Calcium in PDB 6pim: Crystal Structure of Human Protocadherin-1 EC3-4

The structure of Crystal Structure of Human Protocadherin-1 EC3-4, PDB code: 6pim 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)	44.43 / 3.05
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	125.569, 125.569, 45.294, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 26.6

The binding sites of Calcium atom in the Crystal Structure of Human Protocadherin-1 EC3-4 (pdb code 6pim). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Protocadherin-1 EC3-4, PDB code: 6pim:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human Protocadherin-1 EC3-4


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 EC3-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:47.8 occ:1.00 OE1 A:GLU291 1.9 52.1 1.0 OD1 A:ASP322 2.0 54.0 1.0 OE1 A:GLU234 2.2 57.5 1.0 OD1 A:ASP366 2.3 52.0 1.0 O A:MET323 2.3 56.9 1.0 OD1 A:ASP325 2.5 54.0 1.0 CD A:GLU291 2.7 54.2 1.0 OE2 A:GLU291 2.8 54.2 1.0 CG A:ASP322 3.2 58.2 1.0 CD A:GLU234 3.3 53.9 1.0 CG A:ASP325 3.4 53.6 1.0 CG A:ASP366 3.4 50.3 1.0 C A:MET323 3.5 57.8 1.0 N A:MET323 3.5 56.4 1.0 OD2 A:ASP325 3.7 55.3 1.0 OE2 A:GLU234 3.7 52.2 1.0 OD2 A:ASP322 3.8 57.2 1.0 CA A:CA503 3.9 60.9 1.0 CB A:ASP366 4.0 51.5 1.0 CA A:MET323 4.1 57.6 1.0 CG A:GLU291 4.1 52.7 1.0 CA A:ASP366 4.2 54.1 1.0 N A:ASP325 4.2 58.4 1.0 CA A:ASP322 4.3 56.2 1.0 CB A:ASP322 4.3 58.4 1.0 ND2 A:ASN326 4.3 54.2 1.0 C A:ASP322 4.4 56.9 1.0 OD2 A:ASP366 4.4 48.3 1.0 CG A:GLU234 4.5 54.4 1.0 NE A:ARG290 4.6 61.8 1.0 N A:ASN324 4.6 59.7 1.0 CB A:ASP325 4.6 54.8 1.0 CB A:MET323 4.7 56.9 1.0 CB A:ARG290 4.9 54.0 1.0 CA A:ASN324 4.9 61.5 1.0 CA A:ASP325 4.9 57.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human Protocadherin-1 EC3-4


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 EC3-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:48.7 occ:1.00 OD2 A:ASP364 2.2 58.3 1.0 OD1 A:ASP423 2.3 58.0 1.0 O A:ASN326 2.3 47.1 1.0 O A:ASN370 2.4 50.0 1.0 OD2 A:ASP366 2.4 48.3 1.0 OD1 A:ASN324 2.5 64.0 1.0 OD1 A:ASP364 2.7 61.8 1.0 CG A:ASP364 2.8 58.0 1.0 CG A:ASP423 3.0 58.0 1.0 OD2 A:ASP423 3.2 57.8 1.0 CG A:ASP366 3.5 50.3 1.0 C A:ASN326 3.5 49.9 1.0 CG A:ASN324 3.6 66.6 1.0 C A:ASN370 3.6 53.5 1.0 CB A:ASP366 3.8 51.5 1.0 ND2 A:ASN324 4.1 72.2 1.0 CB A:ASP423 4.2 58.4 1.0 CA A:ASN326 4.3 49.2 1.0 CB A:ASP364 4.3 56.6 1.0 N A:ASN326 4.3 50.2 1.0 CB A:ASN326 4.4 49.7 1.0 CA A:ASN370 4.4 57.3 1.0 CB A:ASN370 4.4 58.3 1.0 N A:ALA371 4.5 55.3 1.0 N A:ALA327 4.5 52.1 1.0 OD1 A:ASP366 4.6 52.0 1.0 CD1 A:LEU429 4.6 59.2 1.0 CD A:PRO328 4.7 53.7 1.0 CA A:ALA371 4.7 55.6 1.0 CA A:ASN324 4.7 61.5 1.0 CB A:ASN324 4.8 64.8 1.0 CA A:ALA327 4.8 53.2 1.0 N A:PRO328 4.8 52.2 1.0 C A:ASN324 5.0 60.6 1.0 C A:ALA327 5.0 53.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human Protocadherin-1 EC3-4


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 EC3-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:60.9 occ:1.00 OD2 A:ASP325 2.0 55.3 1.0 OD1 A:ASP289 2.2 54.0 1.0 OE2 A:GLU234 2.5 52.2 1.0 OE1 A:GLU291 2.7 52.1 1.0 CG A:ASP325 2.9 53.6 1.0 CG A:ASP289 3.2 50.2 1.0 OD1 A:ASP325 3.2 54.0 1.0 CD A:GLU234 3.3 53.9 1.0 OE1 A:GLU234 3.6 57.5 1.0 CD A:GLU291 3.6 54.2 1.0 CB A:GLU291 3.8 50.9 1.0 OD2 A:ASP289 3.8 52.9 1.0 CA A:CA501 3.9 47.8 1.0 ND2 A:ASN326 3.9 54.2 1.0 CG A:GLU291 4.0 52.7 1.0 N A:GLU291 4.1 48.2 1.0 CB A:ASP289 4.2 48.2 1.0 CB A:ASP325 4.2 54.8 1.0 CA A:ASP289 4.3 47.9 1.0 N A:ARG290 4.3 51.8 1.0 C A:ASP289 4.6 49.3 1.0 CA A:GLU291 4.6 50.9 1.0 OD1 A:ASN235 4.7 61.7 1.0 CG A:GLU234 4.7 54.4 1.0 OE2 A:GLU291 4.7 54.2 1.0 ND2 A:ASN235 4.7 58.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human Protocadherin-1 EC3-4


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 EC3-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:83.4 occ:1.00 OD2 A:ASP304 2.2 67.6 1.0 OD2 A:ASP249 2.4 78.7 1.0 OD1 A:ASN217 2.4 72.2 1.0 O A:ASN255 2.4 68.3 1.0 OD1 A:ASP249 2.5 85.5 1.0 O A:ASN219 2.5 77.7 1.0 CG A:ASP249 2.7 81.2 1.0 OD2 A:ASP251 2.7 86.9 1.0 CG A:ASP304 3.4 68.1 1.0 CG A:ASP251 3.4 86.9 1.0 CG A:ASN217 3.5 73.7 1.0 C A:ASN219 3.6 80.9 1.0 C A:ASN255 3.7 68.0 1.0 CB A:ASP251 3.8 84.2 1.0 ND2 A:ASN217 4.0 72.3 1.0 N A:ASN219 4.1 80.4 1.0 CA A:ASN219 4.1 81.9 1.0 CB A:ASP249 4.2 78.7 1.0 CB A:ASP304 4.2 68.3 1.0 CB A:ASN219 4.2 81.3 1.0 OD1 A:ASP304 4.3 67.4 1.0 OD1 A:ASP251 4.3 89.2 1.0 CA A:ASN255 4.5 70.7 1.0 CB A:ASN255 4.5 74.8 1.0 N A:ALA256 4.6 65.6 1.0 N A:ALA220 4.6 82.4 1.0 C A:ALA220 4.7 76.8 1.0 CA A:ALA256 4.8 65.7 1.0 CB A:ASN217 4.8 76.2 1.0 O A:ALA220 4.8 79.0 1.0 CD A:PRO221 4.9 72.3 1.0 N A:PRO221 4.9 72.9 1.0 CA A:ALA220 4.9 78.6 1.0 N A:ASP218 4.9 81.5 1.0 C A:ASN217 5.0 80.2 1.0 CA A:ASN217 5.0 78.3 1.0 CG A:LYS310 5.0 80.0 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