Calcium in PDB 4cud: Human NOTCH1 Egf Domains 11-13 Mutant Fucosylated at T466

The structure of Human NOTCH1 Egf Domains 11-13 Mutant Fucosylated at T466, PDB code: 4cud was solved by P.Taylor, H.Takeuchi, D.Sheppard, C.Chillakuri, S.Lea, R.Haltiwanger, P.Handford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.14 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	28.290, 28.290, 282.732, 90.00, 90.00, 120.00
R / Rfree (%)	22.406 / 25.992

The binding sites of Calcium atom in the Human NOTCH1 Egf Domains 11-13 Mutant Fucosylated at T466 (pdb code 4cud). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Human NOTCH1 Egf Domains 11-13 Mutant Fucosylated at T466, PDB code: 4cud:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Human NOTCH1 Egf Domains 11-13 Mutant Fucosylated at T466


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human NOTCH1 Egf Domains 11-13 Mutant Fucosylated at T466 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1531 b:19.0 occ:1.00 O A:VAL453 2.3 19.1 1.0 O A:GLN470 2.4 17.2 1.0 OE1 A:GLU455 2.4 18.7 1.0 OD1 A:ASP452 2.4 20.8 1.0 O A:HOH2012 2.4 17.6 1.0 OD1 A:ASP469 2.4 19.1 1.0 O A:HOH2015 2.5 19.4 1.0 C A:GLN470 3.4 17.3 1.0 CD A:GLU455 3.4 18.7 1.0 CG A:ASP452 3.4 20.7 1.0 CG A:ASP469 3.5 19.1 1.0 C A:VAL453 3.5 20.0 1.0 OE2 A:GLU455 3.7 18.6 1.0 OD2 A:ASP452 3.8 20.9 1.0 OD2 A:ASP469 3.9 18.1 1.0 N A:GLN470 3.9 17.8 1.0 C A:ASP469 4.2 18.4 1.0 CA A:GLN470 4.2 17.6 1.0 N A:ILE471 4.3 16.9 1.0 N A:GLU455 4.3 18.6 1.0 N A:VAL453 4.3 19.7 1.0 CA A:ILE471 4.4 17.6 1.0 C A:ASP452 4.4 20.0 1.0 N A:ASN454 4.4 20.5 1.0 N A:GLY472 4.4 18.2 1.0 CA A:ASN454 4.4 19.8 1.0 CA A:VAL453 4.4 20.0 1.0 O A:ASP469 4.5 18.4 1.0 O A:ASP452 4.6 19.0 1.0 CB A:ASP469 4.7 18.8 1.0 O A:GLU473 4.7 19.8 1.0 CB A:ASP452 4.8 20.3 1.0 O A:GLY443 4.8 19.7 1.0 CG A:GLU455 4.8 19.0 1.0 CA A:ASP469 4.8 18.7 1.0 CB A:VAL453 4.9 19.4 1.0 C A:ILE471 4.9 17.8 1.0 C A:ASN454 4.9 19.5 1.0 CA A:ASP452 5.0 20.5 1.0

Calcium binding site 2 out of 4 in the Human NOTCH1 Egf Domains 11-13 Mutant Fucosylated at T466


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human NOTCH1 Egf Domains 11-13 Mutant Fucosylated at T466 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1532 b:17.4 occ:1.00 O A:THR491 2.2 17.3 1.0 O A:LYS508 2.3 18.8 1.0 OD1 A:ASN490 2.3 18.2 1.0 OE1 A:GLU493 2.3 17.1 1.0 O A:HOH2032 2.4 18.4 1.0 OD2 A:ASP507 2.5 20.4 1.0 OD1 A:ASP507 2.6 19.5 1.0 CG A:ASP507 2.9 20.1 1.0 CD A:GLU493 3.4 17.9 1.0 C A:THR491 3.4 17.4 1.0 C A:LYS508 3.5 19.1 1.0 CG A:ASN490 3.5 18.1 1.0 OE2 A:GLU493 3.7 17.9 1.0 N A:LYS508 4.1 19.9 1.0 N A:GLU493 4.1 18.6 1.0 O A:HOH2037 4.2 24.9 1.0 ND2 A:ASN490 4.2 18.2 1.0 N A:THR491 4.2 17.1 1.0 C A:ASN490 4.3 16.8 1.0 N A:ASN510 4.3 18.5 1.0 N A:ASP492 4.3 17.8 1.0 CA A:ASP492 4.3 18.4 1.0 CB A:ASP507 4.3 20.9 1.0 CA A:ILE509 4.3 19.1 1.0 CA A:THR491 4.3 16.8 1.0 N A:ILE509 4.4 19.1 1.0 O A:ASN490 4.4 17.0 1.0 CA A:LYS508 4.4 20.6 1.0 O A:GLU511 4.5 19.2 1.0 O A:HOH2049 4.6 26.1 1.0 CG A:GLU493 4.7 17.9 1.0 C A:ASP507 4.7 20.8 1.0 CB A:ASN490 4.7 17.4 1.0 O A:GLY481 4.7 19.6 1.0 C A:ASP492 4.8 18.8 1.0 C A:ILE509 4.8 18.4 1.0 CB A:THR491 4.8 16.1 1.0 CB A:GLU493 4.8 18.2 1.0 CA A:ASP507 4.9 20.8 1.0 CA A:ASN490 4.9 17.1 1.0

Calcium binding site 3 out of 4 in the Human NOTCH1 Egf Domains 11-13 Mutant Fucosylated at T466


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human NOTCH1 Egf Domains 11-13 Mutant Fucosylated at T466 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1533 b:23.8 occ:1.00 OD1 A:ASN431 2.3 21.4 1.0 O A:THR432 2.4 21.7 1.0 O A:SER435 2.4 20.4 1.0 OE1 A:GLU415 2.4 21.8 1.0 O A:HOH2004 2.5 27.4 1.0 O A:VAL413 2.5 25.4 1.0 OD1 A:ASP412 2.6 31.8 1.0 OD2 A:ASP412 3.1 30.7 1.0 CG A:ASP412 3.2 31.9 1.0 CD A:GLU415 3.4 22.7 1.0 CG A:ASN431 3.4 22.3 1.0 C A:SER435 3.5 20.3 1.0 C A:THR432 3.6 22.6 1.0 C A:VAL413 3.6 26.9 1.0 OE2 A:GLU415 3.6 23.4 1.0 N A:SER435 3.7 21.1 1.0 N A:GLY434 3.9 24.2 1.0 ND2 A:ASN431 3.9 22.8 1.0 N A:THR432 4.0 21.7 1.0 CA A:SER435 4.1 20.6 1.0 N A:GLU415 4.3 21.9 1.0 CA A:ASP414 4.3 23.9 1.0 C A:GLY434 4.3 22.7 1.0 N A:ASP414 4.4 24.2 1.0 CA A:THR432 4.4 22.1 1.0 N A:VAL413 4.5 30.3 1.0 O A:HOH2005 4.6 26.2 1.0 N A:LEU433 4.6 23.6 1.0 CA A:GLY434 4.6 23.2 1.0 N A:PHE436 4.6 19.8 1.0 CA A:LEU433 4.6 24.5 1.0 CA A:VAL413 4.7 27.8 1.0 C A:LEU433 4.7 24.2 1.0 CB A:ASN431 4.7 22.4 1.0 CB A:ASP412 4.7 32.7 1.0 CG A:GLU415 4.8 22.3 1.0 OG1 A:THR432 4.8 21.9 1.0 C A:ASN431 4.8 21.8 1.0 C A:ASP414 4.9 23.0 1.0 CA A:ASN431 4.9 21.9 1.0 CB A:PHE436 5.0 19.0 1.0

Calcium binding site 4 out of 4 in the Human NOTCH1 Egf Domains 11-13 Mutant Fucosylated at T466


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human NOTCH1 Egf Domains 11-13 Mutant Fucosylated at T466 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1534 b:30.4 occ:0.50 OE2 A:GLU511 2.4 22.2 1.0 NE2 A:HIS523 2.7 25.1 1.0 CD A:GLU511 3.1 22.5 1.0 OE1 A:GLU511 3.2 24.1 1.0 CE1 A:HIS523 3.5 26.2 1.0 CD2 A:HIS523 3.6 25.3 1.0 CE2 A:PHE512 4.0 19.8 1.0 CZ A:PHE512 4.3 19.7 1.0 CD2 A:PHE512 4.5 19.6 1.0 CG A:GLU511 4.6 21.7 1.0 ND1 A:HIS523 4.6 25.5 1.0 O A:PHE512 4.6 18.7 1.0 CG A:HIS523 4.7 25.3 1.0 N A:PHE512 5.0 19.3 1.0 CE1 A:PHE512 5.0 19.6 1.0

P.Taylor, H.Takeuchi, D.Sheppard, C.Chillakuri, S.M.Lea, R.S.Haltiwanger, P.A.Handford. Fringe-Mediated Extension of O-Linked Fucose in the Ligand- Binding Region of NOTCH1 Increases Binding to Mammalian Notch Ligands. Proc.Natl.Acad.Sci.Usa V. 111 7290 2014.
ISSN: ISSN 0027-8424
PubMed: 24803430
DOI: 10.1073/PNAS.1319683111