Calcium in PDB 5uk5: Complex of NOTCH1(EGF8-12) Bound to JAGGED1(N-EGF3)

The structure of Complex of NOTCH1(EGF8-12) Bound to JAGGED1(N-EGF3), PDB code: 5uk5 was solved by K.C.Garcia, V.C.Luca, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.74 / 2.51
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.457, 127.995, 154.288, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 26.3

The binding sites of Calcium atom in the Complex of NOTCH1(EGF8-12) Bound to JAGGED1(N-EGF3) (pdb code 5uk5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Complex of NOTCH1(EGF8-12) Bound to JAGGED1(N-EGF3), PDB code: 5uk5:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Complex of NOTCH1(EGF8-12) Bound to JAGGED1(N-EGF3)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of NOTCH1(EGF8-12) Bound to JAGGED1(N-EGF3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:88.6 occ:0.55 OD1 A:ASP338 2.2 0.6 1.0 O A:HOH701 2.2 69.8 1.0 OD2 A:ASP352 2.2 0.0 1.0 O A:ILE336 2.2 0.2 1.0 OD1 A:ASP352 2.3 0.9 1.0 OD1 A:ASN335 2.3 0.3 1.0 O A:ARG353 2.3 95.4 1.0 CG A:ASP352 2.5 0.4 1.0 CG A:ASN335 3.3 0.0 1.0 CG A:ASP338 3.4 0.9 1.0 C A:ILE336 3.4 0.4 1.0 C A:ARG353 3.4 93.2 1.0 N A:ASP338 3.9 0.1 1.0 ND2 A:ASN335 3.9 0.4 1.0 N A:ALA355 3.9 0.8 1.0 O A:HOH725 4.0 75.2 1.0 CB A:ASP352 4.0 0.9 1.0 N A:ARG353 4.0 95.3 1.0 N A:ILE336 4.1 0.3 1.0 CB A:ASP338 4.2 0.0 1.0 O A:SER356 4.2 99.3 1.0 OD2 A:ASP338 4.2 0.5 1.0 CB A:ASN335 4.3 0.4 1.0 CA A:VAL354 4.3 96.6 1.0 N A:VAL354 4.3 0.8 1.0 CA A:ILE336 4.3 0.6 1.0 CA A:ARG353 4.4 96.3 1.0 C A:ASN335 4.4 0.2 1.0 N A:ASP337 4.4 0.5 1.0 C A:ASP352 4.5 1.0 1.0 CA A:ASP337 4.5 0.2 1.0 CA A:ASP352 4.6 0.5 1.0 C A:VAL354 4.6 94.5 1.0 C A:ASP337 4.6 0.6 1.0 CA A:ASP338 4.7 0.0 1.0 CB A:ILE336 4.7 0.3 1.0 CA A:ASN335 4.7 0.1 1.0 CA A:ALA355 4.8 0.0 1.0 N A:SER356 4.8 97.3 1.0 O A:GLY326 4.8 86.5 1.0 O A:ASN335 4.9 0.0 1.0

Calcium binding site 2 out of 3 in the Complex of NOTCH1(EGF8-12) Bound to JAGGED1(N-EGF3)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of NOTCH1(EGF8-12) Bound to JAGGED1(N-EGF3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:68.4 occ:0.85 OD1 A:ASP412 2.0 0.5 1.0 O A:SER435 2.2 91.2 1.0 O A:VAL413 2.3 73.0 1.0 OE1 A:GLU415 2.3 80.0 1.0 O A:THR432 2.5 93.9 1.0 OD1 A:ASN431 2.6 86.4 1.0 N A:SER435 2.7 0.5 1.0 OD2 A:ASP412 2.7 0.8 1.0 CG A:ASP412 2.7 84.7 1.0 OE2 A:GLU415 3.0 77.6 1.0 CD A:GLU415 3.0 76.2 1.0 C A:SER435 3.1 81.7 1.0 CA A:SER435 3.4 94.3 1.0 C A:VAL413 3.5 89.3 1.0 C A:GLY434 3.5 97.3 1.0 N A:GLY434 3.6 96.9 1.0 C A:THR432 3.7 89.8 1.0 CG A:ASN431 3.7 92.2 1.0 CA A:GLY434 3.8 0.6 1.0 N A:VAL413 4.1 75.0 1.0 N A:THR432 4.1 79.8 1.0 ND2 A:ASN431 4.2 0.7 1.0 CB A:ASP412 4.2 88.6 1.0 N A:GLU415 4.3 61.0 1.0 CA A:VAL413 4.3 80.0 1.0 N A:PHE436 4.4 82.0 1.0 N A:ASP414 4.4 91.5 1.0 C A:LEU433 4.4 94.8 1.0 CA A:ASP414 4.5 67.5 1.0 CA A:THR432 4.5 83.6 1.0 CG A:GLU415 4.5 65.6 1.0 O A:GLY434 4.5 95.2 1.0 O A:GLY403 4.6 0.9 1.0 N A:LEU433 4.6 90.4 1.0 C A:ASP412 4.7 72.5 1.0 CA A:LEU433 4.7 92.6 1.0 CB A:SER435 4.8 0.8 1.0 CA A:ASP412 4.8 84.2 1.0 CB A:VAL413 4.9 84.1 1.0 C A:ASP414 5.0 62.1 1.0 CA A:PHE436 5.0 75.2 1.0 C A:ASN431 5.0 74.0 1.0

Calcium binding site 3 out of 3 in the Complex of NOTCH1(EGF8-12) Bound to JAGGED1(N-EGF3)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of NOTCH1(EGF8-12) Bound to JAGGED1(N-EGF3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:59.5 occ:0.95 O A:HOH705 2.1 53.4 1.0 OD1 A:ASP469 2.2 79.7 1.0 O A:HOH703 2.3 78.2 1.0 O A:VAL453 2.3 83.8 1.0 OD1 A:ASP452 2.4 96.6 1.0 OE1 A:GLU455 2.4 84.0 1.0 O A:GLN470 2.4 68.1 1.0 OE2 A:GLU455 3.1 94.0 1.0 CD A:GLU455 3.1 82.3 1.0 CG A:ASP452 3.1 81.2 1.0 OD2 A:ASP452 3.2 86.8 1.0 C A:GLN470 3.2 65.9 1.0 CG A:ASP469 3.3 77.7 1.0 C A:VAL453 3.6 76.6 1.0 N A:GLN470 3.8 54.4 1.0 OD2 A:ASP469 3.9 84.8 1.0 N A:ILE471 4.1 60.6 1.0 CA A:GLN470 4.1 57.2 1.0 C A:ASP469 4.2 62.9 1.0 CA A:ILE471 4.2 68.0 1.0 N A:GLY472 4.2 83.8 1.0 N A:VAL453 4.3 78.5 1.0 N A:GLU455 4.4 74.0 1.0 CA A:VAL453 4.5 80.6 1.0 CB A:ASP452 4.5 71.6 1.0 N A:ASN454 4.5 74.0 1.0 C A:ASP452 4.5 70.5 1.0 CG A:GLU455 4.5 87.4 1.0 CB A:ASP469 4.5 75.6 1.0 CA A:ASN454 4.6 81.7 1.0 O A:ASP469 4.6 78.3 1.0 O A:GLY443 4.6 70.9 1.0 CA A:ASP469 4.6 64.2 1.0 C A:ILE471 4.7 76.9 1.0 O A:GLU473 4.7 89.3 1.0 CB A:VAL453 4.9 84.2 1.0 O A:ASP452 4.9 66.0 1.0 CA A:ASP452 4.9 66.3 1.0

V.C.Luca, B.C.Kim, C.Ge, S.Kakuda, D.Wu, M.Roein-Peikar, R.S.Haltiwanger, C.Zhu, T.Ha, K.C.Garcia. Notch-Jagged Complex Structure Implicates A Catch Bond in Tuning Ligand Sensitivity. Science V. 355 1320 2017.
ISSN: ESSN 1095-9203
PubMed: 28254785
DOI: 10.1126/SCIENCE.AAF9739