:ASP280 4.6 63.7 1.0 N A:GLU282 4.6 72.8 1.0 CG A:GLU224 4.7 60.4 1.0 CB A:ASP316 4.7 66.2 1.0 CB A:GLU282 4.7 74.0 1.0 O A:LEU279 4.9 57.5 1.0

Calcium binding site 8 out of 18 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


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 Disrupted Trans Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca512 b:60.7 occ:1.00 OE1 A:GLU282 2.4 73.1 1.0 O A:VAL314 2.4 73.2 1.0 OE2 A:GLU224 2.4 75.5 1.0 OD1 A:ASP313 2.5 77.4 1.0 OD1 A:ASP349 2.5 87.9 1.0 OD1 A:ASP316 2.5 78.7 1.0 OE2 A:GLU282 2.8 70.1 1.0 CD A:GLU282 2.9 72.0 1.0 CD A:GLU224 3.3 63.1 1.0 CG A:ASP316 3.5 72.0 1.0 OE1 A:GLU224 3.6 64.4 1.0 CG A:ASP349 3.6 81.8 1.0 C A:VAL314 3.6 70.1 1.0 N A:VAL314 3.7 71.5 1.0 CG A:ASP313 3.8 85.8 1.0 OD2 A:ASP316 3.8 70.2 1.0 CA A:CA511 3.9 66.4 1.0 ND2 A:ASN317 4.2 75.7 1.0 CA A:VAL314 4.2 69.8 1.0 N A:ASP316 4.2 67.4 1.0 CB A:ASP349 4.3 81.0 1.0 CG A:GLU282 4.3 77.2 1.0 OD2 A:ASP349 4.4 84.0 1.0 OD2 A:ASP313 4.5 78.8 1.0 CA A:ASP349 4.6 83.9 1.0 C A:ASP313 4.6 71.4 1.0 N A:ASN315 4.6 71.6 1.0 CA A:ASP313 4.6 72.6 1.0 CG A:GLU224 4.7 60.4 1.0 CB A:PHE281 4.7 71.0 1.0 CB A:ASP316 4.7 66.2 1.0 CB A:ASP313 4.7 72.7 1.0 CB A:VAL314 4.8 66.3 1.0 CA A:ASN315 4.9 75.4 1.0 CA A:ASP316 5.0 65.9 1.0

Calcium binding site 9 out of 18 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


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 Disrupted Trans Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca513 b:65.0 occ:1.00 O A:ASN317 2.3 72.1 1.0 OD1 A:ASN315 2.3 72.7 1.0 O A:ASN353 2.3 73.5 1.0 OD2 A:ASP347 2.4 80.9 1.0 OD2 A:ASP349 2.4 84.0 1.0 OD2 A:ASP400 2.6 77.2 1.0 OD1 A:ASP347 2.8 78.7 1.0 CG A:ASP347 2.9 76.6 1.0 CG A:ASP349 3.4 81.8 1.0 CG A:ASN315 3.5 74.4 1.0 C A:ASN317 3.5 68.8 1.0 C A:ASN353 3.5 85.3 1.0 CG A:ASP400 3.6 75.9 1.0 CB A:ASP349 3.7 81.0 1.0 CB A:ASP400 3.9 78.3 1.0 ND2 A:ASN315 4.1 70.7 1.0 CA A:ASN353 4.3 87.0 1.0 N A:ASN317 4.3 65.0 1.0 CA A:ASN317 4.3 69.6 1.0 CB A:ASP347 4.4 79.0 1.0 CB A:ASN353 4.4 92.1 1.0 N A:ALA318 4.5 65.4 1.0 N A:GLY354 4.5 87.3 1.0 CB A:ASN317 4.5 71.0 1.0 OD1 A:ASP349 4.5 87.9 1.0 CA A:GLY354 4.6 86.5 1.0 OD1 A:ASP400 4.6 79.2 1.0 CA A:ALA318 4.6 60.9 1.0 CB A:ASN315 4.7 73.8 1.0 CD1 A:LEU406 4.7 60.8 1.0 CA A:ASN315 4.7 75.4 1.0 N A:ASP349 4.8 84.4 1.0 CA A:ASP349 4.9 83.9 1.0 C A:ALA318 4.9 62.2 1.0

Calcium binding site 10 out of 18 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:62.3 occ:1.00 OD1 B:ASP62 2.3 70.2 1.0 OE1 B:GLU64 2.4 69.6 1.0 OD2 B:ASP99 2.4 61.7 1.0 O B:HOH660 2.6 59.6 1.0 OE1 B:GLU9 2.6 90.0 1.0 OE1 B:GLU8 2.8 71.5 1.0 CG B:ASP62 3.4 76.3 1.0 CG B:ASP99 3.4 56.3 1.0 CD B:GLU64 3.6 70.5 1.0 CD B:GLU9 3.6 86.7 1.0 OD1 B:ASP99 3.8 57.9 1.0 CD B:GLU8 3.8 69.9 1.0 CG B:GLU9 4.0 81.9 1.0 OD2 B:ASP62 4.2 78.0 1.0 CA B:ASP62 4.2 69.8 1.0 CB B:ASP62 4.3 70.1 1.0 N B:ARG63 4.3 71.0 1.0 OE2 B:GLU8 4.3 70.6 1.0 N B:GLU64 4.3 74.2 1.0 CE1 B:HIS100 4.4 69.9 1.0 CB B:GLU64 4.4 73.6 1.0 CG B:GLU64 4.4 73.2 1.0 OE2 B:GLU64 4.5 69.5 1.0 CA B:CA505 4.5 63.6 1.0 C B:ASP62 4.6 71.0 1.0 OE2 B:GLU9 4.7 90.4 1.0 CB B:ASP99 4.8 54.2 1.0 ND1 B:HIS100 4.9 66.0 1.0 CG B:GLU8 5.0 71.9 1.0

K.M.Goodman, P.S.Katsamba, R.Rubinstein, G.Ahlsen, F.Bahna, S.Mannepalli, H.Dan, R.V.Sampogna, L.Shapiro, B.Honig. How Clustered Protocadherin Binding Specificity Is Tuned For Neuronal Self-/Nonself-Recognition. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 35253643
DOI: 10.7554/ELIFE.72416