Calcium in PDB 5t9t: Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5

The structure of Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5, PDB code: 5t9t 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)	39.75 / 3.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.722, 118.067, 98.190, 90.00, 103.91, 90.00
R / Rfree (%)	21.3 / 25.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Calcium atom in the Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5 (pdb code 5t9t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 26 binding sites of Calcium where determined in the Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5, PDB code: 5t9t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 26 in the Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:66.5 occ:1.00 OD2 A:ASP98 2.4 0.9 1.0 OE1 A:GLU63 2.5 97.0 1.0 OD1 A:ASP61 2.6 0.4 1.0 OE1 A:GLU9 2.9 96.9 1.0 CG A:ASP98 3.1 0.7 1.0 OE2 A:GLU9 3.1 97.0 1.0 OD1 A:ASP98 3.2 0.0 1.0 CD A:GLU9 3.3 96.0 1.0 CA A:CA602 3.5 89.8 1.0 CD A:GLU63 3.5 93.1 1.0 OE2 A:GLU10 3.6 0.3 1.0 CG A:GLU10 3.7 0.1 1.0 CG A:ASP61 3.8 0.7 1.0 OE2 A:GLU63 4.0 90.0 1.0 CD A:GLU10 4.1 0.7 1.0 OD2 A:ASP61 4.5 0.6 1.0 CG A:GLU9 4.6 96.5 1.0 CB A:ASP98 4.6 0.1 1.0 ND2 A:ASN99 4.6 97.8 1.0 N A:ARG62 4.7 0.7 1.0 CG A:GLU63 4.7 94.0 1.0 CA A:ASP61 4.9 0.6 1.0 CB A:ASP61 4.9 0.3 1.0

Calcium binding site 2 out of 26 in the Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:89.8 occ:1.00 OE2 A:GLU63 2.2 90.0 1.0 OE2 A:GLU9 2.2 97.0 1.0 O A:VAL96 2.4 0.4 1.0 OD1 A:ASP98 2.6 0.0 1.0 OD1 A:ASP95 2.7 75.1 1.0 CD A:GLU63 2.9 93.1 1.0 OD1 A:ASP131 3.0 94.9 1.0 OE1 A:GLU63 3.2 97.0 1.0 CD A:GLU9 3.4 96.0 1.0 CA A:CA601 3.5 66.5 1.0 C A:VAL96 3.6 0.6 1.0 CG A:ASP98 3.6 0.7 1.0 N A:VAL96 3.9 0.6 1.0 CG A:ASP95 3.9 82.5 1.0 CG A:ASP131 3.9 91.5 1.0 OE1 A:GLU9 4.0 96.9 1.0 OD2 A:ASP98 4.0 0.9 1.0 CG A:GLU63 4.1 94.0 1.0 CA A:VAL96 4.2 0.1 1.0 N A:ASP98 4.3 0.4 1.0 OD2 A:ASP95 4.4 86.0 1.0 CG A:GLU9 4.6 96.5 1.0 CB A:VAL96 4.6 0.0 1.0 OD2 A:ASP131 4.6 93.2 1.0 CB A:ASP131 4.7 89.5 1.0 N A:ASN97 4.7 0.5 1.0 CB A:ASP98 4.8 0.1 1.0 ND2 A:ASN99 4.8 97.8 1.0 CA A:ASP131 4.8 86.8 1.0 C A:ASP95 4.8 0.8 1.0 N A:ASN99 4.8 0.6 1.0 CA A:ASN97 4.9 0.3 1.0 CA A:ASP95 5.0 97.3 1.0

Calcium binding site 3 out of 26 in the Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:74.2 occ:1.00 OD2 A:ASP129 2.4 77.5 1.0 O A:ASN135 2.5 92.4 1.0 OD1 A:ASN97 2.5 0.7 1.0 OD2 A:ASP131 2.6 93.2 1.0 O A:ASN99 2.7 98.3 1.0 OD1 A:ASP129 2.7 76.9 1.0 OD2 A:ASP186 2.8 0.3 1.0 CG A:ASP129 2.9 76.0 1.0 CG A:ASN97 3.5 0.0 1.0 CG A:ASP186 3.6 0.7 1.0 CG A:ASP131 3.6 91.5 1.0 C A:ASN135 3.7 93.7 1.0 CB A:ASP186 3.8 0.6 1.0 ND2 A:ASN97 3.9 0.8 1.0 C A:ASN99 3.9 97.0 1.0 CB A:ASP131 4.0 89.5 1.0 CD A:PRO101 4.2 70.9 1.0 CB A:ASP129 4.4 79.5 1.0 CA A:ALA100 4.5 89.7 1.0 CA A:ASN135 4.5 97.7 1.0 CB A:ASN135 4.6 0.4 1.0 OD1 A:ASP131 4.6 94.9 1.0 OD1 A:ASP186 4.6 0.4 1.0 N A:SER136 4.6 91.8 1.0 N A:ALA100 4.7 92.8 1.0 CA A:SER136 4.7 89.9 1.0 CB A:ASN97 4.7 0.4 1.0 N A:PRO101 4.7 76.2 1.0 C A:ALA100 4.9 85.9 1.0 CA A:ASN97 4.9 0.3 1.0 C A:SER136 5.0 0.0 1.0

Calcium binding site 4 out of 26 in the Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:62.7 occ:1.00 OD2 A:ASP207 2.1 0.7 1.0 OE2 A:GLU114 2.2 75.7 1.0 OD1 A:ASP171 2.3 90.7 1.0 OE1 A:GLU173 2.8 89.7 1.0 CG A:ASP207 2.9 0.1 1.0 OD1 A:ASP207 3.0 99.7 1.0 CG A:ASP171 3.4 84.8 1.0 CD A:GLU114 3.4 75.4 1.0 CA A:CA605 3.5 40.7 1.0 CD A:GLU173 3.9 87.4 1.0 OD2 A:ASP171 4.0 83.7 1.0 ND2 A:ASN208 4.1 85.1 1.0 OE1 A:GLU114 4.2 74.8 1.0 CB A:ASP207 4.3 91.1 1.0 CB A:ASP171 4.4 82.7 1.0 CA A:ASP171 4.4 76.9 1.0 CG A:GLU114 4.4 77.9 1.0 OE2 A:GLU173 4.5 86.0 1.0 OD1 A:ASN208 4.5 86.8 1.0 CG A:ASN208 4.6 81.6 1.0 N A:ARG172 4.7 65.8 1.0 CB A:GLU173 4.8 86.3 1.0 C A:ASP171 4.9 70.3 1.0 N A:GLU173 4.9 74.3 1.0 CG A:GLU173 4.9 89.1 1.0

Calcium binding site 5 out of 26 in the Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:40.7 occ:1.00 OD1 A:ASP207 2.4 99.7 1.0 OD1 A:ASP240 2.6 79.6 1.0 OE2 A:GLU173 2.7 86.0 1.0 OE1 A:GLU114 2.8 74.8 1.0 O A:ILE205 2.9 75.2 1.0 OD1 A:ASP204 3.0 60.2 1.0 OE2 A:GLU114 3.0 75.7 1.0 OE1 A:GLU173 3.0 89.7 1.0 CD A:GLU173 3.2 87.4 1.0 CD A:GLU114 3.3 75.4 1.0 CA A:CA604 3.5 62.7 1.0 CG A:ASP207 3.5 0.1 1.0 CG A:ASP240 3.6 77.5 1.0 OD2 A:ASP207 4.0 0.7 1.0 C A:ILE205 4.1 76.5 1.0 CG A:ASP204 4.2 63.4 1.0 CG A:ARG172 4.2 57.5 1.0 ND2 A:ASN208 4.3 85.1 1.0 OD2 A:ASP240 4.4 72.3 1.0 N A:ASP207 4.4 76.6 1.0 N A:ILE205 4.4 68.8 1.0 CB A:ASP240 4.5 79.4 1.0 CD A:ARG172 4.6 58.2 1.0 CA A:ASP240 4.7 82.0 1.0 CG A:GLU173 4.7 89.1 1.0 CB A:ASP207 4.8 91.1 1.0 CG A:GLU114 4.8 77.9 1.0 CG A:ASN208 4.9 81.6 1.0 OD2 A:ASP204 4.9 61.5 1.0 N A:ASN208 4.9 80.6 1.0 CA A:ILE205 4.9 73.0 1.0 CA A:ASP204 5.0 66.5 1.0

Calcium binding site 6 out of 26 in the Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:45.5 occ:1.00 OD2 A:ASP293 2.3 45.1 1.0 O A:ASN208 2.4 67.2 1.0 OD2 A:ASP240 2.6 72.3 1.0 OD2 A:ASP238 2.7 84.2 1.0 O A:ASN244 2.7 82.8 1.0 OD1 A:ASN206 2.7 74.4 1.0 OD1 A:ASP238 2.9 91.1 1.0 CG A:ASP238 3.1 85.3 1.0 CG A:ASP293 3.4 47.9 1.0 C A:ASN208 3.6 69.3 1.0 CG A:ASP240 3.7 77.5 1.0 CG A:ASN206 3.7 70.2 1.0 CB A:ASP293 3.8 54.3 1.0 C A:ASN244 3.9 89.1 1.0 ND2 A:ASN206 4.1 75.4 1.0 CB A:ASP240 4.2 79.4 1.0 CA A:PRO209 4.3 58.9 1.0 N A:PRO209 4.4 65.2 1.0 CD A:PRO210 4.4 46.9 1.0 OD1 A:ASP293 4.4 46.6 1.0 N A:ASN208 4.5 80.6 1.0 CD1 A:LEU297 4.5 80.7 1.0 CA A:ASN208 4.6 74.5 1.0 CB A:ASP238 4.6 82.5 1.0 C A:PRO209 4.7 60.3 1.0 OD1 A:ASP240 4.7 79.6 1.0 CA A:ASN244 4.8 87.8 1.0 CB A:ASN244 4.8 90.4 1.0 N A:PRO210 4.8 53.6 1.0 N A:ALA245 4.9 97.3 1.0 CA A:ALA245 4.9 99.9 1.0 CB A:ASN206 4.9 65.9 1.0 CA A:ASN206 5.0 72.5 1.0

Calcium binding site 7 out of 26 in the Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca607 b:56.1 occ:1.00 OD2 A:ASP312 2.2 83.3 1.0 OD1 A:ASP278 2.4 73.4 1.0 OE1 A:GLU280 2.7 90.7 1.0 OE1 A:GLU223 3.0 51.7 1.0 CG A:ASP312 3.1 75.0 1.0 OD1 A:ASP312 3.2 71.0 1.0 CG A:ASP278 3.5 75.1 1.0 CD A:GLU280 3.6 88.2 1.0 CD A:GLU223 4.0 56.7 1.0 OE2 A:GLU280 4.0 88.8 1.0 CA A:CA608 4.0 46.6 1.0 OD2 A:ASP278 4.1 82.5 1.0 OE2 A:GLU223 4.3 64.5 1.0 CB A:ASP312 4.5 72.6 1.0 CB A:ASP278 4.7 73.2 1.0 SG A:CYS313 4.7 87.2 1.0 CG A:GLU280 4.7 89.4 1.0 CA A:ASP278 4.8 71.6 1.0 CB A:GLU280 4.8 91.9 1.0 N A:PHE279 4.9 66.6 1.0 N A:GLU280 5.0 78.1 1.0

Calcium binding site 8 out of 26 in the Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca608 b:46.6 occ:1.00 OE2 A:GLU280 2.1 88.8 1.0 OE2 A:GLU223 2.3 64.5 1.0 OD1 A:ASP309 2.4 46.6 1.0 O A:GLU310 2.4 69.7 1.0 OD1 A:ASP312 2.5 71.0 1.0 OD1 A:ASP345 2.8 76.6 1.0 CD A:GLU280 3.0 88.2 1.0 OE1 A:GLU280 3.2 90.7 1.0 CD A:GLU223 3.3 56.7 1.0 CG A:ASP312 3.5 75.0 1.0 C A:GLU310 3.6 72.7 1.0 CG A:ASP309 3.6 53.5 1.0 OE1 A:GLU223 3.6 51.7 1.0 N A:GLU310 3.8 73.9 1.0 CG A:ASP345 3.9 64.2 1.0 OD2 A:ASP312 4.0 83.3 1.0 CA A:CA607 4.0 56.1 1.0 OD2 A:ASP309 4.2 58.8 1.0 N A:ASP312 4.2 60.6 1.0 CA A:GLU310 4.3 76.5 1.0 CG A:GLU280 4.4 89.4 1.0 CB A:ASP345 4.6 62.7 1.0 CG A:GLU223 4.6 55.5 1.0 CB A:ASP312 4.6 72.6 1.0 CA A:ASP345 4.7 56.0 1.0 N A:ASN311 4.7 60.9 1.0 C A:ASP309 4.7 71.9 1.0 CB A:ASP309 4.7 62.0 1.0 CA A:ASP309 4.8 68.1 1.0 CB A:PHE279 4.8 55.7 1.0 OD2 A:ASP345 4.9 60.0 1.0 CA A:ASP312 4.9 67.7 1.0 CA A:ASN311 4.9 60.4 1.0 CB A:GLU310 4.9 82.0 1.0

Calcium binding site 9 out of 26 in the Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca609 b:51.9 occ:1.00 OD2 A:ASP343 2.3 84.1 1.0 OD2 A:ASP345 2.3 60.0 1.0 O A:CYS313 2.5 47.8 1.0 O A:ASN349 2.5 52.6 1.0 OD1 A:ASN311 2.6 58.4 1.0 OD1 A:ASP343 2.9 94.9 1.0 CG A:ASP343 2.9 84.0 1.0 OD2 A:ASP396 3.0 62.7 1.0 CG A:ASP345 3.4 64.2 1.0 C A:ASN349 3.7 56.0 1.0 C A:CYS313 3.7 50.3 1.0 CG A:ASN311 3.8 66.6 1.0 CG A:ASP396 3.9 53.5 1.0 CB A:ASP345 3.9 62.7 1.0 CB A:ASP396 3.9 50.8 1.0 CD A:PRO315 4.2 44.6 1.0 CB A:ASP343 4.4 74.8 1.0 N A:CYS313 4.4 66.6 1.0 ND2 A:ASN311 4.5 76.5 1.0 OD1 A:ASP345 4.5 76.6 1.0 CA A:CYS313 4.5 63.7 1.0 N A:PRO315 4.5 48.9 1.0 CA A:ASN349 4.5 57.9 1.0 N A:GLY350 4.6 62.7 1.0 CA A:GLY350 4.6 70.5 1.0 CB A:ASN349 4.6 59.7 1.0 CB A:CYS313 4.7 77.0 1.0 N A:VAL314 4.7 41.4 1.0 C A:VAL314 4.8 60.6 1.0 CA A:VAL314 4.8 42.7 1.0 CB A:ASN311 4.9 62.8 1.0

Calcium binding site 10 out of 26 in the Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Protocadherin Gamma B2 Extracellular Cadherin Domains 1-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca610 b:43.7 occ:1.00 OD2 A:ASP417 2.1 66.0 1.0 OD1 A:ASP381 2.4 42.8 1.0 OE1 A:GLU383 2.9 31.4 1.0 CG A:ASP417 2.9 67.8 1.0 OE1 A:GLU328 3.0 90.0 1.0 OD1 A:ASP417 3.1 62.4 1.0 CD A:GLU328 3.4 85.4 1.0 CG A:ASP381 3.4 53.4 1.0 OE2 A:GLU328 3.6 89.4 1.0 CA A:CA611 3.8 50.6 1.0 CD A:GLU383 4.0 45.9 1.0 ND2 A:ASN418 4.0 62.7 1.0 OD2 A:ASP381 4.2 56.4 1.0 CB A:ASP381 4.3 59.3 1.0 CB A:ASP417 4.4 72.7 1.0 OE2 A:GLU383 4.4 53.5 1.0 CA A:ASP381 4.4 48.7 1.0 N A:ARG382 4.5 39.4 1.0 CG A:GLU328 4.5 77.2 1.0 C A:ASP381 5.0 38.4 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