Calcium in PDB 6mga: Crystal Structure of Human Protocadherin-1 EC1-4 with Glycosylation

The structure of Crystal Structure of Human Protocadherin-1 EC1-4 with Glycosylation, PDB code: 6mga 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)	48.53 / 3.15
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	147.227, 147.227, 149.366, 90.00, 90.00, 120.00
R / Rfree (%)	21.5 / 26.3

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

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


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 with Glycosylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:0.0 occ:1.00 OD1 A:ASP59 1.8 0.3 1.0 OD2 A:ASP106 2.2 0.9 1.0 OE1 A:GLU61 2.3 0.4 1.0 OE1 A:GLU9 2.7 0.1 1.0 OE1 A:GLU10 2.7 0.3 1.0 CG A:ASP59 2.9 0.8 1.0 CG A:ASP106 3.0 0.1 1.0 OD1 A:ASP106 3.1 0.2 1.0 OD2 A:ASP59 3.4 0.4 1.0 CD A:GLU10 3.4 0.2 1.0 CD A:GLU61 3.5 0.8 1.0 CD A:GLU9 3.5 0.3 1.0 OE2 A:GLU9 3.7 0.1 1.0 OE2 A:GLU10 4.0 0.5 1.0 ND2 A:ASN107 4.0 0.4 1.0 CB A:ASP59 4.2 0.7 1.0 CG A:GLU10 4.3 0.8 1.0 CB A:GLU61 4.3 0.9 1.0 CG A:GLU61 4.3 0.9 1.0 CA A:CA504 4.4 0.9 1.0 OE2 A:GLU61 4.4 0.5 1.0 CB A:ASP106 4.4 0.2 1.0 CA A:ASP59 4.4 0.1 1.0 N A:GLU61 4.6 0.7 1.0 N A:ARG60 4.7 0.5 1.0 C A:ASP59 4.9 0.7 1.0 CG A:GLU9 4.9 0.2 1.0

Calcium binding site 2 out of 9 in the Crystal Structure of Human Protocadherin-1 EC1-4 with Glycosylation


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 with Glycosylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:0.9 occ:1.00 OD1 A:ASP103 2.2 0.8 1.0 OE2 A:GLU9 2.3 0.1 1.0 O A:ILE104 2.4 0.4 1.0 OD1 A:ASP106 2.4 0.2 1.0 OE2 A:GLU61 2.4 0.5 1.0 OD1 A:ASP139 2.5 0.3 1.0 OE1 A:GLU61 2.9 0.4 1.0 CD A:GLU61 3.0 0.8 1.0 CG A:ASP103 3.4 0.6 1.0 CD A:GLU9 3.5 0.3 1.0 CG A:ASP139 3.5 0.8 1.0 C A:ILE104 3.5 0.7 1.0 CG A:ASP106 3.6 0.1 1.0 N A:ILE104 3.7 0.7 1.0 ND2 A:ASN107 3.9 0.4 1.0 OD2 A:ASP103 4.1 0.6 1.0 N A:ASP106 4.1 0.2 1.0 CB A:ASP139 4.1 0.1 1.0 OE1 A:GLU9 4.1 0.1 1.0 NH1 A:ARG60 4.1 0.1 1.0 CA A:ILE104 4.2 0.1 1.0 CA A:ASP139 4.3 0.1 1.0 CA A:CA503 4.4 0.0 1.0 CG A:GLU61 4.4 0.9 1.0 OD2 A:ASP106 4.4 0.9 1.0 CB A:ASP103 4.4 0.4 1.0 OD2 A:ASP139 4.5 0.4 1.0 CA A:ASP103 4.5 0.3 1.0 C A:ASP103 4.6 0.5 1.0 N A:ASN105 4.6 0.2 1.0 CG1 A:ILE104 4.6 0.3 1.0 CB A:ASP106 4.6 0.2 1.0 CG A:GLU9 4.6 0.2 1.0 CA A:ASP106 4.8 0.1 1.0 CA A:ASN105 4.9 0.8 1.0 CD A:ARG60 4.9 0.5 1.0

Calcium binding site 3 out of 9 in the Crystal Structure of Human Protocadherin-1 EC1-4 with Glycosylation


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 with Glycosylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:0.7 occ:1.00 O A:ASN107 2.2 0.7 1.0 O A:ASN143 2.2 0.4 1.0 OD2 A:ASP139 2.2 0.4 1.0 OD2 A:ASP137 2.3 0.5 1.0 OD2 A:ASP197 2.3 0.7 1.0 OD1 A:ASN105 2.3 0.8 1.0 OD1 A:ASP137 2.9 0.4 1.0 CG A:ASP137 3.0 0.0 1.0 CG A:ASP197 3.3 0.5 1.0 CG A:ASP139 3.3 0.8 1.0 C A:ASN107 3.4 0.9 1.0 C A:ASN143 3.5 0.4 1.0 CG A:ASN105 3.5 0.6 1.0 CB A:ASP197 3.7 0.2 1.0 CB A:ASP139 3.8 0.1 1.0 ND2 A:ASN105 4.3 0.0 1.0 OD1 A:ASP197 4.3 0.4 1.0 CA A:ASN107 4.4 0.6 1.0 N A:THR108 4.4 0.1 1.0 N A:GLY144 4.4 0.4 1.0 N A:ASN107 4.4 0.6 1.0 CD A:PRO109 4.4 1.0 1.0 CA A:ASN143 4.4 0.3 1.0 CA A:GLY144 4.4 0.8 1.0 OD1 A:ASP139 4.4 0.3 1.0 CB A:ASP137 4.5 0.0 1.0 CB A:ASN143 4.5 0.7 1.0 CA A:THR108 4.6 0.2 1.0 CB A:ASN107 4.6 0.5 1.0 CA A:ASN105 4.6 0.8 1.0 CB A:ASN105 4.7 0.1 1.0 CD A:ARG203 4.7 0.3 1.0 N A:PRO109 4.7 0.6 1.0 C A:THR108 4.8 0.9 1.0 C A:ASN105 4.9 0.4 1.0

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


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 with Glycosylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:0.8 occ:1.00 OD1 A:ASP182 1.9 0.1 1.0 OE1 A:GLU184 2.0 0.5 1.0 OD2 A:ASP218 2.0 0.6 1.0 OE2 A:GLU122 2.1 0.0 1.0 CG A:ASP182 3.0 0.6 1.0 CG A:ASP218 3.1 0.9 1.0 CD A:GLU184 3.1 0.1 1.0 CD A:GLU122 3.3 0.1 1.0 OD2 A:ASP182 3.5 0.6 1.0 OD1 A:ASP218 3.6 0.1 1.0 OE2 A:GLU184 3.7 0.1 1.0 OE1 A:GLU122 4.0 0.1 1.0 OD1 A:ASN219 4.1 0.7 1.0 CB A:ASP182 4.2 0.6 1.0 CG A:GLU184 4.3 0.3 1.0 CG A:GLU122 4.3 0.1 1.0 CB A:ASP218 4.3 0.2 1.0 CA A:CA507 4.4 0.5 1.0 N A:ARG183 4.4 0.7 1.0 CA A:ASP182 4.4 0.1 1.0 CB A:GLU184 4.4 0.1 1.0 OD1 A:ASN123 4.7 0.4 1.0 N A:GLU184 4.7 0.1 1.0 ND2 A:ASN123 4.8 0.4 1.0 C A:ASP182 4.8 0.0 1.0

Calcium binding site 5 out of 9 in the Crystal Structure of Human Protocadherin-1 EC1-4 with Glycosylation


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 with Glycosylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:0.5 occ:1.00 OE2 A:GLU184 1.9 0.1 1.0 OD1 A:ASP215 2.0 0.9 1.0 OD1 A:ASP218 2.2 0.1 1.0 O A:THR216 2.3 0.2 1.0 OE1 A:GLU122 2.4 0.1 1.0 OD1 A:ASP251 2.5 0.5 1.0 CD A:GLU184 3.0 0.1 1.0 CG A:ASP215 3.1 0.8 1.0 CD A:GLU122 3.3 0.1 1.0 CG A:ASP218 3.3 0.9 1.0 CG A:ASP251 3.4 0.3 1.0 OE2 A:GLU122 3.5 0.0 1.0 OE1 A:GLU184 3.5 0.5 1.0 C A:THR216 3.5 0.4 1.0 OD2 A:ASP215 3.7 0.6 1.0 N A:THR216 3.8 0.8 1.0 OD2 A:ASP218 3.8 0.6 1.0 CB A:ASP251 3.8 0.7 1.0 CA A:ASP251 4.0 0.1 1.0 N A:ASP218 4.1 99.5 1.0 NE A:ARG183 4.2 0.4 1.0 CB A:ASP215 4.2 0.7 1.0 NH2 A:ARG183 4.3 0.7 1.0 CA A:THR216 4.3 0.1 1.0 CG A:GLU184 4.3 0.3 1.0 CA A:CA506 4.4 0.8 1.0 CA A:ASP215 4.4 0.7 1.0 OD1 A:ASN219 4.4 0.7 1.0 OD2 A:ASP251 4.5 0.8 1.0 C A:ASP215 4.5 0.5 1.0 CB A:ASP218 4.6 0.2 1.0 N A:ASN217 4.6 0.1 1.0 CG A:GLU122 4.7 0.1 1.0 CZ A:ARG183 4.7 0.7 1.0 CA A:ASN217 4.8 99.0 1.0 CA A:ASP218 4.9 0.5 1.0 N A:ASP251 4.9 0.3 1.0 CB A:ARG183 4.9 0.6 1.0 OG1 A:THR216 4.9 0.2 1.0

Calcium binding site 6 out of 9 in the Crystal Structure of Human Protocadherin-1 EC1-4 with Glycosylation


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 with Glycosylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:0.6 occ:1.00 O A:ASN219 2.1 0.4 1.0 O A:ASN255 2.3 0.3 1.0 OD2 A:ASP251 2.3 0.8 1.0 OD2 A:ASP249 2.3 0.1 1.0 OD2 A:ASP304 2.3 0.3 1.0 OD1 A:ASN217 2.4 0.4 1.0 OD1 A:ASP249 2.5 0.7 1.0 CG A:ASP249 2.7 0.9 1.0 CG A:ASP304 3.3 0.5 1.0 C A:ASN219 3.3 0.8 1.0 CG A:ASP251 3.4 0.3 1.0 C A:ASN255 3.5 0.9 1.0 CG A:ASN217 3.6 0.8 1.0 CB A:ASP304 3.8 1.0 1.0 CB A:ASP251 4.0 0.7 1.0 CB A:ASP249 4.2 0.4 1.0 ND2 A:ASN217 4.2 0.8 1.0 CA A:ASN219 4.2 0.9 1.0 CB A:ASN219 4.3 0.1 1.0 N A:ALA220 4.3 0.3 1.0 OD1 A:ASP304 4.3 0.2 1.0 N A:ASN219 4.3 0.8 1.0 CA A:ASN255 4.4 0.1 1.0 CA A:ALA220 4.4 99.4 1.0 CB A:ASN255 4.5 0.6 1.0 OD1 A:ASP251 4.5 0.5 1.0 N A:ALA256 4.5 0.3 1.0 CA A:ALA256 4.6 0.9 1.0 C A:ALA220 4.6 0.2 1.0 CB A:ASN217 4.8 98.6 1.0 CD A:PRO221 4.8 0.4 1.0 CA A:ASN217 4.9 99.0 1.0 N A:PRO221 4.9 0.9 1.0 CB A:LYS310 4.9 0.2 1.0 N A:ASP251 5.0 0.3 1.0

Calcium binding site 7 out of 9 in the Crystal Structure of Human Protocadherin-1 EC1-4 with Glycosylation


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 with Glycosylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca509 b:0.9 occ:1.00 OE2 A:GLU234 2.0 0.5 1.0 OD1 A:ASP289 2.2 0.3 1.0 OD2 A:ASP325 2.3 0.7 1.0 OE2 A:GLU291 2.6 0.7 1.0 CG A:ASP289 3.1 0.6 1.0 CG A:ASP325 3.1 0.9 1.0 CD A:GLU234 3.2 0.7 1.0 OD1 A:ASP325 3.3 0.9 1.0 CB A:ASP289 3.8 0.5 1.0 OD2 A:ASP289 3.9 0.9 1.0 CD A:GLU291 3.9 0.3 1.0 CA A:ASP289 4.0 0.7 1.0 ND2 A:ASN326 4.0 0.7 1.0 CG A:GLU234 4.0 0.3 1.0 ND2 A:ASN235 4.1 0.8 1.0 OE1 A:GLU234 4.1 0.6 1.0 OD1 A:ASN235 4.2 0.7 1.0 CA A:CA510 4.3 0.6 1.0 N A:ARG290 4.5 0.1 1.0 CB A:ASP325 4.5 0.4 1.0 C A:ASP289 4.5 0.1 1.0 N A:GLU291 4.6 0.8 1.0 CB A:GLU291 4.6 0.6 1.0 CG A:ASN235 4.6 0.2 1.0 CG A:GLU291 4.7 0.4 1.0 OE1 A:GLU291 4.7 0.8 1.0

Calcium binding site 8 out of 9 in the Crystal Structure of Human Protocadherin-1 EC1-4 with Glycosylation


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 with Glycosylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca510 b:0.6 occ:1.00 OD1 A:ASP322 2.1 0.8 1.0 O A:MET323 2.2 0.7 1.0 OD1 A:ASP366 2.3 0.4 1.0 OD1 A:ASP325 2.3 0.9 1.0 OE1 A:GLU234 2.6 0.6 1.0 OE1 A:GLU291 2.7 0.8 1.0 OE2 A:GLU291 2.9 0.7 1.0 CD A:GLU291 3.1 0.3 1.0 CG A:ASP366 3.2 0.6 1.0 CD A:GLU234 3.3 0.7 1.0 OE2 A:GLU234 3.3 0.5 1.0 CG A:ASP322 3.3 0.2 1.0 C A:MET323 3.3 0.7 1.0 N A:MET323 3.5 0.1 1.0 CG A:ASP325 3.5 0.9 1.0 CB A:ASP366 3.9 0.4 1.0 CA A:MET323 4.0 0.8 1.0 OD2 A:ASP366 4.0 0.1 1.0 OD2 A:ASP322 4.0 0.3 1.0 N A:ASP325 4.0 0.0 1.0 ND2 A:ASN326 4.1 0.7 1.0 OD2 A:ASP325 4.2 0.7 1.0 CA A:CA509 4.3 0.9 1.0 CA A:ASP366 4.3 0.8 1.0 CB A:MET323 4.4 0.4 1.0 N A:ASN324 4.5 0.0 1.0 CB A:ASP322 4.5 0.9 1.0 C A:ASP322 4.5 0.2 1.0 CA A:ASP322 4.5 0.3 1.0 CG A:GLU291 4.6 0.4 1.0 CB A:ASP325 4.6 0.4 1.0 CA A:ASN324 4.7 0.9 1.0 CG A:GLU234 4.8 0.3 1.0 CA A:ASP325 4.8 0.1 1.0 NE A:ARG290 4.8 0.6 1.0 C A:ASN324 4.9 0.0 1.0

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


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 with Glycosylation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca511 b:0.1 occ:1.00 O A:ASN326 2.1 0.9 1.0 OD2 A:ASP364 2.3 0.7 1.0 OD1 A:ASN324 2.3 0.3 1.0 O A:ASN370 2.4 0.7 1.0 OD2 A:ASP423 2.5 0.1 1.0 OD1 A:ASP364 2.7 0.1 1.0 OD2 A:ASP366 2.7 0.1 1.0 CG A:ASP364 2.8 0.7 1.0 C A:ASN326 3.3 0.6 1.0 CG A:ASP423 3.5 0.1 1.0 CG A:ASN324 3.5 0.4 1.0 C A:ASN370 3.6 0.4 1.0 CG A:ASP366 3.7 0.6 1.0 CB A:ASP423 3.9 0.7 1.0 CB A:ASP366 4.0 0.4 1.0 ND2 A:ASN324 4.1 0.7 1.0 CA A:ASN326 4.1 0.8 1.0 N A:ASN326 4.2 0.7 1.0 CB A:ASP364 4.3 0.6 1.0 N A:ALA327 4.4 0.6 1.0 CD1 A:LEU429 4.4 0.6 1.0 CB A:ASN370 4.4 0.6 1.0 CB A:ASN326 4.4 0.8 1.0 OD1 A:ASP423 4.5 0.7 1.0 N A:ALA371 4.5 0.7 1.0 CA A:ALA371 4.5 0.7 1.0 CA A:ASN370 4.5 0.6 1.0 CA A:ALA327 4.6 0.9 1.0 CB A:ASN324 4.6 0.9 1.0 CD A:PRO328 4.7 0.8 1.0 CA A:ASN324 4.7 0.9 1.0 OD1 A:ASP366 4.7 0.4 1.0 N A:ASP366 4.8 0.1 1.0 N A:PRO328 5.0 0.7 1.0 C A:ALA327 5.0 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