Calcium in PDB 6mer: PCDHGB3 EC1-4 in 50 Mm Hepes

The structure of PCDHGB3 EC1-4 in 50 Mm Hepes, PDB code: 6mer was solved by J.M.Nicoludis, R.Gaudet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.83 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	128.390, 161.770, 52.160, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 27.2

The binding sites of Calcium atom in the PCDHGB3 EC1-4 in 50 Mm Hepes (pdb code 6mer). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the PCDHGB3 EC1-4 in 50 Mm Hepes, PDB code: 6mer:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the PCDHGB3 EC1-4 in 50 Mm Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of PCDHGB3 EC1-4 in 50 Mm Hepes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:66.6 occ:1.00 OD1 A:ASN97 2.5 77.5 1.0 O A:ASN135 2.5 76.8 1.0 OD1 A:ASP129 2.6 86.4 1.0 O A:ASN99 2.6 80.0 1.0 OD1 A:ASP131 2.6 79.4 1.0 OD2 A:ASP129 2.6 84.8 1.0 OD2 A:ASP186 2.6 77.2 1.0 CG A:ASP129 2.9 85.7 1.0 CG A:ASP131 3.3 80.8 1.0 CG A:ASN97 3.6 77.8 1.0 C A:ASN135 3.7 80.0 1.0 CG A:ASP186 3.7 76.8 1.0 C A:ASN99 3.8 80.9 1.0 CB A:ASP131 3.9 81.3 1.0 OD2 A:ASP131 4.1 82.0 1.0 CB A:ASP186 4.2 75.7 1.0 CB A:ASN135 4.2 85.7 1.0 CB A:ASP129 4.3 86.1 1.0 ND2 A:ASN97 4.3 77.0 1.0 CA A:ASN135 4.4 82.1 1.0 N A:ASN99 4.5 80.1 1.0 CB A:ASN97 4.6 79.6 1.0 CA A:ASN99 4.6 82.0 1.0 CA A:ASN97 4.6 80.9 1.0 N A:SER136 4.7 79.9 1.0 N A:PRO100 4.8 82.4 1.0 CB A:ASN99 4.8 81.3 1.0 OD1 A:ASP186 4.8 78.0 1.0 CA A:PRO100 4.8 81.2 1.0 N A:ASP131 4.8 81.5 1.0 CA A:SER136 4.9 78.5 1.0 C A:PRO100 4.9 81.0 1.0 CA A:ASP131 5.0 82.5 1.0

Calcium binding site 2 out of 9 in the PCDHGB3 EC1-4 in 50 Mm Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of PCDHGB3 EC1-4 in 50 Mm Hepes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:63.8 occ:1.00 OD1 A:ASP61 2.5 99.3 1.0 OD2 A:ASP98 2.5 87.3 1.0 OE1 A:GLU63 2.6 88.6 1.0 OE2 A:GLU10 2.6 85.3 1.0 OE1 A:GLU9 3.0 81.9 1.0 CG A:ASP98 3.4 85.3 1.0 CG A:ASP61 3.5 97.6 1.0 CD A:GLU10 3.5 84.9 1.0 CD A:GLU9 3.6 81.1 1.0 OD1 A:ASP98 3.6 84.2 1.0 OE2 A:GLU9 3.6 81.7 1.0 CG A:GLU10 3.8 83.3 1.0 CD A:GLU63 3.8 89.5 1.0 OD1 A:ASN99 4.0 84.5 1.0 CA A:CA503 4.2 57.1 1.0 CA A:ASP61 4.2 89.2 1.0 N A:ARG62 4.2 88.2 1.0 NH2 A:ARG59 4.3 91.0 1.0 OD2 A:ASP61 4.3 0.2 1.0 CB A:ASP61 4.3 93.2 1.0 OE2 A:GLU63 4.4 84.1 1.0 C A:ASP61 4.6 89.2 1.0 OE1 A:GLU10 4.7 86.0 1.0 N A:GLU63 4.7 94.8 1.0 CB A:ASP98 4.7 89.8 1.0 CG A:GLU9 4.8 79.7 1.0 CG A:GLU63 4.8 93.5 1.0 CG A:ASN99 4.9 83.0 1.0 CB A:GLU63 5.0 96.6 1.0

Calcium binding site 3 out of 9 in the PCDHGB3 EC1-4 in 50 Mm Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of PCDHGB3 EC1-4 in 50 Mm Hepes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:57.1 occ:1.00 OD2 A:ASP131 2.4 82.0 1.0 OE2 A:GLU9 2.4 81.7 1.0 OE2 A:GLU63 2.4 84.1 1.0 OD1 A:ASP95 2.5 80.8 1.0 O A:ILE96 2.6 84.2 1.0 OD1 A:ASP98 2.7 84.2 1.0 CD A:GLU63 3.2 89.5 1.0 OE1 A:GLU63 3.3 88.6 1.0 CG A:ASP131 3.4 80.8 1.0 CG A:ASP95 3.5 81.0 1.0 CD A:GLU9 3.6 81.1 1.0 CG A:ASP98 3.6 85.3 1.0 C A:ILE96 3.8 84.3 1.0 N A:ILE96 3.9 88.0 1.0 OD2 A:ASP98 3.9 87.3 1.0 CB A:ASP131 4.0 81.3 1.0 OD1 A:ASN99 4.0 84.5 1.0 OD2 A:ASP95 4.1 80.8 1.0 OE1 A:GLU9 4.1 81.9 1.0 CA A:CA502 4.2 63.8 1.0 CA A:ASP131 4.4 82.5 1.0 NE A:ARG62 4.4 80.5 1.0 N A:ASP98 4.4 81.8 1.0 OD1 A:ASP131 4.4 79.4 1.0 CA A:ILE96 4.5 86.5 1.0 CG1 A:ILE96 4.5 88.1 1.0 CG A:GLU63 4.6 93.5 1.0 CB A:ASP95 4.6 78.8 1.0 CA A:ASP95 4.6 88.8 1.0 C A:ASP95 4.7 78.3 1.0 CG A:GLU9 4.7 79.7 1.0 N A:ASN97 4.8 82.8 1.0 CB A:ASP98 4.9 89.8 1.0 CB A:ARG62 4.9 79.3 1.0

Calcium binding site 4 out of 9 in the PCDHGB3 EC1-4 in 50 Mm Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of PCDHGB3 EC1-4 in 50 Mm Hepes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:66.0 occ:1.00 OD2 A:ASP343 2.4 85.5 1.0 O A:ASN313 2.4 83.4 1.0 OD1 A:ASN311 2.5 79.6 1.0 OD2 A:ASP396 2.5 71.5 1.0 OD1 A:ASP343 2.6 82.3 1.0 OD2 A:ASP345 2.6 77.6 1.0 O A:ASN349 2.7 73.4 1.0 CG A:ASP343 2.8 85.2 1.0 CG A:ASP396 3.5 70.3 1.0 CG A:ASP345 3.6 79.0 1.0 CG A:ASN311 3.6 79.4 1.0 C A:ASN313 3.7 84.6 1.0 C A:ASN349 3.8 74.5 1.0 CB A:ASP396 3.9 69.3 1.0 CB A:ASP345 4.1 79.0 1.0 CB A:ASP343 4.2 90.4 1.0 ND2 A:ASN311 4.3 78.0 1.0 CD A:PRO315 4.5 95.8 1.0 CA A:ASN349 4.5 75.9 1.0 CB A:ASN349 4.5 77.9 1.0 CA A:ASN313 4.5 84.4 1.0 N A:ASN313 4.5 82.1 1.0 N A:ALA314 4.6 74.7 1.0 CA A:ALA314 4.6 72.5 1.0 OD1 A:ASP345 4.6 80.7 1.0 OD1 A:ASP396 4.7 70.2 1.0 CG A:PRO315 4.7 91.1 1.0 CB A:ASN313 4.7 85.7 1.0 N A:GLY350 4.8 74.8 1.0 CB A:ASN311 4.8 79.8 1.0 N A:PRO315 4.8 97.5 1.0 CA A:ASN311 4.9 82.8 1.0 C A:ALA314 4.9 0.8 1.0 CA A:GLY350 5.0 73.9 1.0

Calcium binding site 5 out of 9 in the PCDHGB3 EC1-4 in 50 Mm Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of PCDHGB3 EC1-4 in 50 Mm Hepes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:65.5 occ:1.00 OE2 A:GLU280 2.4 98.2 1.0 OE2 A:GLU223 2.5 97.9 1.0 OD1 A:ASP345 2.5 80.7 1.0 O A:GLU310 2.5 88.2 1.0 OD1 A:ASP312 2.5 80.2 1.0 OD1 A:ASP309 2.6 79.1 1.0 OE1 A:GLU280 3.1 98.4 1.0 CD A:GLU280 3.1 99.1 1.0 CG A:ASP345 3.3 79.0 1.0 CD A:GLU223 3.4 97.5 1.0 CG A:ASP312 3.5 79.6 1.0 OE1 A:GLU223 3.6 98.9 1.0 CA A:CA506 3.6 61.6 1.0 C A:GLU310 3.7 88.4 1.0 CG A:ASP309 3.8 92.8 1.0 ND2 A:ASN313 3.8 84.8 1.0 CB A:ASP345 3.9 79.0 1.0 OD2 A:ASP312 3.9 79.6 1.0 N A:GLU310 4.0 90.2 1.0 OD2 A:ASP345 4.1 77.6 1.0 N A:ASP312 4.2 83.7 1.0 CA A:ASP345 4.3 80.0 1.0 OD2 A:ASP309 4.4 80.0 1.0 CA A:GLU310 4.4 89.6 1.0 CG A:GLU280 4.5 0.0 1.0 C A:ASP309 4.7 89.5 1.0 N A:ASN311 4.7 84.1 1.0 CG A:GLU223 4.7 95.4 1.0 CB A:PHE279 4.7 80.3 1.0 CB A:ASP312 4.8 85.2 1.0 CA A:ASP309 4.8 89.2 1.0 CB A:ASP309 4.9 91.1 1.0 N A:ASP345 4.9 78.9 1.0 CA A:ASP312 4.9 84.8 1.0 CA A:ASN311 4.9 82.8 1.0 CG A:ASN313 4.9 86.4 1.0 N A:ASN313 5.0 82.1 1.0

Calcium binding site 6 out of 9 in the PCDHGB3 EC1-4 in 50 Mm Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of PCDHGB3 EC1-4 in 50 Mm Hepes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:61.6 occ:1.00 OE1 A:GLU280 2.5 98.4 1.0 OE1 A:GLU223 2.5 98.9 1.0 OD1 A:ASP278 2.5 84.9 1.0 OD2 A:ASP312 2.5 79.6 1.0 O A:HOH620 2.6 60.4 1.0 OD1 A:ASP312 3.1 80.2 1.0 CG A:ASP312 3.1 79.6 1.0 O A:HOH657 3.3 42.9 1.0 CD A:GLU223 3.4 97.5 1.0 ND2 A:ASN313 3.5 84.8 1.0 CD A:GLU280 3.6 99.1 1.0 CG A:ASP278 3.6 85.7 1.0 CA A:CA505 3.6 65.5 1.0 OE2 A:GLU223 3.8 97.9 1.0 OD2 A:ASP278 4.2 87.5 1.0 OE2 A:GLU280 4.2 98.2 1.0 N A:PHE279 4.4 88.1 1.0 CA A:ASP278 4.5 84.3 1.0 CB A:ASP312 4.5 85.2 1.0 CG A:GLU223 4.5 95.4 1.0 CG A:GLU280 4.6 0.0 1.0 CB A:ASP278 4.6 85.1 1.0 N A:GLU280 4.6 96.2 1.0 O A:HOH649 4.6 42.9 1.0 CB A:GLU280 4.7 0.8 1.0 CG A:ASN313 4.8 86.4 1.0 C A:ASP278 4.9 86.5 1.0 CB A:GLU223 5.0 95.8 1.0

Calcium binding site 7 out of 9 in the PCDHGB3 EC1-4 in 50 Mm Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of PCDHGB3 EC1-4 in 50 Mm Hepes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:93.2 occ:1.00 OD2 A:ASP240 2.5 0.7 1.0 O A:ASN208 2.5 0.9 1.0 O A:ASN244 2.5 0.3 1.0 OD2 A:ASP293 2.6 0.5 1.0 OD1 A:ASP238 2.6 0.7 1.0 OD2 A:ASP238 2.6 0.5 1.0 ND2 A:ASN206 2.7 0.5 1.0 CG A:ASP238 3.0 0.7 1.0 CG A:ASP240 3.5 0.5 1.0 C A:ASN208 3.6 0.4 1.0 CG A:ASN206 3.7 0.5 1.0 C A:ASN244 3.7 0.8 1.0 CG A:ASP293 3.8 0.5 1.0 CB A:ASP240 4.0 0.1 1.0 OD1 A:ASN206 4.2 0.6 1.0 N A:ASN208 4.3 0.7 1.0 CB A:ASN244 4.4 0.5 1.0 CA A:ASN244 4.4 0.3 1.0 CB A:ASP293 4.4 0.8 1.0 CA A:ASN208 4.4 0.1 1.0 OD1 A:ASP240 4.4 0.7 1.0 N A:PRO209 4.4 0.7 1.0 CA A:PRO209 4.5 0.7 1.0 CB A:ASP238 4.5 1.0 1.0 CB A:ASN206 4.7 0.8 1.0 CA A:ASN206 4.7 0.0 1.0 CB A:ASN208 4.7 0.6 1.0 N A:ALA245 4.7 0.7 1.0 OD1 A:ASP293 4.8 0.4 1.0 C A:PRO209 4.8 0.3 1.0 CD A:PRO210 4.9 98.8 1.0 CA A:ALA245 4.9 99.3 1.0

Calcium binding site 8 out of 9 in the PCDHGB3 EC1-4 in 50 Mm Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of PCDHGB3 EC1-4 in 50 Mm Hepes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:0.2 occ:1.00 OD1 A:ASP171 2.4 0.6 1.0 OD2 A:ASP207 2.4 0.7 1.0 OE1 A:GLU114 2.5 1.0 1.0 OE1 A:GLU173 2.5 0.2 1.0 CG A:ASP207 3.3 0.9 1.0 CG A:ASP171 3.3 0.3 1.0 OD1 A:ASP207 3.4 0.2 1.0 CD A:GLU114 3.7 0.1 1.0 CD A:GLU173 3.7 0.4 1.0 OD1 A:ASN208 3.8 0.0 1.0 OD2 A:ASP171 3.9 0.3 1.0 O A:HOH660 4.0 57.7 1.0 CA A:CA509 4.2 92.4 1.0 OE2 A:GLU114 4.2 0.7 1.0 CB A:ASP171 4.3 0.3 1.0 CA A:ASP171 4.3 0.4 1.0 OE2 A:GLU173 4.5 0.3 1.0 CG A:GLU173 4.5 0.8 1.0 CB A:GLU173 4.6 0.9 1.0 N A:ARG172 4.6 0.6 1.0 CG A:ASN208 4.6 0.5 1.0 N A:GLU173 4.7 0.8 1.0 CB A:ASP207 4.7 0.8 1.0 ND2 A:ASN208 4.8 0.5 1.0 C A:ASP171 4.8 0.8 1.0 CG A:GLU114 4.8 0.2 1.0 CB A:GLU114 5.0 0.7 1.0

Calcium binding site 9 out of 9 in the PCDHGB3 EC1-4 in 50 Mm Hepes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of PCDHGB3 EC1-4 in 50 Mm Hepes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca509 b:92.4 occ:1.00 OE2 A:GLU114 2.5 0.7 1.0 O A:ALA205 2.5 0.3 1.0 OE2 A:GLU173 2.5 0.3 1.0 OD1 A:ASP240 2.6 0.7 1.0 OD1 A:ASP204 2.7 0.1 1.0 OD1 A:ASP207 2.7 0.2 1.0 OE1 A:GLU173 3.1 0.2 1.0 CD A:GLU173 3.1 0.4 1.0 CD A:GLU114 3.2 0.1 1.0 CG A:ASP240 3.4 0.5 1.0 OE1 A:GLU114 3.4 1.0 1.0 C A:ALA205 3.6 0.2 1.0 CG A:ASP204 3.6 0.5 1.0 N A:ALA205 3.7 0.6 1.0 CG A:ASP207 3.8 0.9 1.0 CB A:ASP240 4.0 0.1 1.0 OD2 A:ASP240 4.1 0.7 1.0 OD2 A:ASP204 4.1 1.0 1.0 CA A:CA508 4.2 0.2 1.0 CA A:ALA205 4.2 0.6 1.0 CA A:ASP240 4.3 0.4 1.0 N A:ASP207 4.4 0.1 1.0 OD2 A:ASP207 4.4 0.7 1.0 NE A:ARG172 4.5 0.4 1.0 CG A:GLU173 4.5 0.8 1.0 CG A:GLU114 4.6 0.2 1.0 C A:ASP204 4.6 0.7 1.0 CA A:ASP204 4.6 0.1 1.0 N A:ASN206 4.7 0.9 1.0 OD1 A:ASN208 4.7 0.0 1.0 CB A:ASP204 4.7 0.5 1.0 CB A:ALA205 4.9 0.1 1.0 CB A:ASP207 4.9 0.8 1.0 CA A:ASN206 4.9 0.0 1.0 NH2 A:ARG172 4.9 0.5 1.0 CG A:ASN208 4.9 0.5 1.0

J.M.Nicoludis, A.G.Green, S.Walujkar, E.J.May, M.Sotomayor, D.S.Marks, R.Gaudet. Interaction Specificity of Clustered Protocadherins Inferred From Sequence Covariation and Structural Analysis. Proc.Natl.Acad.Sci.Usa V. 116 17825 2019.
ISSN: ESSN 1091-6490
PubMed: 31431536
DOI: 10.1073/PNAS.1821063116