Calcium in PDB 4cuf: Uman NOTCH1 Egf Domains 11-13 Mutant T466S

The structure of Uman NOTCH1 Egf Domains 11-13 Mutant T466S, PDB code: 4cuf 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)	17.66 / 2.29
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	61.770, 61.770, 126.560, 90.00, 90.00, 120.00
R / Rfree (%)	25.59 / 28.65

The binding sites of Calcium atom in the Uman NOTCH1 Egf Domains 11-13 Mutant T466S (pdb code 4cuf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Uman NOTCH1 Egf Domains 11-13 Mutant T466S, PDB code: 4cuf:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Uman NOTCH1 Egf Domains 11-13 Mutant T466S


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Uman NOTCH1 Egf Domains 11-13 Mutant T466S within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1531 b:82.2 occ:1.00 O A:GLN470 2.3 84.6 1.0 O A:VAL453 2.3 78.1 1.0 OD1 A:ASP452 2.3 97.2 1.0 OD1 A:ASP469 2.5 97.9 1.0 OE1 A:GLU455 2.5 75.5 1.0 C A:GLN470 3.3 83.0 1.0 CG A:ASP452 3.4 98.9 1.0 CG A:ASP469 3.5 96.8 1.0 C A:VAL453 3.5 82.6 1.0 CD A:GLU455 3.6 93.3 1.0 OD2 A:ASP452 3.8 0.8 1.0 OE2 A:GLU455 3.9 86.8 1.0 N A:GLN470 4.0 77.4 1.0 OD2 A:ASP469 4.0 98.8 1.0 CA A:GLN470 4.1 76.8 1.0 N A:ILE471 4.2 81.2 1.0 CA A:ILE471 4.3 82.0 1.0 C A:ASP469 4.3 82.4 1.0 N A:GLY472 4.3 80.2 1.0 N A:VAL453 4.3 78.4 1.0 C A:ASP452 4.4 83.6 1.0 N A:ASN454 4.5 82.4 1.0 CA A:VAL453 4.5 80.0 1.0 N A:GLU455 4.5 77.4 1.0 CA A:ASN454 4.6 82.5 1.0 O A:ASP452 4.6 84.2 1.0 O A:ASP469 4.6 85.8 1.0 CB A:ASP452 4.7 83.6 1.0 O A:GLU473 4.7 78.0 1.0 O A:GLY443 4.7 81.7 1.0 CB A:ASP469 4.7 81.5 1.0 C A:ILE471 4.8 84.3 1.0 CA A:ASP469 4.8 77.7 1.0 CG A:GLU455 4.9 78.8 1.0 CA A:ASP452 5.0 81.7 1.0 CB A:VAL453 5.0 83.9 1.0

Calcium binding site 2 out of 3 in the Uman NOTCH1 Egf Domains 11-13 Mutant T466S


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Uman NOTCH1 Egf Domains 11-13 Mutant T466S within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1532 b:70.6 occ:1.00 O A:LYS508 2.2 66.0 1.0 OD1 A:ASN490 2.2 67.7 1.0 O A:THR491 2.3 73.4 1.0 OE1 A:GLU493 2.4 70.4 1.0 OD2 A:ASP507 2.4 75.1 1.0 OD1 A:ASP507 2.6 79.9 1.0 CG A:ASP507 2.8 76.2 1.0 CD A:GLU493 3.4 95.6 1.0 CG A:ASN490 3.4 75.7 1.0 C A:LYS508 3.5 68.2 1.0 C A:THR491 3.5 74.2 1.0 OE2 A:GLU493 3.8 89.5 1.0 N A:LYS508 4.0 64.5 1.0 ND2 A:ASN490 4.1 69.1 1.0 N A:THR491 4.2 68.8 1.0 N A:GLU493 4.2 73.4 1.0 C A:ASN490 4.2 72.3 1.0 CB A:ASP507 4.3 67.0 1.0 N A:ILE509 4.3 67.0 1.0 N A:ASN510 4.3 67.5 1.0 CA A:LYS508 4.4 64.5 1.0 CA A:ILE509 4.4 64.7 1.0 CA A:THR491 4.4 69.1 1.0 O A:ASN490 4.4 73.5 1.0 N A:ASP492 4.4 72.7 1.0 CA A:ASP492 4.4 72.7 1.0 O A:GLU511 4.5 72.4 1.0 C A:ASP507 4.6 68.2 1.0 CB A:ASN490 4.6 70.3 1.0 CG A:GLU493 4.7 83.7 1.0 O A:GLY481 4.7 64.9 1.0 CA A:ASP507 4.8 63.5 1.0 CA A:ASN490 4.8 67.9 1.0 C A:ASP492 4.9 78.1 1.0 C A:ILE509 4.9 69.7 1.0 CB A:GLU493 4.9 73.8 1.0 CB A:THR491 4.9 74.8 1.0

Calcium binding site 3 out of 3 in the Uman NOTCH1 Egf Domains 11-13 Mutant T466S


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Uman NOTCH1 Egf Domains 11-13 Mutant T466S within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1533 b:0.9 occ:1.00 O A:SER435 2.3 0.2 1.0 OE1 A:GLU415 2.3 100.0 1.0 O A:VAL413 2.4 96.9 1.0 O A:THR432 2.4 0.1 1.0 OD1 A:ASN431 2.5 0.8 1.0 O A:HOH2001 3.0 71.2 1.0 CD A:GLU415 3.3 0.6 1.0 C A:SER435 3.4 0.4 1.0 OE2 A:GLU415 3.5 93.8 1.0 N A:SER435 3.6 0.1 1.0 CG A:ASN431 3.6 0.3 1.0 C A:VAL413 3.6 98.2 1.0 C A:THR432 3.6 0.8 1.0 CA A:SER435 3.9 0.9 1.0 N A:GLY434 4.0 0.8 1.0 ND2 A:ASN431 4.1 98.2 1.0 N A:THR432 4.1 0.6 1.0 C A:GLY434 4.3 0.9 1.0 N A:GLU415 4.4 87.5 1.0 CA A:ASP414 4.4 91.2 1.0 N A:VAL413 4.4 0.1 1.0 N A:ASP414 4.5 92.9 1.0 N A:PHE436 4.5 0.1 1.0 CA A:THR432 4.5 0.8 1.0 CA A:LEU433 4.6 1.0 1.0 N A:LEU433 4.6 0.3 1.0 CA A:VAL413 4.6 98.3 1.0 C A:LEU433 4.6 0.7 1.0 CG A:GLU415 4.7 95.3 1.0 CA A:GLY434 4.7 1.0 1.0 CB A:ASN431 4.8 92.8 1.0 OG1 A:THR432 4.9 0.0 1.0 C A:ASP414 5.0 91.3 1.0 CA A:PHE436 5.0 0.5 1.0 CB A:PHE436 5.0 0.5 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