Calcium in PDB 6bx7: Crystal Structure of Human Protocadherin-1 EC1-4

The structure of Crystal Structure of Human Protocadherin-1 EC1-4, PDB code: 6bx7 was solved by D.Modak, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.26 / 2.85
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	146.981, 146.981, 147.686, 90.00, 90.00, 120.00
R / Rfree (%)	22.1 / 24.3

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Human Protocadherin-1 EC1-4 (pdb code 6bx7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the Crystal Structure of Human Protocadherin-1 EC1-4, PDB code: 6bx7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in the Crystal Structure of Human Protocadherin-1 EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Protocadherin-1 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:75.2 occ:1.00 OD1 A:ASP59 2.2 79.4 1.0 OD2 A:ASP106 2.2 69.5 1.0 OE1 A:GLU61 2.3 69.4 1.0 OE1 A:GLU9 2.4 67.6 1.0 OE1 A:GLU10 3.0 78.1 1.0 CG A:ASP106 3.0 67.0 1.0 OD1 A:ASP106 3.2 66.5 1.0 CD A:GLU9 3.3 69.7 1.0 CG A:ASP59 3.3 78.1 1.0 CD A:GLU61 3.5 70.7 1.0 OE2 A:GLU9 3.6 69.4 1.0 CG A:GLU10 3.7 77.5 1.0 CD A:GLU10 3.8 79.2 1.0 CA A:CA503 4.0 61.0 1.0 ND2 A:ASN107 4.1 52.7 1.0 OD2 A:ASP59 4.1 79.9 1.0 CB A:ASP59 4.2 77.2 1.0 OE2 A:GLU61 4.3 70.3 1.0 N A:ARG60 4.3 70.6 1.0 N A:GLU61 4.4 71.6 1.0 CA A:ASP59 4.4 75.0 1.0 CB A:ASP106 4.4 66.9 1.0 CG A:GLU61 4.6 71.3 1.0 CB A:GLU61 4.6 72.4 1.0 C A:ASP59 4.6 73.0 1.0 CG A:GLU9 4.6 71.1 1.0

Calcium binding site 2 out of 11 in the Crystal Structure of Human Protocadherin-1 EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Protocadherin-1 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:61.0 occ:1.00 OE2 A:GLU61 2.2 70.3 1.0 OE2 A:GLU9 2.3 69.4 1.0 OD1 A:ASP139 2.3 55.7 1.0 OD1 A:ASP103 2.3 65.0 1.0 OD1 A:ASP106 2.4 66.5 1.0 O A:ILE104 2.6 64.1 1.0 CD A:GLU61 2.9 70.7 1.0 OE1 A:GLU61 2.9 69.4 1.0 CD A:GLU9 3.4 69.7 1.0 CG A:ASP139 3.5 56.3 1.0 CG A:ASP106 3.5 67.0 1.0 CG A:ASP103 3.6 67.0 1.0 NH1 A:ARG60 3.7 68.0 1.0 C A:ILE104 3.8 65.1 1.0 OE1 A:GLU9 3.9 67.6 1.0 ND2 A:ASN107 3.9 52.7 1.0 CA A:CA502 4.0 75.2 1.0 N A:ILE104 4.0 66.3 1.0 OD2 A:ASP106 4.1 69.5 1.0 CB A:ASP139 4.2 57.8 1.0 N A:ASP106 4.2 64.5 1.0 CA A:ASP139 4.4 59.2 1.0 CG A:GLU61 4.4 71.3 1.0 OD2 A:ASP103 4.4 67.3 1.0 OD2 A:ASP139 4.4 54.0 1.0 CB A:ASP103 4.5 68.6 1.0 CA A:ILE104 4.5 66.4 1.0 CA A:ASP103 4.6 68.7 1.0 CG A:GLU9 4.6 71.1 1.0 CG1 A:ILE104 4.6 65.7 1.0 CB A:ASP106 4.7 66.9 1.0 C A:ASP103 4.7 67.1 1.0 CB A:ARG60 4.8 68.5 1.0 N A:ASN105 4.8 65.0 1.0 CA A:ASP106 4.9 65.6 1.0 CD A:ARG60 4.9 68.9 1.0 CZ A:ARG60 5.0 70.2 1.0

Calcium binding site 3 out of 11 in the Crystal Structure of Human Protocadherin-1 EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Protocadherin-1 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:50.4 occ:1.00 OD1 A:ASN105 2.3 62.8 1.0 O A:ASN107 2.3 45.5 1.0 OD2 A:ASP197 2.3 44.2 1.0 O A:ASN143 2.4 53.3 1.0 OD2 A:ASP137 2.4 53.1 1.0 OD2 A:ASP139 2.5 54.0 1.0 OD1 A:ASP137 2.8 55.5 1.0 CG A:ASP137 2.9 54.6 1.0 CG A:ASP197 3.3 45.8 1.0 CG A:ASN105 3.4 63.7 1.0 CG A:ASP139 3.5 56.3 1.0 C A:ASN107 3.5 47.6 1.0 C A:ASN143 3.6 54.5 1.0 CB A:ASP139 3.7 57.8 1.0 CB A:ASP197 3.8 46.0 1.0 ND2 A:ASN105 4.1 64.4 1.0 OD1 A:ASP197 4.3 46.8 1.0 N A:ASN107 4.3 49.4 1.0 CA A:ASN107 4.3 48.9 1.0 CD A:PRO109 4.4 53.0 1.0 CB A:ASP137 4.5 54.6 1.0 N A:GLY144 4.5 54.0 1.0 N A:THR108 4.5 49.9 1.0 CA A:GLY144 4.5 52.3 1.0 CB A:ASN107 4.5 50.6 1.0 CA A:ASN143 4.5 56.4 1.0 CD A:ARG203 4.6 57.0 1.0 CB A:ASN143 4.6 57.4 1.0 CB A:ASN105 4.6 64.5 1.0 OD1 A:ASP139 4.7 55.7 1.0 CA A:THR108 4.7 50.0 1.0 CA A:ASN105 4.7 64.4 1.0 N A:PRO109 4.8 51.7 1.0 C A:THR108 4.9 50.1 1.0 C A:ASN105 4.9 64.7 1.0 N A:ASP139 4.9 58.8 1.0 CA A:ASP139 4.9 59.2 1.0

Calcium binding site 4 out of 11 in the Crystal Structure of Human Protocadherin-1 EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Protocadherin-1 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:53.0 occ:1.00 OD1 A:ASP182 1.9 58.7 1.0 OE2 A:GLU122 2.0 49.3 1.0 OE1 A:GLU184 2.2 54.3 1.0 O A:HOH611 2.3 47.2 1.0 OD2 A:ASP218 2.4 44.8 1.0 O A:HOH601 2.4 45.9 1.0 CG A:ASP182 3.0 58.9 1.0 CG A:ASP218 3.1 44.4 1.0 CD A:GLU122 3.2 48.1 1.0 OD1 A:ASP218 3.2 43.1 1.0 CD A:GLU184 3.4 53.8 1.0 OD2 A:ASP182 3.6 59.5 1.0 O A:HOH621 3.7 48.6 1.0 CG A:GLU122 4.1 48.1 1.0 CA A:CA506 4.1 45.8 1.0 OD1 A:ASN219 4.1 43.6 1.0 OE1 A:GLU122 4.1 45.6 1.0 CB A:ASP182 4.2 58.2 1.0 CB A:GLU184 4.2 57.1 1.0 N A:ARG183 4.2 51.9 1.0 OE2 A:GLU184 4.3 52.5 1.0 CG A:GLU184 4.3 55.6 1.0 CA A:ASP182 4.4 55.2 1.0 N A:GLU184 4.4 55.4 1.0 CB A:ASP218 4.5 44.2 1.0 C A:ASP182 4.7 54.6 1.0 OD1 A:ASN123 4.7 47.2 1.0 ND2 A:ASN123 4.9 44.2 1.0 CA A:GLU184 5.0 57.2 1.0

Calcium binding site 5 out of 11 in the Crystal Structure of Human Protocadherin-1 EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human Protocadherin-1 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:45.8 occ:1.00 OD1 A:ASP215 2.1 42.9 1.0 OD1 A:ASP251 2.3 43.0 1.0 OE2 A:GLU184 2.4 52.5 1.0 OD1 A:ASP218 2.4 43.1 1.0 O A:THR216 2.4 40.3 1.0 OE1 A:GLU122 2.7 45.6 1.0 OE1 A:GLU184 2.9 54.3 1.0 CD A:GLU184 3.0 53.8 1.0 OE2 A:GLU122 3.1 49.3 1.0 CG A:ASP215 3.2 43.0 1.0 CD A:GLU122 3.3 48.1 1.0 CG A:ASP251 3.4 41.1 1.0 CG A:ASP218 3.5 44.4 1.0 C A:THR216 3.6 42.1 1.0 OD2 A:ASP215 3.8 42.5 1.0 N A:THR216 3.8 43.6 1.0 CB A:ASP251 4.0 39.5 1.0 CA A:CA505 4.1 53.0 1.0 OD2 A:ASP218 4.1 44.8 1.0 N A:ASP218 4.1 41.2 1.0 CA A:ASP251 4.2 40.8 1.0 NE A:ARG183 4.3 51.7 1.0 OD1 A:ASN219 4.3 43.6 1.0 CA A:THR216 4.3 44.0 1.0 OD2 A:ASP251 4.3 40.2 1.0 CG A:GLU184 4.4 55.6 1.0 CB A:ASP215 4.4 43.5 1.0 CA A:ASP215 4.5 42.8 1.0 OG1 A:THR216 4.6 46.1 1.0 N A:ASN217 4.6 40.9 1.0 C A:ASP215 4.6 42.5 1.0 CB A:ASP218 4.6 44.2 1.0 CG A:GLU122 4.8 48.1 1.0 CB A:ARG183 4.8 50.6 1.0 CA A:ASN217 4.9 40.5 1.0 CA A:ASP218 4.9 43.1 1.0 NH2 A:ARG183 5.0 49.2 1.0 CD A:ARG183 5.0 51.2 1.0

Calcium binding site 6 out of 11 in the Crystal Structure of Human Protocadherin-1 EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Human Protocadherin-1 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:40.9 occ:1.00 O A:ASN219 2.3 39.2 1.0 O A:ASN255 2.3 40.6 1.0 OD2 A:ASP304 2.4 40.4 1.0 OD1 A:ASN217 2.4 43.2 1.0 OD2 A:ASP249 2.4 45.8 1.0 OD2 A:ASP251 2.4 40.2 1.0 OD1 A:ASP249 2.5 46.0 1.0 CG A:ASP249 2.8 46.4 1.0 CG A:ASP251 3.4 41.1 1.0 CG A:ASP304 3.4 43.4 1.0 C A:ASN219 3.4 40.4 1.0 C A:ASN255 3.5 41.3 1.0 CG A:ASN217 3.6 41.3 1.0 CB A:ASP251 3.7 39.5 1.0 CB A:ASP304 4.0 44.4 1.0 ND2 A:ASN217 4.3 41.7 1.0 CA A:ASN219 4.3 41.0 1.0 CB A:ASP249 4.3 46.4 1.0 CB A:ASN255 4.3 41.8 1.0 N A:ASN219 4.3 42.0 1.0 CA A:ASN255 4.3 41.9 1.0 CB A:ASN219 4.4 41.1 1.0 OD1 A:ASP304 4.4 45.2 1.0 N A:ALA256 4.4 43.1 1.0 N A:ALA220 4.4 41.4 1.0 CA A:ALA256 4.5 43.9 1.0 OD1 A:ASP251 4.6 43.0 1.0 CA A:ALA220 4.6 41.5 1.0 CA A:ASN217 4.7 40.5 1.0 CB A:ASN217 4.7 40.5 1.0 CD A:PRO221 4.8 43.0 1.0 N A:ASP251 4.9 42.1 1.0 C A:ASN217 4.9 40.4 1.0 C A:ALA220 4.9 41.1 1.0 CA A:ASP251 4.9 40.8 1.0

Calcium binding site 7 out of 11 in the Crystal Structure of Human Protocadherin-1 EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Human Protocadherin-1 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:66.8 occ:1.00 OE2 A:GLU234 2.2 48.3 1.0 O A:HOH603 2.2 34.1 1.0 OD1 A:ASP289 2.3 58.3 1.0 OE2 A:GLU291 2.3 52.3 1.0 OD2 A:ASP325 2.4 51.6 1.0 CG A:ASP325 3.0 51.2 1.0 OD1 A:ASP325 3.1 49.7 1.0 CG A:ASP289 3.3 58.4 1.0 CD A:GLU234 3.4 49.4 1.0 CD A:GLU291 3.5 54.1 1.0 ND2 A:ASN326 3.6 59.9 1.0 OD2 A:ASP289 3.9 62.6 1.0 CB A:GLU291 4.0 57.8 1.0 CA A:CA509 4.0 49.5 1.0 CG A:GLU291 4.1 56.2 1.0 OE1 A:GLU234 4.2 47.0 1.0 CG A:GLU234 4.4 49.2 1.0 CB A:ASP289 4.4 55.6 1.0 CB A:ASP325 4.4 51.3 1.0 N A:GLU291 4.4 54.5 1.0 OE1 A:GLU291 4.5 54.6 1.0 CA A:ASP289 4.6 52.8 1.0 N A:ARG290 4.7 50.6 1.0 CG A:ASN326 4.8 60.0 1.0 ND2 A:ASN235 4.9 49.8 1.0 CA A:GLU291 4.9 57.8 1.0 C A:ASP289 4.9 52.0 1.0 NH2 A:ARG365 4.9 69.1 1.0 OD1 A:ASN235 5.0 52.4 1.0

Calcium binding site 8 out of 11 in the Crystal Structure of Human Protocadherin-1 EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human Protocadherin-1 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca509 b:49.5 occ:1.00 OD1 A:ASP322 2.1 50.4 1.0 OD1 A:ASP366 2.2 51.6 1.0 O A:MET323 2.4 54.0 1.0 OD1 A:ASP325 2.4 49.7 1.0 OE2 A:GLU291 2.5 52.3 1.0 OE1 A:GLU234 2.6 47.0 1.0 OE1 A:GLU291 2.6 54.6 1.0 CD A:GLU291 2.9 54.1 1.0 OE2 A:GLU234 3.2 48.3 1.0 CD A:GLU234 3.3 49.4 1.0 CG A:ASP366 3.3 51.6 1.0 CG A:ASP322 3.3 53.0 1.0 CG A:ASP325 3.5 51.2 1.0 C A:MET323 3.6 53.3 1.0 N A:MET323 3.7 53.7 1.0 CB A:ASP366 3.9 53.3 1.0 OD2 A:ASP322 4.0 55.7 1.0 ND2 A:ASN326 4.0 59.9 1.0 CA A:CA508 4.0 66.8 1.0 OD2 A:ASP325 4.1 51.6 1.0 N A:ASP325 4.2 50.3 1.0 OD2 A:ASP366 4.2 50.3 1.0 CA A:ASP366 4.2 55.8 1.0 CA A:MET323 4.3 52.9 1.0 CG A:GLU291 4.3 56.2 1.0 NE A:ARG290 4.4 52.0 1.0 CA A:ASP322 4.5 52.0 1.0 CB A:ASP322 4.5 53.0 1.0 C A:ASP322 4.6 52.7 1.0 N A:ASN324 4.7 52.2 1.0 CG A:GLU234 4.7 49.2 1.0 CB A:ASP325 4.7 51.3 1.0 CB A:MET323 4.8 53.7 1.0 CB A:ARG290 4.8 50.5 1.0 CA A:ASN324 4.8 50.7 1.0 CA A:ASP325 4.9 51.6 1.0

Calcium binding site 9 out of 11 in the Crystal Structure of Human Protocadherin-1 EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Human Protocadherin-1 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca510 b:53.4 occ:1.00 OD1 A:ASN324 2.2 52.6 1.0 OD1 A:ASP364 2.2 58.6 1.0 O A:ASN370 2.3 55.4 1.0 O A:ASN326 2.3 56.1 1.0 OD1 A:ASP423 2.5 56.3 1.0 OD2 A:ASP366 2.5 50.3 1.0 CG A:ASP364 2.8 60.5 1.0 OD2 A:ASP364 2.8 60.9 1.0 CG A:ASP423 3.2 54.5 1.0 OD2 A:ASP423 3.3 55.5 1.0 CG A:ASN324 3.3 51.8 1.0 CG A:ASP366 3.5 51.6 1.0 C A:ASN326 3.5 57.5 1.0 C A:ASN370 3.5 57.9 1.0 CB A:ASP366 3.8 53.3 1.0 ND2 A:ASN324 3.9 52.3 1.0 CA A:ASN326 4.2 58.2 1.0 N A:ASN326 4.3 58.0 1.0 CB A:ASP364 4.3 62.1 1.0 CB A:ASN326 4.3 59.6 1.0 CA A:ASN370 4.4 58.2 1.0 N A:ALA371 4.4 58.2 1.0 CB A:ASN370 4.5 57.1 1.0 CD1 A:LEU429 4.5 53.6 1.0 CA A:ALA371 4.5 58.6 1.0 CB A:ASN324 4.5 51.2 1.0 CB A:ASP423 4.6 54.8 1.0 N A:ALA327 4.6 57.5 1.0 OD1 A:ASP366 4.6 51.6 1.0 CA A:ASN324 4.7 50.7 1.0 CA A:ALA327 4.8 58.0 1.0 N A:ASP366 4.8 57.8 1.0 C A:ALA327 4.9 58.5 1.0 CA A:ASP366 5.0 55.8 1.0 C A:ASN324 5.0 49.4 1.0

Calcium binding site 10 out of 11 in the Crystal Structure of Human Protocadherin-1 EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Human Protocadherin-1 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca511 b:0.8 occ:1.00 OE2 A:GLU349 2.2 0.5 1.0 OD1 A:ASP441 2.4 0.4 1.0 OD1 A:ASP408 2.6 0.4 1.0 CD A:GLU349 2.9 0.0 1.0 OE1 A:GLU349 3.0 0.5 1.0 O A:VAL442 3.0 0.3 1.0 CG A:ASP441 3.2 0.9 1.0 OD2 A:ASP441 3.5 0.0 1.0 CG A:ASP408 3.6 0.7 1.0 OD2 A:ASP408 3.9 0.4 1.0 CB A:TYR409 3.9 0.6 1.0 N A:TYR409 4.1 0.1 1.0 C A:VAL442 4.2 0.8 1.0 N A:VAL442 4.2 0.3 1.0 CG A:GLU349 4.4 0.0 1.0 CB A:ASP441 4.4 0.3 1.0 CA A:TYR409 4.5 0.1 1.0 CA A:ASP441 4.7 0.1 1.0 CB A:ASP408 4.8 0.8 1.0 CA A:VAL442 4.8 0.9 1.0 C A:ASP441 4.9 0.5 1.0 C A:TYR409 4.9 0.0 1.0

D.Modak, M.Sotomayor. Identification of An Adhesive Interface For the Non-Clustered Delta 1 Protocadherin-1 Involved in Respiratory Diseases. Commun Biol V. 2 354 2019.
ISSN: ESSN 2399-3642
PubMed: 31583286
DOI: 10.1038/S42003-019-0586-0