Calcium in PDB 4d0e: Human NOTCH1 Egf Domains 11-13 Mutant Glcnac-Fucose Disaccharide Modified at T466

The structure of Human NOTCH1 Egf Domains 11-13 Mutant Glcnac-Fucose Disaccharide Modified at T466, PDB code: 4d0e 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)	47.07 / 1.61
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	28.440, 28.440, 282.390, 90.00, 90.00, 120.00
R / Rfree (%)	23.052 / 27.031

The binding sites of Calcium atom in the Human NOTCH1 Egf Domains 11-13 Mutant Glcnac-Fucose Disaccharide Modified at T466 (pdb code 4d0e). 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 Glcnac-Fucose Disaccharide Modified at T466, PDB code: 4d0e:
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 Glcnac-Fucose Disaccharide Modified 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 Glcnac-Fucose Disaccharide Modified at T466 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1531 b:20.9 occ:1.00 O A:VAL453 2.3 21.1 1.0 O A:GLN470 2.3 20.3 1.0 O A:HOH2066 2.4 26.7 1.0 O A:HOH2060 2.4 20.3 1.0 OD1 A:ASP469 2.4 25.2 1.0 OD1 A:ASP452 2.4 23.7 1.0 OE1 A:GLU455 2.4 22.4 1.0 C A:GLN470 3.4 21.0 1.0 CG A:ASP469 3.5 25.6 1.0 CD A:GLU455 3.5 22.1 1.0 CG A:ASP452 3.5 25.0 1.0 C A:VAL453 3.5 22.4 1.0 OE2 A:GLU455 3.8 20.8 1.0 OD2 A:ASP452 3.9 25.1 1.0 OD2 A:ASP469 3.9 25.7 1.0 N A:GLN470 4.0 21.6 1.0 C A:ASP469 4.2 23.7 1.0 CA A:GLN470 4.2 21.4 1.0 N A:ILE471 4.2 19.9 1.0 N A:GLY472 4.2 20.9 1.0 CA A:ILE471 4.3 20.1 1.0 O A:HOH2064 4.3 28.4 1.0 N A:GLU455 4.4 21.5 1.0 N A:VAL453 4.4 23.8 1.0 N A:ASN454 4.4 23.0 1.0 C A:ASP452 4.4 24.4 1.0 CA A:ASN454 4.5 22.5 1.0 CA A:VAL453 4.5 22.7 1.0 O A:ASP469 4.5 23.4 1.0 O A:ASP452 4.6 25.3 1.0 CB A:ASP469 4.7 24.1 1.0 O A:GLU473 4.7 21.4 1.0 CA A:ASP469 4.8 23.9 1.0 C A:ILE471 4.8 20.7 1.0 O A:GLY443 4.8 20.9 1.0 CB A:ASP452 4.8 24.5 1.0 CG A:GLU455 4.8 21.6 1.0 CB A:VAL453 4.9 23.2 1.0 C A:ASN454 5.0 22.5 1.0 CA A:ASP452 5.0 24.6 1.0

Calcium binding site 2 out of 4 in the Human NOTCH1 Egf Domains 11-13 Mutant Glcnac-Fucose Disaccharide Modified 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 Glcnac-Fucose Disaccharide Modified at T466 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1532 b:23.2 occ:1.00 O A:THR491 2.3 22.1 1.0 OE1 A:GLU493 2.3 23.6 1.0 O A:LYS508 2.3 22.6 1.0 OD1 A:ASN490 2.3 24.4 1.0 O A:HOH2095 2.5 21.9 1.0 OD2 A:ASP507 2.5 27.3 1.0 OD1 A:ASP507 2.6 23.5 1.0 CG A:ASP507 2.9 25.1 1.0 CD A:GLU493 3.3 23.2 1.0 C A:THR491 3.5 24.3 1.0 CG A:ASN490 3.5 23.5 1.0 C A:LYS508 3.5 24.1 1.0 OE2 A:GLU493 3.7 23.8 1.0 O A:HOH2105 4.1 30.0 1.0 N A:LYS508 4.1 25.7 1.0 ND2 A:ASN490 4.1 23.3 1.0 N A:GLU493 4.1 24.0 1.0 N A:THR491 4.2 24.1 1.0 N A:ASN510 4.3 21.8 1.0 C A:ASN490 4.3 23.3 1.0 CB A:ASP507 4.3 25.8 1.0 CA A:ILE509 4.3 23.8 1.0 CA A:THR491 4.4 23.3 1.0 CA A:ASP492 4.4 24.7 1.0 N A:ASP492 4.4 23.3 1.0 N A:ILE509 4.4 23.6 1.0 CA A:LYS508 4.5 25.5 1.0 O A:ASN490 4.5 25.5 1.0 O A:GLU511 4.5 23.1 1.0 CG A:GLU493 4.6 23.8 1.0 O A:HOH2123 4.6 38.4 1.0 C A:ASP507 4.6 25.4 1.0 CB A:ASN490 4.7 23.1 1.0 O A:GLY481 4.7 22.5 1.0 C A:ASP492 4.8 24.8 1.0 C A:ILE509 4.8 22.8 1.0 CB A:GLU493 4.8 23.8 1.0 CB A:THR491 4.8 23.0 1.0 CA A:ASP507 4.9 25.9 1.0 CA A:ASN490 4.9 23.1 1.0

Calcium binding site 3 out of 4 in the Human NOTCH1 Egf Domains 11-13 Mutant Glcnac-Fucose Disaccharide Modified 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 Glcnac-Fucose Disaccharide Modified at T466 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1533 b:24.2 occ:1.00 O A:THR432 2.3 24.2 1.0 OD1 A:ASN431 2.4 21.4 1.0 O A:SER435 2.4 23.0 1.0 O A:VAL413 2.4 28.9 1.0 OE1 A:GLU415 2.5 22.4 1.0 OD1 A:ASP412 2.5 31.1 1.0 O A:HOH2023 2.5 28.6 1.0 OD2 A:ASP412 3.1 30.9 1.0 CG A:ASP412 3.1 31.8 1.0 CG A:ASN431 3.4 21.3 1.0 CD A:GLU415 3.5 24.2 1.0 C A:SER435 3.5 22.5 1.0 C A:THR432 3.6 24.7 1.0 C A:VAL413 3.6 28.7 1.0 N A:SER435 3.7 25.4 1.0 OE2 A:GLU415 3.7 25.6 1.0 ND2 A:ASN431 3.9 22.8 1.0 N A:GLY434 3.9 26.7 1.0 N A:THR432 4.0 22.4 1.0 CA A:SER435 4.0 24.6 1.0 C A:GLY434 4.3 26.3 1.0 N A:GLU415 4.4 23.9 1.0 CA A:ASP414 4.4 24.8 1.0 CA A:THR432 4.4 23.2 1.0 N A:ASP414 4.4 25.8 1.0 N A:VAL413 4.5 31.6 1.0 N A:LEU433 4.5 26.9 1.0 CA A:LEU433 4.6 27.7 1.0 CA A:GLY434 4.6 27.1 1.0 C A:LEU433 4.6 27.5 1.0 N A:PHE436 4.6 21.5 1.0 CB A:ASP412 4.6 32.2 1.0 CA A:VAL413 4.6 29.8 1.0 O A:HOH2024 4.7 30.8 1.0 CB A:ASN431 4.8 21.9 1.0 CG A:GLU415 4.8 23.7 1.0 OG1 A:THR432 4.9 23.9 1.0 C A:ASN431 4.9 21.2 1.0 C A:ASP414 4.9 24.9 1.0 CA A:ASN431 4.9 21.1 1.0

Calcium binding site 4 out of 4 in the Human NOTCH1 Egf Domains 11-13 Mutant Glcnac-Fucose Disaccharide Modified 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 Glcnac-Fucose Disaccharide Modified at T466 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1535 b:20.6 occ:0.50 OE2 A:GLU511 2.3 26.9 1.0 NE2 A:HIS523 2.4 27.9 1.0 OE1 A:GLU511 2.8 30.2 1.0 CD A:GLU511 2.9 27.3 1.0 CD2 A:HIS523 3.3 27.0 1.0 CE1 A:HIS523 3.4 27.6 1.0 CE1 A:PHE512 4.3 23.0 1.0 CG A:GLU511 4.3 26.3 1.0 CG A:HIS523 4.4 27.8 1.0 ND1 A:HIS523 4.4 28.1 1.0 CZ A:PHE512 4.5 24.2 1.0 CD1 A:PHE512 4.8 23.7 1.0 O A:PHE512 4.8 25.0 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