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

The structure of PCDHGB3 EC1-4 in 50 Mm Hepes, PDB code: 6meq 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)	49.92 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	126.811, 162.912, 52.857, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 27.1

The binding sites of Calcium atom in the PCDHGB3 EC1-4 in 50 Mm Hepes (pdb code 6meq). 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: 6meq:
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:74.7 occ:1.00 OD1 A:ASN206 2.4 99.9 1.0 OD2 A:ASP238 2.5 0.5 1.0 O A:ASN208 2.5 0.1 1.0 OD2 A:ASP240 2.5 0.1 1.0 OD1 A:ASP238 2.6 0.3 1.0 O A:ASN244 2.6 88.7 1.0 OD2 A:ASP293 2.8 0.2 1.0 CG A:ASP238 2.9 0.4 1.0 CG A:ASN206 3.5 99.4 1.0 CG A:ASP240 3.5 0.0 1.0 C A:ASN208 3.7 0.2 1.0 C A:ASN244 3.8 0.2 1.0 CB A:ASP240 3.9 0.8 1.0 CG A:ASP293 3.9 0.6 1.0 ND2 A:ASN206 4.0 0.4 1.0 CB A:ASP293 4.3 0.2 1.0 CB A:ASP238 4.4 0.6 1.0 CA A:PRO209 4.4 0.2 1.0 CB A:ASN244 4.4 0.1 1.0 CA A:ASN244 4.5 0.8 1.0 N A:PRO209 4.5 0.5 1.0 OD1 A:ASP240 4.6 0.8 1.0 CA A:ASN208 4.6 0.5 1.0 N A:ASN208 4.6 0.7 1.0 C A:PRO209 4.6 0.7 1.0 CD A:PRO210 4.7 98.2 1.0 CB A:ASN206 4.7 97.2 1.0 N A:ALA245 4.8 0.4 1.0 N A:PRO210 4.8 0.5 1.0 CA A:ASN206 4.9 95.2 1.0 CB A:ASN208 4.9 0.5 1.0 N A:ASP240 5.0 0.3 1.0 CA A:ALA245 5.0 0.7 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:66.3 occ:1.00 OD2 A:ASP343 2.5 78.9 1.0 O A:ASN313 2.5 86.7 1.0 O A:ASN349 2.6 72.5 1.0 OD1 A:ASN311 2.6 83.8 1.0 OD2 A:ASP345 2.7 64.6 1.0 OD1 A:ASP343 2.9 77.8 1.0 CG A:ASP343 2.9 77.7 1.0 OD2 A:ASP396 3.1 78.6 1.0 CG A:ASP396 3.3 78.3 1.0 CB A:ASP396 3.6 76.3 1.0 CG A:ASN311 3.7 83.5 1.0 C A:ASN313 3.7 87.8 1.0 CG A:ASP345 3.8 64.8 1.0 C A:ASN349 3.8 72.7 1.0 OD1 A:ASP396 4.0 80.8 1.0 CB A:ASP345 4.1 64.7 1.0 CB A:ASP343 4.3 76.5 1.0 ND2 A:ASN311 4.3 84.1 1.0 CA A:ASN349 4.5 74.5 1.0 CB A:ASN349 4.6 67.4 1.0 CA A:ASN313 4.6 86.0 1.0 N A:ASN313 4.6 82.6 1.0 CB A:ASN313 4.7 85.9 1.0 N A:ALA314 4.7 71.0 1.0 CD A:PRO315 4.7 77.8 1.0 N A:GLY350 4.8 74.9 1.0 CA A:ALA314 4.8 73.5 1.0 CB A:ASN311 4.8 83.5 1.0 OD1 A:ASP345 4.9 71.6 1.0 C A:ALA314 4.9 75.1 1.0 N A:PRO315 4.9 77.9 1.0 CA A:GLY350 4.9 74.7 1.0 CG A:PRO315 4.9 76.3 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:59.9 occ:1.00 OE2 A:GLU223 2.5 88.5 1.0 O A:GLU310 2.5 89.2 1.0 OE2 A:GLU280 2.5 91.7 1.0 OD1 A:ASP312 2.5 76.5 1.0 OD1 A:ASP345 2.6 71.6 1.0 OD1 A:ASP309 2.8 87.9 1.0 OE1 A:GLU280 3.0 91.4 1.0 CD A:GLU280 3.1 92.5 1.0 OE1 A:GLU223 3.1 89.8 1.0 CD A:GLU223 3.1 88.3 1.0 ND2 A:ASN313 3.6 83.7 1.0 CG A:ASP345 3.6 64.8 1.0 CG A:ASP312 3.6 77.2 1.0 C A:GLU310 3.6 88.1 1.0 CG A:ASP309 3.8 87.6 1.0 CA A:CA508 3.9 62.8 1.0 N A:GLU310 3.9 84.9 1.0 OD2 A:ASP312 4.2 77.5 1.0 N A:ASP312 4.3 77.3 1.0 CB A:ASP345 4.3 64.7 1.0 OD2 A:ASP309 4.3 88.4 1.0 CA A:GLU310 4.3 87.3 1.0 OD2 A:ASP345 4.4 64.6 1.0 CG A:GLU280 4.5 95.7 1.0 CA A:ASP345 4.5 70.8 1.0 CG A:GLU223 4.6 86.4 1.0 N A:ASN311 4.7 85.8 1.0 CB A:ASP312 4.8 81.6 1.0 CG A:ASN313 4.8 85.3 1.0 CB A:PHE279 4.8 84.8 1.0 C A:ASP309 4.8 84.9 1.0 CB A:GLU310 4.9 89.8 1.0 CA A:ASP309 4.9 85.4 1.0 CB A:ASP309 4.9 86.9 1.0 CA A:ASN311 4.9 85.1 1.0 CA A:ASP312 5.0 78.6 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:79.5 occ:1.00 OD2 A:ASP131 2.4 79.4 1.0 OD2 A:ASP129 2.5 92.6 1.0 OD1 A:ASN97 2.5 92.7 1.0 O A:ASN135 2.5 78.0 1.0 O A:ASN99 2.6 95.5 1.0 OD2 A:ASP186 2.7 70.8 1.0 OD1 A:ASP129 3.0 96.5 1.0 CG A:ASP129 3.0 94.0 1.0 CG A:ASP131 3.5 81.9 1.0 C A:ASN135 3.6 77.0 1.0 CG A:ASN97 3.6 91.2 1.0 C A:ASN99 3.8 96.1 1.0 CB A:ASP131 3.8 80.7 1.0 CG A:ASP186 3.8 70.5 1.0 CB A:ASN135 4.2 79.8 1.0 CB A:ASP186 4.2 70.6 1.0 CA A:ASN135 4.3 78.1 1.0 ND2 A:ASN97 4.3 94.5 1.0 CB A:ASP129 4.5 92.3 1.0 N A:SER136 4.5 77.5 1.0 N A:ASN99 4.5 90.3 1.0 OD1 A:ASP131 4.6 84.4 1.0 CA A:ASN99 4.6 93.7 1.0 CB A:ASN97 4.6 87.2 1.0 CA A:SER136 4.7 76.5 1.0 N A:PRO100 4.7 75.9 1.0 CA A:ASN97 4.7 84.7 1.0 CA A:PRO100 4.7 73.7 1.0 CB A:ASN99 4.8 93.8 1.0 CD A:PRO101 4.9 67.7 1.0 C A:PRO100 4.9 73.5 1.0 OD1 A:ASP186 4.9 70.6 1.0 N A:PRO101 5.0 69.6 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:67.7 occ:1.00 OD1 A:ASP61 2.5 91.1 1.0 OE1 A:GLU63 2.5 81.0 1.0 OD2 A:ASP98 2.6 83.1 1.0 OE1 A:GLU9 2.9 79.5 1.0 OE2 A:GLU10 2.9 0.2 1.0 CG A:ASP98 3.4 84.9 1.0 CD A:GLU9 3.5 79.7 1.0 OD1 A:ASP98 3.5 85.5 1.0 CG A:ASP61 3.6 92.9 1.0 OE2 A:GLU9 3.6 80.5 1.0 CD A:GLU10 3.7 0.6 1.0 CD A:GLU63 3.7 87.2 1.0 CG A:GLU10 3.8 97.2 1.0 CA A:CA506 3.9 60.7 1.0 OD1 A:ASN99 4.0 91.2 1.0 OD2 A:ASP61 4.3 95.0 1.0 N A:ARG62 4.3 84.9 1.0 CA A:ASP61 4.4 85.5 1.0 OE2 A:GLU63 4.4 81.8 1.0 NH2 A:ARG59 4.5 0.4 1.0 CB A:ASP61 4.5 90.2 1.0 N A:GLU63 4.7 90.1 1.0 CG A:GLU9 4.7 79.8 1.0 CG A:GLU63 4.7 91.9 1.0 CB A:ASP98 4.8 86.3 1.0 C A:ASP61 4.8 86.8 1.0 CB A:GLU63 4.9 95.2 1.0 OE1 A:GLU10 4.9 0.4 1.0 CG A:ASN99 5.0 93.3 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:60.7 occ:1.00 OE2 A:GLU63 2.4 81.8 1.0 OE2 A:GLU9 2.5 80.5 1.0 O A:ILE96 2.5 79.4 1.0 OD1 A:ASP98 2.5 85.5 1.0 OD1 A:ASP95 2.6 82.3 1.0 OD1 A:ASP131 2.6 84.4 1.0 CD A:GLU63 3.0 87.2 1.0 OE1 A:GLU63 3.1 81.0 1.0 CG A:ASP131 3.5 81.9 1.0 CG A:ASP98 3.6 84.9 1.0 CD A:GLU9 3.6 79.7 1.0 CG A:ASP95 3.6 82.3 1.0 C A:ILE96 3.7 78.7 1.0 OD1 A:ASN99 3.9 91.2 1.0 N A:ILE96 3.9 76.9 1.0 CA A:CA505 3.9 67.7 1.0 OD2 A:ASP98 4.0 83.1 1.0 OE1 A:GLU9 4.1 79.5 1.0 OD2 A:ASP95 4.1 84.6 1.0 OD2 A:ASP131 4.2 79.4 1.0 N A:ASP98 4.3 86.4 1.0 CB A:ASP131 4.3 80.7 1.0 CG1 A:ILE96 4.4 75.4 1.0 CA A:ILE96 4.4 77.3 1.0 CG A:GLU63 4.4 91.9 1.0 NE A:ARG62 4.5 77.5 1.0 CA A:ASP131 4.6 82.3 1.0 NH2 A:ARG62 4.7 86.0 1.0 N A:ASN97 4.7 80.5 1.0 CB A:ASP95 4.8 79.8 1.0 C A:ASP95 4.8 77.5 1.0 CB A:ASP98 4.8 86.3 1.0 CG A:GLU9 4.8 79.8 1.0 CA A:ASP95 4.8 77.2 1.0 CG A:ASN99 4.9 93.3 1.0 CA A:ASN97 4.9 84.7 1.0 CA A:ASP98 5.0 87.6 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:0.7 occ:1.00 OE1 A:GLU173 2.5 0.3 1.0 OD2 A:ASP207 2.5 90.0 1.0 O A:HOH638 2.5 86.4 1.0 OD1 A:ASP171 2.5 0.6 1.0 CD A:GLU173 3.1 0.2 1.0 CG A:ASP207 3.3 92.5 1.0 CB A:GLU173 3.4 0.5 1.0 CG A:GLU173 3.4 0.2 1.0 O A:HOH613 3.4 64.0 1.0 CG A:ASP171 3.4 0.7 1.0 OD1 A:ASP207 3.5 93.4 1.0 OD2 A:ASP171 3.7 0.7 1.0 CA A:CA509 4.1 79.7 1.0 ND2 A:ASN208 4.1 0.1 1.0 OE2 A:GLU173 4.1 0.5 1.0 OE1 A:GLU114 4.1 1.0 1.0 N A:GLU173 4.2 0.8 1.0 CA A:GLU173 4.4 0.4 1.0 CB A:ASP207 4.6 93.6 1.0 CB A:ASP171 4.8 97.4 1.0 O A:ASP207 4.8 0.7 1.0 OE2 A:GLU114 4.8 0.4 1.0 CD A:GLU114 4.9 0.0 1.0 CG A:ASN208 5.0 0.3 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:62.8 occ:1.00 OE1 A:GLU223 2.4 89.8 1.0 OD1 A:ASP278 2.5 93.5 1.0 OD2 A:ASP312 2.6 77.5 1.0 OE1 A:GLU280 2.9 91.4 1.0 CG A:ASP312 3.4 77.2 1.0 CD A:GLU223 3.4 88.3 1.0 OD1 A:ASP312 3.4 76.5 1.0 O A:HOH645 3.4 50.5 1.0 CG A:ASP278 3.5 94.8 1.0 CA A:CA503 3.9 59.9 1.0 ND2 A:ASN313 4.0 83.7 1.0 CD A:GLU280 4.0 92.5 1.0 OD2 A:ASP278 4.0 95.9 1.0 OE2 A:GLU223 4.1 88.5 1.0 CG A:GLU223 4.3 86.4 1.0 CB A:ASP278 4.5 91.4 1.0 OD1 A:ASN224 4.5 0.7 1.0 CA A:ASP278 4.5 87.3 1.0 N A:PHE279 4.7 83.9 1.0 OE2 A:GLU280 4.7 91.7 1.0 CB A:ASP312 4.9 81.6 1.0 CG A:GLU280 4.9 95.7 1.0 N A:GLU280 5.0 94.2 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:79.7 occ:1.00 OD1 A:ASP207 2.4 93.4 1.0 OD1 A:ASP204 2.4 0.7 1.0 OE2 A:GLU114 2.4 0.4 1.0 OE2 A:GLU173 2.4 0.5 1.0 OE1 A:GLU173 2.7 0.3 1.0 OD1 A:ASP240 2.8 0.8 1.0 CD A:GLU173 2.9 0.2 1.0 O A:ALA205 2.9 92.7 1.0 CG A:ASP207 3.2 92.5 1.0 CD A:GLU114 3.3 0.0 1.0 CG A:ASP204 3.5 0.1 1.0 OD2 A:ASP207 3.5 90.0 1.0 OE1 A:GLU114 3.5 1.0 1.0 CG A:ASP240 3.8 0.0 1.0 NH1 A:ARG172 4.0 98.8 1.0 N A:ALA205 4.0 98.9 1.0 CA A:CA507 4.1 0.7 1.0 NE A:ARG172 4.1 95.9 1.0 C A:ALA205 4.1 93.7 1.0 OD2 A:ASP204 4.1 0.6 1.0 CG A:GLU173 4.3 0.2 1.0 N A:ASP207 4.5 94.7 1.0 CB A:ASP240 4.5 0.8 1.0 CA A:ASP240 4.5 0.7 1.0 CZ A:ARG172 4.5 97.4 1.0 CB A:ASP207 4.5 93.6 1.0 CB A:ASP204 4.6 0.9 1.0 CA A:ASP204 4.6 0.6 1.0 CA A:ALA205 4.7 94.7 1.0 CB A:ARG172 4.7 93.7 1.0 CG A:GLU114 4.7 0.1 1.0 OD2 A:ASP240 4.8 0.1 1.0 C A:ASP204 4.8 0.7 1.0 O A:MET239 5.0 0.4 1.0 CA A:ASP207 5.0 96.5 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