Calcium in PDB 5szl: Protocadherin Gamma A1 Extracellular Cadherin Domains 1-4

The structure of Protocadherin Gamma A1 Extracellular Cadherin Domains 1-4, PDB code: 5szl was solved by K.M.Goodman, F.Bahna, 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)	39.96 / 4.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.867, 107.867, 463.081, 90.00, 90.00, 120.00
R / Rfree (%)	28.7 / 31.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Calcium atom in the Protocadherin Gamma A1 Extracellular Cadherin Domains 1-4 (pdb code 5szl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 36 binding sites of Calcium where determined in the Protocadherin Gamma A1 Extracellular Cadherin Domains 1-4, PDB code: 5szl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 36 in the Protocadherin Gamma A1 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 A1 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:1.0 occ:1.00 OD1 A:ASN208 2.4 0.2 1.0 OD2 A:ASP295 2.4 0.8 1.0 OD2 A:ASP242 2.5 0.8 1.0 O A:ASN210 2.5 0.7 1.0 O A:ASN246 2.6 0.7 1.0 OD2 A:ASP240 3.0 0.5 1.0 OD1 A:ASP240 3.1 0.4 1.0 CG A:ASP240 3.3 0.1 1.0 CG A:ASP295 3.4 0.0 1.0 CG A:ASP242 3.5 0.5 1.0 CG A:ASN208 3.6 0.5 1.0 C A:ASN210 3.7 0.9 1.0 C A:ASN246 3.7 0.4 1.0 CB A:ASP295 3.8 0.6 1.0 CB A:ASP242 4.0 1.0 1.0 CB A:ASN246 4.2 0.2 1.0 CD1 A:LEU299 4.2 0.1 1.0 CA A:ASN246 4.2 0.8 1.0 ND2 A:ASN208 4.4 0.9 1.0 N A:ASN210 4.4 0.1 1.0 CA A:ASN210 4.5 0.8 1.0 OD1 A:ASP295 4.5 0.9 1.0 CB A:ASP240 4.6 0.2 1.0 N A:PRO211 4.6 0.1 1.0 OD1 A:ASP242 4.6 0.8 1.0 CA A:PRO211 4.7 0.1 1.0 CB A:ASN208 4.7 0.7 1.0 CB A:ASN210 4.8 0.7 1.0 N A:GLY247 4.8 0.6 1.0 CB A:LEU299 4.8 0.1 1.0 CA A:ASN208 4.9 0.0 1.0 C A:PRO211 5.0 0.1 1.0 CA A:GLY247 5.0 1.0 1.0

Calcium binding site 2 out of 36 in the Protocadherin Gamma A1 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 A1 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:0.4 occ:1.00 OE2 A:GLU175 2.2 0.4 1.0 O A:VAL207 2.3 0.9 1.0 OD1 A:ASP209 2.4 0.8 1.0 OD1 A:ASP206 2.4 0.0 1.0 OD1 A:ASP242 2.5 0.8 1.0 OE1 A:GLU116 2.5 0.6 1.0 CD A:GLU175 2.8 0.4 1.0 OE1 A:GLU175 3.2 0.2 1.0 C A:VAL207 3.4 0.7 1.0 CD A:GLU116 3.4 0.2 1.0 CG A:ASP242 3.4 0.5 1.0 CG A:ASP209 3.5 0.8 1.0 OE2 A:GLU116 3.6 0.7 1.0 CG A:ASP206 3.6 0.5 1.0 N A:VAL207 3.6 0.5 1.0 N A:ASP209 4.0 0.7 1.0 OD2 A:ASP209 4.0 0.6 1.0 CG A:GLU175 4.0 0.9 1.0 CB A:ASP242 4.0 1.0 1.0 CA A:VAL207 4.1 0.2 1.0 OD2 A:ASP206 4.2 0.7 1.0 CA A:ASP242 4.3 0.8 1.0 N A:ASN208 4.3 0.3 1.0 OD2 A:ASP242 4.3 0.8 1.0 NE A:ARG174 4.4 0.5 1.0 CA A:ASN208 4.5 0.0 1.0 OD1 A:ASN210 4.5 0.4 1.0 NH2 A:ARG174 4.6 0.5 1.0 C A:ASP206 4.6 0.0 1.0 CB A:ASP209 4.6 0.5 1.0 CA A:ASP206 4.6 0.7 1.0 CB A:ASP206 4.7 0.1 1.0 C A:ASN208 4.8 0.8 1.0 CG A:GLU116 4.8 0.8 1.0 CA A:CA505 4.8 95.5 1.0 CA A:ASP209 4.8 0.6 1.0 CB A:VAL207 4.9 0.0 1.0 CZ A:ARG174 5.0 0.0 1.0

Calcium binding site 3 out of 36 in the Protocadherin Gamma A1 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 A1 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:95.5 occ:1.00 OD1 A:ASP173 2.2 0.1 1.0 OD2 A:ASP209 2.2 0.6 1.0 OE1 A:GLU175 2.3 0.2 1.0 OE2 A:GLU116 2.4 0.7 1.0 CG A:ASP173 3.0 1.0 1.0 CG A:ASP209 3.4 0.8 1.0 CD A:GLU175 3.5 0.4 1.0 CA A:ASP173 3.5 0.2 1.0 CD A:GLU116 3.6 0.2 1.0 OD2 A:ASP173 3.7 0.9 1.0 CB A:ASP173 3.7 0.8 1.0 N A:ARG174 3.8 0.3 1.0 OD1 A:ASP209 3.9 0.8 1.0 C A:ASP173 4.1 0.4 1.0 OE2 A:GLU175 4.2 0.4 1.0 N A:GLU175 4.2 0.1 1.0 OE1 A:GLU116 4.4 0.6 1.0 OD1 A:ASN210 4.4 0.4 1.0 O A:LEU172 4.5 0.3 1.0 CB A:GLU175 4.5 0.1 1.0 CG A:GLU175 4.5 0.9 1.0 CG A:GLU116 4.5 0.8 1.0 CB A:ASP209 4.6 0.5 1.0 CB A:GLU116 4.7 0.8 1.0 N A:ASP173 4.8 0.5 1.0 CA A:CA504 4.8 0.4 1.0 CA A:ARG174 4.9 0.9 1.0

Calcium binding site 4 out of 36 in the Protocadherin Gamma A1 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 A1 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:0.0 occ:1.00 OE2 A:GLU65 2.4 0.7 1.0 OD1 A:ASP100 2.4 0.8 1.0 O A:ILE98 2.5 0.1 1.0 OD1 A:ASP133 2.5 0.1 1.0 OE2 A:GLU9 2.5 0.7 1.0 CD A:GLU65 3.0 0.2 1.0 OD1 A:ASP97 3.2 0.4 1.0 CG A:ASP133 3.2 0.9 1.0 OE1 A:GLU65 3.4 0.7 1.0 CG A:ASP100 3.5 0.7 1.0 C A:ILE98 3.5 0.7 1.0 CD A:GLU9 3.5 0.8 1.0 CB A:ASP133 3.7 0.2 1.0 OE1 A:GLU9 3.8 0.8 1.0 N A:ASP100 3.8 0.4 1.0 CG A:GLU65 3.9 0.1 1.0 CA A:ASP133 4.0 0.7 1.0 OD2 A:ASP100 4.1 0.4 1.0 OD2 A:ASP133 4.1 0.6 1.0 CG A:ASP97 4.1 1.0 1.0 CA A:CA508 4.2 0.1 1.0 N A:ASN99 4.3 0.3 1.0 CA A:ASN99 4.3 0.1 1.0 N A:ILE98 4.3 0.9 1.0 OD2 A:ASP97 4.4 0.7 1.0 CA A:ILE98 4.5 0.9 1.0 ND2 A:ASN101 4.5 0.8 1.0 C A:ASN99 4.5 0.1 1.0 CB A:ASP100 4.5 0.9 1.0 CA A:ASP100 4.7 0.8 1.0 N A:ASP133 4.8 0.2 1.0 CG A:GLU9 4.9 0.3 1.0

Calcium binding site 5 out of 36 in the Protocadherin Gamma A1 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 A1 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:0.1 occ:1.00 O A:ASN101 2.3 0.9 1.0 OD2 A:ASP131 2.3 0.6 1.0 O A:ASN137 2.3 0.8 1.0 OD2 A:ASP133 2.4 0.6 1.0 OD1 A:ASN99 2.4 0.7 1.0 OD2 A:ASP188 2.6 0.3 1.0 OD1 A:ASP131 2.6 0.9 1.0 CG A:ASP131 2.8 0.7 1.0 CG A:ASP133 3.4 0.9 1.0 C A:ASN101 3.4 0.6 1.0 CG A:ASP188 3.5 0.4 1.0 CG A:ASN99 3.5 0.5 1.0 C A:ASN137 3.5 0.9 1.0 CB A:ASP133 3.7 0.2 1.0 CB A:ASP188 3.7 0.1 1.0 ND2 A:ASN99 4.0 0.0 1.0 N A:ASN101 4.2 0.5 1.0 CA A:ASN101 4.2 0.9 1.0 CB A:ASP131 4.3 0.6 1.0 CA A:ASN137 4.3 0.2 1.0 N A:THR102 4.3 0.7 1.0 CB A:ASN137 4.4 0.8 1.0 CB A:ASN101 4.4 0.8 1.0 OD1 A:ASP133 4.5 0.1 1.0 N A:SER138 4.5 0.0 1.0 CD A:PRO103 4.6 0.4 1.0 CA A:THR102 4.6 0.1 1.0 OD1 A:ASP188 4.7 0.6 1.0 CA A:SER138 4.7 0.9 1.0 N A:ASP133 4.7 0.2 1.0 CB A:ASN99 4.8 0.4 1.0 CA A:ASP133 4.8 0.7 1.0 N A:PRO103 5.0 1.0 1.0

Calcium binding site 6 out of 36 in the Protocadherin Gamma A1 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 A1 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:0.1 occ:1.00 OD1 A:ASP63 2.4 0.3 1.0 OE1 A:GLU65 2.4 0.7 1.0 OE2 A:GLU10 2.4 0.4 1.0 OD2 A:ASP100 2.4 0.4 1.0 OE1 A:GLU9 3.2 0.8 1.0 CG A:ASP100 3.3 0.7 1.0 CG A:ASP63 3.4 0.2 1.0 CD A:GLU65 3.5 0.2 1.0 CD A:GLU10 3.5 1.0 1.0 OD1 A:ASP100 3.5 0.8 1.0 NH2 A:ARG61 3.9 0.2 1.0 OD2 A:ASP63 4.0 0.5 1.0 CG A:GLU10 4.0 0.3 1.0 CD A:GLU9 4.1 0.8 1.0 OE2 A:GLU65 4.1 0.7 1.0 CA A:CA506 4.2 0.0 1.0 CB A:ASP63 4.4 0.2 1.0 CG A:GLU65 4.4 0.1 1.0 OE2 A:GLU9 4.4 0.7 1.0 ND2 A:ASN101 4.5 0.8 1.0 OE1 A:GLU10 4.6 0.1 1.0 CA A:ASP63 4.6 0.1 1.0 CB A:GLU65 4.6 0.6 1.0 CB A:ASP100 4.7 0.9 1.0 CZ A:ARG61 4.9 0.6 1.0 NE A:ARG61 5.0 0.7 1.0

Calcium binding site 7 out of 36 in the Protocadherin Gamma A1 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 A1 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca509 b:0.7 occ:1.00 O A:VAL312 2.4 0.2 1.0 OD1 A:ASP311 2.6 0.2 1.0 OE1 A:GLU225 2.6 0.8 1.0 OD1 A:ASP347 2.6 0.4 1.0 OD1 A:ASP314 2.9 0.3 1.0 OE2 A:GLU282 3.1 0.2 1.0 OD2 A:ASP347 3.1 0.2 1.0 CG A:ASP347 3.1 1.0 1.0 CD A:GLU225 3.4 0.2 1.0 OE2 A:GLU225 3.4 0.7 1.0 C A:VAL312 3.5 0.6 1.0 N A:VAL312 3.6 0.3 1.0 CA A:CA510 3.7 0.8 1.0 CG A:ASP311 3.8 0.8 1.0 CG A:ASP314 3.8 0.5 1.0 CD A:GLU282 4.0 0.6 1.0 N A:ASP314 4.2 0.9 1.0 CA A:VAL312 4.2 0.2 1.0 CB A:PHE281 4.2 0.7 1.0 OE1 A:GLU282 4.3 0.2 1.0 CD2 A:PHE281 4.3 0.9 1.0 OD2 A:ASP314 4.3 0.9 1.0 CB A:ASP347 4.4 0.3 1.0 N A:ASN313 4.5 0.2 1.0 OD2 A:ASP311 4.5 0.7 1.0 CG A:PHE281 4.5 0.9 1.0 C A:ASP311 4.6 0.9 1.0 CA A:ASN313 4.6 0.6 1.0 CA A:ASP311 4.7 0.8 1.0 CG A:GLU225 4.8 0.9 1.0 CB A:ASP311 4.8 0.5 1.0 C A:ASN313 4.9 0.2 1.0 CB A:ASP314 4.9 0.6 1.0

Calcium binding site 8 out of 36 in the Protocadherin Gamma A1 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 A1 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca510 b:0.8 occ:1.00 OE1 A:GLU282 2.3 0.2 1.0 OD1 A:ASP280 2.4 0.4 1.0 OD2 A:ASP314 2.4 0.9 1.0 OE2 A:GLU282 2.7 0.2 1.0 OE2 A:GLU225 2.7 0.7 1.0 OD1 A:ASP314 2.8 0.3 1.0 CD A:GLU282 2.8 0.6 1.0 CG A:ASP314 2.9 0.5 1.0 CG A:ASP280 3.5 0.9 1.0 CD A:GLU225 3.6 0.2 1.0 ND2 A:ASN315 3.7 0.1 1.0 CA A:CA509 3.7 0.7 1.0 N A:PHE281 3.9 0.7 1.0 OE1 A:GLU225 3.9 0.8 1.0 CG A:ASN315 4.1 0.4 1.0 OD1 A:ASN315 4.1 0.4 1.0 OD2 A:ASP280 4.1 0.2 1.0 CG A:GLU282 4.2 0.9 1.0 N A:GLU282 4.4 0.4 1.0 CB A:ASP314 4.4 0.6 1.0 CB A:PHE281 4.4 0.7 1.0 CA A:ASP280 4.5 0.5 1.0 C A:ASP280 4.6 0.9 1.0 CB A:ASP280 4.6 0.4 1.0 CA A:PHE281 4.7 0.4 1.0 CG A:GLU225 4.7 0.9 1.0 OD1 A:ASP347 4.8 0.4 1.0 CB A:GLU282 4.9 0.3 1.0

Calcium binding site 9 out of 36 in the Protocadherin Gamma A1 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 A1 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca511 b:0.5 occ:1.00 OD1 A:ASN313 2.4 0.3 1.0 OD2 A:ASP347 2.6 0.2 1.0 O A:ASN315 2.6 0.3 1.0 O A:ASN351 2.7 0.0 1.0 CG A:ASP347 3.0 1.0 1.0 CB A:ASP347 3.1 0.3 1.0 OD1 A:ASP345 3.1 0.3 1.0 OD2 A:ASP345 3.1 0.2 1.0 OD2 A:ASP398 3.2 0.4 1.0 CG A:ASP345 3.5 0.1 1.0 CG A:ASN313 3.6 0.1 1.0 C A:ASN315 3.8 0.6 1.0 C A:ASN351 3.9 0.3 1.0 N A:ASP347 4.1 0.6 1.0 OD1 A:ASP347 4.1 0.4 1.0 CA A:ASP347 4.2 0.6 1.0 N A:ASN315 4.2 0.5 1.0 CB A:ASN351 4.3 0.3 1.0 ND2 A:ASN313 4.4 0.4 1.0 CG A:ASP398 4.4 0.2 1.0 CA A:ASN315 4.5 1.0 1.0 CA A:ASN313 4.5 0.6 1.0 CB A:ASN313 4.6 0.3 1.0 CA A:ASN351 4.6 0.1 1.0 CB A:ASN315 4.6 0.9 1.0 N A:ASP314 4.7 0.9 1.0 N A:ALA316 4.8 0.1 1.0 N A:GLY352 4.9 0.5 1.0 CB A:ASP345 4.9 0.3 1.0 C A:ASN313 4.9 0.2 1.0 CA A:GLY352 5.0 0.3 1.0 CB A:ASP398 5.0 0.2 1.0

Calcium binding site 10 out of 36 in the Protocadherin Gamma A1 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 10 of Protocadherin Gamma A1 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:0.3 occ:1.00 OD1 B:ASN99 2.3 0.2 1.0 OD2 B:ASP131 2.4 0.3 1.0 OD2 B:ASP133 2.5 0.4 1.0 OD1 B:ASP131 2.5 0.4 1.0 O B:ASN137 2.6 0.0 1.0 OD2 B:ASP188 2.6 0.7 1.0 O B:ASN101 2.6 0.4 1.0 CG B:ASP131 2.8 0.4 1.0 CG B:ASP133 3.4 0.6 1.0 CG B:ASN99 3.5 1.0 1.0 CG B:ASP188 3.7 0.9 1.0 CB B:ASP133 3.8 0.1 1.0 C B:ASN101 3.8 0.4 1.0 C B:ASN137 3.8 0.3 1.0 CB B:ASP188 4.1 0.6 1.0 ND2 B:ASN99 4.2 0.2 1.0 CB B:ASP131 4.3 0.6 1.0 N B:ASN101 4.4 0.1 1.0 CB B:ASN137 4.4 0.6 1.0 OD1 B:ASP133 4.4 0.4 1.0 CA B:ASN101 4.5 0.1 1.0 CA B:ASN137 4.5 0.6 1.0 N B:ASP133 4.6 0.9 1.0 CB B:ASN99 4.6 0.3 1.0 CD B:PRO103 4.7 0.3 1.0 CA B:ASN99 4.7 0.3 1.0 OD1 B:ASP188 4.7 0.7 1.0 CB B:ASN101 4.8 0.6 1.0 N B:THR102 4.8 0.2 1.0 N B:SER138 4.8 0.2 1.0 CA B:ASP133 4.8 1.0 1.0 CB B:HIS194 4.9 0.2 1.0 CA B:SER138 4.9 0.6 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