Calcium in PDB 5szm: Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4

The structure of Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4, PDB code: 5szm was solved by K.M.Goodman, S.Mannepalli, F.Bahna, B.Honig, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 3.60
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	257.560, 257.560, 105.190, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 23.8

The binding sites of Calcium atom in the Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4 (pdb code 5szm). 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 Gamma A8 Extracellular Cadherin Domains 1-4, PDB code: 5szm:
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 Gamma A8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:0.3 occ:1.00 OE2 A:GLU9 2.3 0.8 1.0 OE1 A:GLU8 2.4 0.4 1.0 OD2 A:ASP99 2.4 0.7 1.0 OD1 A:ASP62 2.4 0.3 1.0 OE1 A:GLU64 2.4 0.4 1.0 CG A:GLU9 2.5 0.8 1.0 CD A:GLU9 2.8 0.8 1.0 CD A:GLU8 2.8 0.3 1.0 OE2 A:GLU8 2.9 0.6 1.0 OD1 A:ASP99 3.0 0.1 1.0 CG A:ASP99 3.0 0.8 1.0 CD A:GLU64 3.5 0.0 1.0 CG A:ASP62 3.6 0.8 1.0 OE1 A:GLU9 3.9 0.8 1.0 OE2 A:GLU64 4.0 0.1 1.0 CB A:GLU9 4.0 0.5 1.0 CA A:CA506 4.1 0.2 1.0 CG A:GLU8 4.1 0.0 1.0 CA A:ASP62 4.3 0.0 1.0 CD1 A:ILE97 4.3 0.0 1.0 CB A:ASP99 4.4 0.5 1.0 CB A:ASP62 4.4 0.7 1.0 OD2 A:ASP62 4.5 0.7 1.0 CG1 A:ILE97 4.6 0.8 1.0 N A:ARG63 4.7 0.7 1.0 OD1 A:ASN100 4.7 0.9 1.0 CG A:GLU64 4.7 0.4 1.0 CB A:GLU8 4.8 0.5 1.0 O A:ILE97 4.9 0.1 1.0 NH2 A:ARG60 4.9 0.2 1.0 C A:ASP62 4.9 0.6 1.0 N A:GLU9 5.0 0.4 1.0 O A:ILE61 5.0 0.3 1.0 CA A:GLU9 5.0 0.1 1.0

Calcium binding site 2 out of 9 in the Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:0.2 occ:1.00 O A:ILE97 1.7 0.1 1.0 OE2 A:GLU8 2.3 0.6 1.0 OE2 A:GLU64 2.3 0.1 1.0 OD1 A:ASP132 2.4 1.0 1.0 OD1 A:ASP96 2.7 0.9 1.0 C A:ILE97 2.7 0.1 1.0 N A:ILE97 2.7 0.2 1.0 CA A:ILE97 3.2 0.1 1.0 OD1 A:ASP99 3.2 0.1 1.0 CD A:GLU64 3.3 0.0 1.0 CG1 A:ILE97 3.4 0.8 1.0 CD A:GLU8 3.5 0.3 1.0 CG A:ASP132 3.6 0.4 1.0 OE1 A:GLU64 3.6 0.4 1.0 CG A:ASP96 3.8 0.6 1.0 C A:ASP96 3.8 0.5 1.0 N A:ASN98 3.9 0.9 1.0 CB A:ILE97 3.9 0.1 1.0 CA A:CA505 4.1 0.3 1.0 CA A:ASP96 4.1 0.3 1.0 CD1 A:ILE97 4.1 0.0 1.0 N A:ASP99 4.2 0.4 1.0 CG A:ASP99 4.2 0.8 1.0 OD2 A:ASP132 4.2 0.4 1.0 CG A:GLU8 4.3 0.0 1.0 OE1 A:GLU8 4.4 0.4 1.0 CA A:ASN98 4.4 0.8 1.0 CG A:GLU64 4.5 0.4 1.0 CB A:ASP96 4.5 0.8 1.0 NH2 A:ARG63 4.5 0.2 1.0 OD2 A:ASP96 4.6 0.3 1.0 CB A:ASP132 4.7 0.2 1.0 C A:ASN98 4.8 0.2 1.0 OD2 A:ASP99 4.9 0.7 1.0 O A:ASP96 4.9 0.2 1.0 CA A:ASP132 5.0 0.5 1.0

Calcium binding site 3 out of 9 in the Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:0.8 occ:1.00 OD2 A:ASP132 2.3 0.4 1.0 OD2 A:ASP130 2.4 0.1 1.0 OD1 A:ASP130 2.4 0.3 1.0 OD1 A:ASN98 2.4 0.5 1.0 O A:ASN136 2.4 1.0 1.0 OD2 A:ASP187 2.5 0.6 1.0 CB A:ASP132 2.5 0.2 1.0 O A:ASN100 2.5 0.0 1.0 CG A:ASP130 2.7 0.1 1.0 CG A:ASP132 2.8 0.4 1.0 CG A:ASN98 3.6 0.6 1.0 C A:ASN136 3.6 0.9 1.0 CG A:ASP187 3.6 0.9 1.0 C A:ASN100 3.7 1.0 1.0 CA A:ASP132 3.8 0.5 1.0 OD1 A:ASP132 4.0 1.0 1.0 CB A:ASN136 4.1 0.9 1.0 N A:ASP132 4.1 0.0 1.0 CB A:ASP130 4.1 1.0 1.0 CB A:ASP187 4.2 0.1 1.0 CA A:ASN136 4.3 0.8 1.0 N A:ASN100 4.3 0.3 1.0 CA A:ASN100 4.4 0.4 1.0 CB A:ASN100 4.4 0.6 1.0 CA A:ASN98 4.5 0.8 1.0 ND2 A:ASN98 4.5 0.9 1.0 CB A:ASN98 4.5 0.5 1.0 C A:ASP132 4.6 0.6 1.0 N A:SER137 4.6 1.0 1.0 O A:ASP132 4.6 0.8 1.0 OD1 A:ASP187 4.6 0.1 1.0 CA A:SER137 4.8 1.0 1.0 N A:ASN101 4.8 0.2 1.0

Calcium binding site 4 out of 9 in the Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:0.1 occ:1.00 OE2 A:GLU174 2.4 0.3 1.0 O A:THR206 2.4 0.1 1.0 OD2 A:ASP241 2.4 0.2 1.0 OD1 A:ASP205 2.4 0.6 1.0 OD1 A:ASP208 2.4 0.4 1.0 OE1 A:GLU115 2.4 0.5 1.0 OE1 A:GLU174 2.8 0.5 1.0 CD A:GLU174 2.8 0.6 1.0 OE2 A:GLU115 3.0 0.4 1.0 CD A:GLU115 3.1 0.4 1.0 CG A:ASP208 3.4 0.2 1.0 C A:THR206 3.5 0.2 1.0 CG A:ASP205 3.6 0.2 1.0 CG A:ASP241 3.6 0.4 1.0 N A:THR206 3.7 0.2 1.0 OD2 A:ASP208 3.8 0.2 1.0 CA A:CA510 3.9 0.1 1.0 N A:ASP208 4.1 0.5 1.0 CA A:THR206 4.1 0.3 1.0 OD2 A:ASP205 4.1 0.6 1.0 CG A:GLU174 4.2 0.7 1.0 OD1 A:ASP241 4.4 0.8 1.0 CG A:ARG173 4.5 0.5 1.0 N A:ASN207 4.5 0.9 1.0 CA A:ASP241 4.5 0.4 1.0 OD1 A:ASP172 4.5 0.2 1.0 CG A:GLU115 4.6 0.9 1.0 CB A:ASP208 4.6 0.3 1.0 CB A:ASP241 4.6 0.2 1.0 C A:ASP205 4.7 0.3 1.0 CA A:ASP205 4.7 0.1 1.0 CB A:ASP205 4.7 1.0 1.0 CA A:ASN207 4.7 0.8 1.0 CB A:THR206 4.8 1.0 1.0 CA A:ASP208 4.8 0.8 1.0 N A:ASN209 4.9 0.4 1.0 CD A:ARG173 4.9 0.9 1.0 C A:ASN207 5.0 0.4 1.0

Calcium binding site 5 out of 9 in the Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca509 b:0.1 occ:1.00 OD1 A:ASP241 2.3 0.8 1.0 O A:ASN245 2.4 0.1 1.0 OD2 A:ASP239 2.4 0.6 1.0 OD1 A:ASP239 2.4 0.6 1.0 OD1 A:ASN207 2.4 0.8 1.0 O A:ASN209 2.5 0.5 1.0 OD2 A:ASP294 2.5 0.2 1.0 CB A:ASP241 2.5 0.2 1.0 CG A:ASP239 2.7 0.5 1.0 CG A:ASP241 2.8 0.4 1.0 C A:ASN245 3.6 0.1 1.0 CG A:ASN207 3.6 0.7 1.0 CG A:ASP294 3.6 0.5 1.0 C A:ASN209 3.7 0.5 1.0 CA A:ASP241 3.9 0.4 1.0 OD2 A:ASP241 4.0 0.2 1.0 N A:ASP241 4.1 0.9 1.0 CB A:ASP294 4.2 0.7 1.0 CB A:ASN245 4.2 0.5 1.0 CB A:ASP239 4.2 0.2 1.0 ND2 A:ASN207 4.3 1.0 1.0 CA A:ASN245 4.3 0.1 1.0 N A:ASN209 4.5 0.4 1.0 CA A:ASN209 4.5 0.0 1.0 N A:GLY246 4.6 0.1 1.0 CB A:ASN209 4.6 0.2 1.0 CD1 A:LEU298 4.6 0.3 1.0 OD1 A:ASP294 4.7 0.6 1.0 CB A:ASN207 4.7 0.2 1.0 N A:ALA210 4.7 0.8 1.0 CA A:GLY246 4.7 0.1 1.0 CA A:ASN207 4.7 0.8 1.0 C A:ASP241 4.7 0.9 1.0 CA A:ALA210 4.9 0.9 1.0

Calcium binding site 6 out of 9 in the Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca510 b:0.1 occ:1.00 OD1 A:ASP172 2.3 0.2 1.0 OD2 A:ASP208 2.3 0.2 1.0 OE1 A:GLU174 2.4 0.5 1.0 OD2 A:ASP172 2.4 1.0 1.0 OE2 A:GLU115 2.4 0.4 1.0 CG A:ASP172 2.6 0.2 1.0 CG A:ASP208 3.0 0.2 1.0 OD1 A:ASP208 3.0 0.4 1.0 CD A:GLU174 3.3 0.6 1.0 OD1 A:ASN209 3.5 0.2 1.0 CD A:GLU115 3.6 0.4 1.0 CG A:GLU174 3.8 0.7 1.0 CA A:CA508 3.9 0.1 1.0 CB A:GLU174 4.0 0.8 1.0 CB A:ASP172 4.1 0.8 1.0 CG A:ASN209 4.1 0.1 1.0 OE2 A:GLU174 4.2 0.3 1.0 OE1 A:GLU115 4.3 0.5 1.0 ND2 A:ASN209 4.3 0.7 1.0 CB A:ASP208 4.3 0.3 1.0 CG A:GLU115 4.6 0.9 1.0 CA A:ASP172 4.8 0.1 1.0 N A:GLU174 4.8 0.3 1.0

Calcium binding site 7 out of 9 in the Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca511 b:0.5 occ:1.00 OE1 A:GLU281 2.3 0.2 1.0 OD1 A:ASP313 2.3 0.8 1.0 OD1 A:ASP279 2.4 0.2 1.0 OE1 A:GLU224 2.4 0.3 1.0 OE2 A:GLU281 2.4 0.3 1.0 OE2 A:GLU224 2.4 0.8 1.0 CD A:GLU281 2.6 0.8 1.0 CD A:GLU224 2.7 0.1 1.0 CA A:CA512 2.8 0.0 1.0 OD2 A:ASP313 2.9 0.7 1.0 CG A:ASP313 2.9 0.0 1.0 CG A:ASP279 3.4 0.9 1.0 OD2 A:ASP279 3.6 0.7 1.0 CG A:GLU281 4.0 0.1 1.0 OD1 A:ASP310 4.1 0.9 1.0 CG A:GLU224 4.2 0.3 1.0 OD1 A:ASN314 4.3 1.0 1.0 N A:TYR280 4.4 0.8 1.0 OD1 A:ASP346 4.4 0.3 1.0 CB A:ASP313 4.4 0.8 1.0 O A:VAL311 4.5 0.9 1.0 N A:GLU281 4.6 0.4 1.0 CG A:ASN314 4.7 0.5 1.0 CB A:ASP279 4.7 0.2 1.0 ND2 A:ASN314 4.7 0.9 1.0 CB A:GLU281 4.7 0.5 1.0 CB A:TYR280 4.8 0.3 1.0 CA A:ASP279 5.0 0.5 1.0

Calcium binding site 8 out of 9 in the Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca512 b:0.0 occ:1.00 O A:VAL311 2.1 0.9 1.0 OE2 A:GLU224 2.3 0.8 1.0 OD1 A:ASP346 2.3 0.3 1.0 OD2 A:ASP313 2.3 0.7 1.0 OD1 A:ASP310 2.3 0.9 1.0 CA A:CA511 2.8 0.5 1.0 CG A:ASP313 2.8 0.0 1.0 OE2 A:GLU281 3.0 0.3 1.0 OD1 A:ASP313 3.2 0.8 1.0 C A:VAL311 3.3 0.3 1.0 CG A:ASP346 3.3 0.5 1.0 CD A:GLU224 3.5 0.1 1.0 N A:ASP313 3.5 0.3 1.0 CG A:ASP310 3.6 0.8 1.0 OD2 A:ASP346 3.7 0.8 1.0 CB A:ASP313 3.9 0.8 1.0 C A:ASN312 4.0 0.5 1.0 CA A:ASN312 4.0 0.2 1.0 CD A:GLU281 4.0 0.8 1.0 N A:ASN312 4.1 0.0 1.0 OE1 A:GLU224 4.1 0.3 1.0 N A:VAL311 4.1 0.3 1.0 C A:ASP310 4.2 0.7 1.0 CA A:ASP313 4.3 0.5 1.0 OD2 A:ASP310 4.3 0.1 1.0 OE1 A:GLU281 4.3 0.2 1.0 CA A:VAL311 4.4 0.1 1.0 CA A:ASP310 4.5 0.5 1.0 CG A:GLU224 4.6 0.3 1.0 CB A:ASP310 4.6 0.3 1.0 N A:ASN314 4.6 0.2 1.0 CB A:ASP346 4.7 0.0 1.0 O A:ASP310 4.7 0.7 1.0 CG2 A:VAL311 4.8 0.7 1.0 O A:ASN312 4.8 0.7 1.0 C A:ASP313 4.9 0.2 1.0

Calcium binding site 9 out of 9 in the Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Protocadherin Gamma A8 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca513 b:0.7 occ:1.00 OD2 A:ASP344 2.3 0.4 1.0 OD2 A:ASP346 2.3 0.8 1.0 O A:ASN314 2.4 0.4 1.0 O A:ASN350 2.4 0.1 1.0 OD1 A:ASP344 2.4 0.5 1.0 CB A:ASP346 2.5 0.0 1.0 CG A:ASP344 2.7 0.2 1.0 CG A:ASP346 2.8 0.5 1.0 OD2 A:ASP397 2.9 0.1 1.0 OD1 A:ASN312 3.1 0.1 1.0 C A:ASN350 3.5 0.8 1.0 C A:ASN314 3.6 0.1 1.0 CA A:ASP346 3.8 0.4 1.0 N A:ASP346 3.8 0.7 1.0 CG A:ASN312 3.9 0.8 1.0 CG A:ASP397 3.9 0.8 1.0 OD1 A:ASP346 4.0 0.3 1.0 N A:ASN314 4.2 0.2 1.0 CB A:ASP344 4.2 0.9 1.0 CA A:ASN314 4.2 0.2 1.0 CB A:ASP397 4.2 0.5 1.0 CB A:ASN350 4.3 0.9 1.0 CB A:ASN314 4.3 0.9 1.0 CA A:ASN350 4.4 0.5 1.0 N A:GLY351 4.4 0.6 1.0 ND2 A:ASN312 4.4 0.6 1.0 CA A:GLY351 4.5 0.4 1.0 N A:ARG315 4.6 0.7 1.0 C A:ASP346 4.7 0.7 1.0 N A:ASP313 4.8 0.3 1.0 CA A:ARG315 4.9 0.9 1.0 CB A:ASN312 4.9 0.1 1.0 CA A:ASP344 5.0 0.8 1.0 C A:ASP344 5.0 0.3 1.0 CA A:ASN312 5.0 0.2 1.0

K.M.Goodman, R.Rubinstein, C.A.Thu, S.Mannepalli, F.Bahna, G.Ahlsen, C.Rittenhouse, T.Maniatis, B.Honig, L.Shapiro. Gamma-Protocadherin Structural Diversity and Functional Implications. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27782885
DOI: 10.7554/ELIFE.20930