Calcium in PDB 5dzx: Protocadherin Beta 6 Extracellular Cadherin Domains 1-4

The structure of Protocadherin Beta 6 Extracellular Cadherin Domains 1-4, PDB code: 5dzx 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)	29.97 / 2.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.040, 90.530, 258.130, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 28.9

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Protocadherin Beta 6 Extracellular Cadherin Domains 1-4 (pdb code 5dzx). 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 Beta 6 Extracellular Cadherin Domains 1-4, PDB code: 5dzx:
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 Beta 6 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 Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca512 b:63.4 occ:1.00 OE2 A:GLU9 2.2 50.4 1.0 OD2 A:ASP100 2.3 46.2 1.0 OD1 A:ASP63 2.5 60.3 1.0 OE2 A:GLU10 2.6 67.9 1.0 OE1 A:GLU65 2.7 52.9 1.0 CG A:ASP100 3.3 54.0 1.0 CD A:GLU9 3.4 50.4 1.0 CE1 A:HIS101 3.5 55.1 1.0 CD A:GLU10 3.5 74.7 1.0 CG A:ASP63 3.6 63.6 1.0 CG A:GLU10 3.7 64.9 1.0 OD1 A:ASP100 3.7 59.1 1.0 CD A:GLU65 3.8 51.5 1.0 OE1 A:GLU9 4.1 50.3 1.0 OD2 A:ASP63 4.2 65.8 1.0 ND1 A:HIS101 4.3 48.8 1.0 OE2 A:GLU65 4.4 48.5 1.0 CA A:CA513 4.4 39.8 1.0 CG A:GLU9 4.4 56.6 1.0 NE2 A:HIS101 4.5 51.0 1.0 CB A:ASP100 4.6 65.9 1.0 CB A:ASP63 4.7 66.2 1.0 OE1 A:GLU10 4.7 82.8 1.0 CA A:ASP63 4.8 59.1 1.0 CG A:GLU65 4.9 57.8 1.0 N A:ARG64 5.0 48.6 1.0

Calcium binding site 2 out of 18 in the Protocadherin Beta 6 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 Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca513 b:39.8 occ:1.00 OE2 A:GLU65 2.2 48.5 1.0 OE1 A:GLU9 2.4 50.3 1.0 OD1 A:ASP97 2.4 39.4 1.0 OD1 A:ASP100 2.4 59.1 1.0 OD1 A:ASP133 2.5 50.6 1.0 O A:ILE98 2.5 60.4 1.0 CD A:GLU65 3.2 51.5 1.0 CD A:GLU9 3.4 50.4 1.0 CG A:ASP100 3.4 54.0 1.0 OE1 A:GLU65 3.5 52.9 1.0 CG A:ASP133 3.5 55.0 1.0 OE2 A:GLU9 3.6 50.4 1.0 CG A:ASP97 3.6 44.7 1.0 C A:ILE98 3.6 62.0 1.0 N A:ILE98 3.9 56.4 1.0 OD2 A:ASP100 3.9 46.2 1.0 OD2 A:ASP97 4.2 60.0 1.0 N A:ASP100 4.2 51.1 1.0 OD2 A:ASP133 4.3 62.0 1.0 CA A:ILE98 4.4 58.2 1.0 ND1 A:HIS101 4.4 48.8 1.0 CA A:CA512 4.4 63.4 1.0 CB A:ASP133 4.4 47.3 1.0 CG A:GLU65 4.5 57.8 1.0 CG1 A:ILE98 4.5 57.9 1.0 CD1 A:ILE98 4.6 55.2 1.0 CB A:ASP100 4.6 65.9 1.0 N A:ASN99 4.7 69.0 1.0 CA A:ASP133 4.7 40.4 1.0 C A:ASP97 4.7 55.4 1.0 CG A:GLU9 4.7 56.6 1.0 CB A:ASP97 4.8 55.8 1.0 CA A:ASP97 4.8 51.5 1.0 CE1 A:HIS101 4.8 55.1 1.0 NH1 A:ARG64 4.8 53.8 1.0 CA A:ASN99 4.8 49.6 1.0 CA A:ASP100 4.9 49.8 1.0 CB A:ARG64 5.0 50.3 1.0

Calcium binding site 3 out of 18 in the Protocadherin Beta 6 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 Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca514 b:36.9 occ:1.00 O A:HIS101 2.3 38.4 1.0 OD1 A:ASN99 2.4 63.4 1.0 O A:ASN137 2.5 47.4 1.0 OD2 A:ASP133 2.6 62.0 1.0 OD2 A:ASP188 2.6 50.7 1.0 OD2 A:ASP131 2.7 60.7 1.0 OD1 A:ASP131 3.0 56.2 1.0 CG A:ASP131 3.2 54.2 1.0 C A:HIS101 3.4 42.6 1.0 CG A:ASP133 3.5 55.0 1.0 CG A:ASN99 3.6 65.4 1.0 CG A:ASP188 3.6 54.9 1.0 CB A:ASP133 3.7 47.3 1.0 C A:ASN137 3.7 45.6 1.0 OD1 A:ASP188 4.0 64.8 1.0 CA A:HIS101 4.1 51.7 1.0 N A:HIS101 4.1 58.8 1.0 ND2 A:ASN99 4.2 64.3 1.0 CB A:HIS101 4.2 50.0 1.0 N A:SER102 4.5 46.8 1.0 CA A:ALA138 4.6 49.1 1.0 CD A:PRO103 4.6 59.4 1.0 N A:ALA138 4.6 47.8 1.0 OD1 A:ASP133 4.6 50.6 1.0 CA A:ASN137 4.7 49.8 1.0 CA A:SER102 4.7 53.9 1.0 CB A:ASP131 4.7 54.6 1.0 CB A:ASN99 4.7 52.6 1.0 CB A:ASN137 4.7 55.9 1.0 CB A:ASP188 4.8 61.0 1.0 CA A:ASN99 4.8 49.6 1.0 CA A:ASP133 4.9 40.4 1.0 N A:ASP133 4.9 42.6 1.0 N A:PRO103 4.9 51.5 1.0 C A:SER102 4.9 53.1 1.0 C A:ALA138 5.0 57.0 1.0

Calcium binding site 4 out of 18 in the Protocadherin Beta 6 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 Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca515 b:47.8 occ:1.00 OE2 A:GLU116 2.2 59.4 1.0 OD2 A:ASP209 2.3 56.2 1.0 OE1 A:GLU175 2.4 57.2 1.0 OD1 A:ASP173 2.5 71.9 1.0 CD A:GLU175 3.2 50.7 1.0 CG A:ASP209 3.3 59.1 1.0 CG A:ASP173 3.3 69.7 1.0 CD A:GLU116 3.4 63.6 1.0 OD2 A:ASP173 3.5 77.5 1.0 ND2 A:ASN210 3.7 71.2 1.0 OD1 A:ASP209 3.7 57.7 1.0 OE2 A:GLU175 3.8 46.4 1.0 CG A:GLU175 4.0 59.5 1.0 OE1 A:GLU116 4.0 61.7 1.0 OD1 A:ASN210 4.1 67.5 1.0 CG A:ASN210 4.2 64.3 1.0 CA A:CA516 4.4 39.8 1.0 CB A:GLU175 4.4 70.3 1.0 CG A:GLU116 4.5 61.5 1.0 CB A:ASP209 4.5 63.5 1.0 CB A:ASP173 4.7 68.0 1.0 N A:GLU175 4.9 59.1 1.0 N A:ARG174 5.0 50.4 1.0 CA A:ASP173 5.0 60.4 1.0

Calcium binding site 5 out of 18 in the Protocadherin Beta 6 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 Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca516 b:39.8 occ:1.00 OE2 A:GLU175 2.4 46.4 1.0 OD1 A:ASP206 2.4 54.5 1.0 OE1 A:GLU116 2.5 61.7 1.0 OD1 A:ASP242 2.6 56.5 1.0 O A:ILE207 2.8 50.6 1.0 OD1 A:ASP209 2.8 57.7 1.0 CD A:GLU175 3.3 50.7 1.0 CD A:GLU116 3.5 63.6 1.0 CG A:ASP242 3.5 53.2 1.0 OE1 A:GLU175 3.6 57.2 1.0 CG A:ASP206 3.7 58.7 1.0 OE2 A:GLU116 3.7 59.4 1.0 N A:ILE207 3.8 54.4 1.0 CG A:ASP209 3.8 59.1 1.0 C A:ILE207 3.9 57.1 1.0 OD2 A:ASP209 4.1 56.2 1.0 NH1 A:ARG174 4.1 64.4 1.0 CB A:ASP242 4.2 53.7 1.0 CA A:CA515 4.4 47.8 1.0 CA A:ASP242 4.4 54.7 1.0 OD2 A:ASP242 4.4 56.0 1.0 OD2 A:ASP206 4.4 55.2 1.0 CA A:ILE207 4.5 59.3 1.0 CA A:ASP206 4.5 62.3 1.0 C A:ASP206 4.6 58.5 1.0 CB A:ASP206 4.6 73.2 1.0 CG1 A:ILE207 4.6 52.9 1.0 ND2 A:ASN210 4.6 71.2 1.0 CG A:GLU175 4.7 59.5 1.0 CB A:ARG174 4.7 44.0 1.0 N A:ASP209 4.7 63.9 1.0 CD A:ARG174 4.8 56.9 1.0 CG A:GLU116 4.9 61.5 1.0 N A:ASN208 5.0 63.7 1.0

Calcium binding site 6 out of 18 in the Protocadherin Beta 6 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 Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca517 b:52.1 occ:1.00 OD2 A:ASP240 2.3 58.2 1.0 O A:ASN210 2.4 52.7 1.0 OD2 A:ASP294 2.5 74.6 1.0 O A:HIS246 2.7 46.9 1.0 OD1 A:ASP240 2.8 51.1 1.0 CG A:ASP240 2.9 54.4 1.0 OD2 A:ASP242 2.9 56.0 1.0 OD1 A:ASN208 2.9 55.5 1.0 CG A:ASP294 3.2 55.7 1.0 C A:ASN210 3.6 56.4 1.0 CG A:ASP242 3.8 53.2 1.0 OD1 A:ASP294 3.9 67.0 1.0 C A:HIS246 3.9 54.1 1.0 CB A:ASP294 4.0 46.5 1.0 CG A:ASN208 4.1 49.4 1.0 CB A:ASP242 4.1 53.7 1.0 CD A:PRO212 4.2 43.8 1.0 CD1 A:LEU298 4.3 35.0 1.0 CB A:ASP240 4.4 57.1 1.0 CA A:ALA211 4.5 50.4 1.0 N A:PRO212 4.5 44.1 1.0 N A:ALA211 4.5 57.7 1.0 CA A:ASN210 4.6 67.7 1.0 ND2 A:ASN208 4.6 65.5 1.0 C A:ALA211 4.6 46.7 1.0 N A:ASN210 4.6 61.6 1.0 CA A:HIS246 4.7 59.4 1.0 CB A:LEU298 4.8 60.9 1.0 CB A:HIS246 4.9 65.0 1.0 CB A:ASN210 4.9 63.6 1.0 OD1 A:ASP242 4.9 56.5 1.0 N A:GLY247 4.9 57.7 1.0 CG A:LEU298 5.0 34.6 1.0 N A:ASP242 5.0 59.2 1.0

Calcium binding site 7 out of 18 in the Protocadherin Beta 6 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 Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca518 b:62.1 occ:1.00 OD2 A:ASP313 2.4 47.7 1.0 OE1 A:GLU281 2.5 53.5 1.0 OD1 A:ASP279 2.5 66.1 1.0 OE1 A:GLU225 3.0 70.4 1.0 OE2 A:GLU225 3.0 40.0 1.0 CD A:GLU225 3.2 50.5 1.0 CG A:ASP313 3.3 46.0 1.0 CG A:ASP279 3.4 64.7 1.0 OD1 A:ASP313 3.4 51.1 1.0 CD A:GLU281 3.4 45.7 1.0 OD1 A:ASN314 3.7 64.2 1.0 CA A:CA519 3.8 27.6 1.0 OD2 A:ASP279 3.8 64.7 1.0 OE2 A:GLU281 3.9 42.5 1.0 CB A:ASP279 4.4 57.2 1.0 CG A:GLU225 4.5 62.5 1.0 CA A:ASP279 4.6 68.6 1.0 CG A:ASN314 4.6 54.1 1.0 CG A:GLU281 4.6 49.3 1.0 N A:PHE280 4.6 59.1 1.0 CB A:ASP313 4.7 49.2 1.0 ND2 A:ASN314 4.7 47.3 1.0 N A:GLU281 4.9 46.7 1.0 CB A:GLU281 5.0 65.8 1.0

Calcium binding site 8 out of 18 in the Protocadherin Beta 6 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 Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca519 b:27.6 occ:1.00 O A:VAL311 2.4 49.3 1.0 OE2 A:GLU281 2.5 42.5 1.0 OE1 A:GLU225 2.5 70.4 1.0 OD1 A:ASP313 2.6 51.1 1.0 OD1 A:ASP345 2.8 46.6 1.0 OD1 A:ASP310 2.8 47.1 1.0 CD A:GLU281 3.4 45.7 1.0 C A:VAL311 3.4 56.1 1.0 CD A:GLU225 3.5 50.5 1.0 CG A:ASP313 3.5 46.0 1.0 OE1 A:GLU281 3.5 53.5 1.0 CG A:ASP310 3.6 48.5 1.0 N A:VAL311 3.7 40.2 1.0 CG A:ASP345 3.8 53.5 1.0 CA A:CA518 3.8 62.1 1.0 OE2 A:GLU225 3.8 40.0 1.0 OD2 A:ASP310 4.0 46.4 1.0 OD2 A:ASP313 4.0 47.7 1.0 N A:ASP313 4.1 57.5 1.0 CA A:VAL311 4.2 51.1 1.0 OD1 A:ASN314 4.3 64.2 1.0 C A:ASP310 4.4 44.7 1.0 CB A:ASP345 4.4 54.9 1.0 N A:ASN312 4.4 57.6 1.0 CA A:ASP310 4.5 46.9 1.0 CB A:ASP313 4.6 49.2 1.0 CB A:ASP310 4.6 54.2 1.0 CB A:PHE280 4.6 44.1 1.0 CA A:ASN312 4.6 59.5 1.0 OD2 A:ASP345 4.6 59.3 1.0 CA A:ASP345 4.6 53.8 1.0 CG A:GLU225 4.7 62.5 1.0 CG A:GLU281 4.8 49.3 1.0 CA A:ASP313 4.9 54.1 1.0 C A:ASN312 4.9 60.6 1.0 CB A:VAL311 4.9 48.7 1.0

Calcium binding site 9 out of 18 in the Protocadherin Beta 6 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 Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca520 b:41.8 occ:1.00 OD2 A:ASP345 2.3 59.3 1.0 OD1 A:ASN312 2.3 55.7 1.0 O A:ASN349 2.4 48.5 1.0 O A:ASN314 2.5 39.0 1.0 OD2 A:ASP343 2.6 36.4 1.0 OD1 A:ASP343 2.7 54.8 1.0 OD2 A:ASP396 2.8 58.7 1.0 CG A:ASP343 3.0 48.0 1.0 CG A:ASP345 3.3 53.5 1.0 CG A:ASN312 3.5 60.6 1.0 C A:ASN349 3.5 51.5 1.0 CB A:ASP345 3.6 54.9 1.0 C A:ASN314 3.7 46.6 1.0 CG A:ASP396 3.8 62.0 1.0 ND2 A:ASN312 4.0 62.6 1.0 CB A:ASP396 4.1 57.4 1.0 CD A:PRO316 4.3 57.6 1.0 CA A:ASN349 4.3 50.8 1.0 CB A:ASN349 4.4 52.1 1.0 OD1 A:ASP345 4.5 46.6 1.0 N A:GLY350 4.5 54.3 1.0 CD1 A:LEU402 4.5 50.6 1.0 CB A:ASP343 4.5 46.3 1.0 CA A:ASN314 4.6 59.2 1.0 N A:ALA315 4.6 56.8 1.0 N A:ASN314 4.6 55.4 1.0 CA A:GLY350 4.6 50.6 1.0 CA A:ALA315 4.7 58.0 1.0 CB A:ASN312 4.7 56.4 1.0 CB A:ASN314 4.8 53.0 1.0 N A:PRO316 4.8 54.5 1.0 CA A:ASP345 4.8 53.8 1.0 C A:ALA315 4.9 53.1 1.0 N A:ASP345 4.9 58.6 1.0 CA A:ASN312 4.9 59.5 1.0 OD1 A:ASP396 4.9 58.6 1.0

Calcium binding site 10 out of 18 in the Protocadherin Beta 6 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 Beta 6 Extracellular Cadherin Domains 1-4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:53.1 occ:1.00 OD1 B:ASP63 2.3 52.2 1.0 OE2 B:GLU9 2.3 36.9 1.0 OD2 B:ASP100 2.4 52.4 1.0 OE1 B:GLU65 2.4 49.2 1.0 OE2 B:GLU10 2.8 49.6 1.0 CE1 B:HIS101 3.3 58.5 1.0 CG B:ASP100 3.3 55.3 1.0 CG B:ASP63 3.4 56.3 1.0 CD B:GLU9 3.6 43.2 1.0 CD B:GLU65 3.6 47.3 1.0 OD1 B:ASP100 3.6 53.2 1.0 OD2 B:ASP63 3.8 79.3 1.0 CD B:GLU10 3.9 57.8 1.0 ND1 B:HIS101 4.0 55.4 1.0 CG B:GLU10 4.1 51.0 1.0 OE1 B:GLU9 4.2 39.7 1.0 OE2 B:GLU65 4.3 45.1 1.0 NE2 B:HIS101 4.3 43.9 1.0 CA B:CA506 4.5 37.3 1.0 CG B:GLU65 4.6 54.8 1.0 CB B:ASP63 4.6 61.6 1.0 CB B:GLU65 4.6 58.3 1.0 CB B:ASP100 4.7 66.7 1.0 CG B:GLU9 4.7 56.0 1.0 N B:GLU65 4.9 59.0 1.0 CA B:ASP63 4.9 59.7 1.0 N B:ARG64 5.0 45.1 1.0

K.M.Goodman, R.Rubinstein, C.A.Thu, F.Bahna, S.Mannepalli, G.Ahlsen, C.Rittenhouse, T.Maniatis, B.Honig, L.Shapiro. Structural Basis of Diverse Homophilic Recognition By Clustered Alpha- and Beta-Protocadherins. Neuron V. 90 709 2016.
ISSN: ISSN 0896-6273
PubMed: 27161523
DOI: 10.1016/J.NEURON.2016.04.004