Calcium in PDB 4d0f: Human NOTCH1 Egf Domains 11-13 Mutant T466A

The structure of Human NOTCH1 Egf Domains 11-13 Mutant T466A, PDB code: 4d0f 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)	41.19 / 2.80
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	62.620, 62.620, 126.630, 90.00, 90.00, 120.00
R / Rfree (%)	22.29 / 26.45

The binding sites of Calcium atom in the Human NOTCH1 Egf Domains 11-13 Mutant T466A (pdb code 4d0f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Human NOTCH1 Egf Domains 11-13 Mutant T466A, PDB code: 4d0f:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human NOTCH1 Egf Domains 11-13 Mutant T466A


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 T466A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1535 b:86.6 occ:1.00 OD1 A:ASP452 2.1 97.1 1.0 O A:GLN470 2.2 74.8 1.0 OE1 A:GLU455 2.4 83.0 1.0 O A:VAL453 2.4 81.1 1.0 OD1 A:ASP469 2.6 92.3 1.0 CG A:ASP452 3.1 95.7 1.0 C A:GLN470 3.3 73.8 1.0 CD A:GLU455 3.4 95.1 1.0 OD2 A:ASP452 3.5 0.7 1.0 OE2 A:GLU455 3.6 87.2 1.0 CG A:ASP469 3.7 91.9 1.0 C A:VAL453 3.7 83.4 1.0 N A:GLN470 4.0 69.6 1.0 OD2 A:ASP469 4.1 96.5 1.0 CA A:GLN470 4.2 68.7 1.0 N A:GLY472 4.2 71.2 1.0 N A:ILE471 4.2 71.4 1.0 C A:ASP452 4.3 80.0 1.0 C A:ASP469 4.3 77.4 1.0 N A:VAL453 4.3 75.7 1.0 CA A:ILE471 4.3 72.2 1.0 O A:ASP452 4.4 80.6 1.0 CB A:ASP452 4.4 80.1 1.0 N A:GLU455 4.5 78.1 1.0 CA A:VAL453 4.5 77.9 1.0 O A:ASP469 4.6 80.3 1.0 N A:ASN454 4.6 82.7 1.0 O A:GLU473 4.6 79.1 1.0 CA A:ASN454 4.7 82.7 1.0 CG A:GLU455 4.7 79.3 1.0 C A:ILE471 4.7 74.7 1.0 CA A:ASP452 4.8 77.2 1.0 O A:GLY443 4.8 69.0 1.0 CB A:ASP469 4.8 80.1 1.0 CA A:ASP469 4.9 75.2 1.0

Calcium binding site 2 out of 3 in the Human NOTCH1 Egf Domains 11-13 Mutant T466A


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 T466A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1536 b:88.0 occ:1.00 O A:SER435 2.3 87.2 1.0 O A:THR432 2.4 98.9 1.0 OE1 A:GLU415 2.4 72.3 1.0 O A:VAL413 2.5 70.6 1.0 OD1 A:ASN431 2.8 95.2 1.0 O A:HOH2001 3.2 67.6 1.0 CD A:GLU415 3.3 86.1 1.0 C A:SER435 3.3 88.0 1.0 N A:SER435 3.3 94.0 1.0 OE2 A:GLU415 3.3 81.0 1.0 C A:THR432 3.6 0.6 1.0 N A:GLY434 3.7 0.5 1.0 CA A:SER435 3.7 89.5 1.0 C A:VAL413 3.7 70.2 1.0 CG A:ASN431 3.9 0.3 1.0 C A:GLY434 4.0 0.8 1.0 N A:THR432 4.2 89.8 1.0 N A:VAL413 4.3 73.5 1.0 CA A:GLY434 4.3 0.7 1.0 ND2 A:ASN431 4.3 0.8 1.0 C A:LEU433 4.4 0.2 1.0 N A:PHE436 4.5 80.7 1.0 CA A:LEU433 4.5 0.7 1.0 O A:GLN411 4.5 89.1 1.0 N A:LEU433 4.5 0.4 1.0 CA A:THR432 4.5 95.3 1.0 N A:GLU415 4.6 58.4 1.0 CA A:VAL413 4.6 68.5 1.0 CA A:ASP414 4.7 63.9 1.0 N A:ASP414 4.7 64.9 1.0 CG A:GLU415 4.7 65.2 1.0 OG1 A:THR432 4.8 87.4 1.0 CG1 A:VAL413 4.9 69.8 1.0 O A:GLY434 4.9 0.1 1.0

Calcium binding site 3 out of 3 in the Human NOTCH1 Egf Domains 11-13 Mutant T466A


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 T466A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1537 b:68.5 occ:1.00 OE1 A:GLU493 2.2 80.7 1.0 OD1 A:ASP507 2.2 67.4 1.0 O A:THR491 2.2 58.7 1.0 O A:HOH2005 2.2 37.0 1.0 OD2 A:ASP507 2.3 68.3 1.0 O A:LYS508 2.5 59.9 1.0 CG A:ASP507 2.5 67.4 1.0 OD1 A:ASN490 2.6 47.0 1.0 CD A:GLU493 3.2 77.0 1.0 C A:THR491 3.4 58.9 1.0 C A:LYS508 3.7 62.0 1.0 OE2 A:GLU493 3.8 53.3 1.0 CG A:ASN490 3.8 61.0 1.0 N A:GLU493 3.8 62.3 1.0 CB A:ASP507 4.0 61.1 1.0 N A:LYS508 4.0 58.0 1.0 CA A:ASP492 4.1 59.0 1.0 N A:ASP492 4.2 57.0 1.0 N A:THR491 4.4 52.4 1.0 O A:GLU511 4.4 63.0 1.0 ND2 A:ASN490 4.4 62.1 1.0 CG A:GLU493 4.4 69.0 1.0 CA A:THR491 4.4 53.0 1.0 C A:ASP507 4.5 63.5 1.0 C A:ASP492 4.5 66.8 1.0 CB A:GLU493 4.5 62.6 1.0 CA A:LYS508 4.5 58.0 1.0 C A:ASN490 4.5 55.2 1.0 N A:ASN510 4.6 63.8 1.0 CA A:ASP507 4.6 58.3 1.0 N A:ILE509 4.7 59.6 1.0 CA A:ILE509 4.7 58.9 1.0 O A:ASN490 4.7 58.8 1.0 CA A:GLU493 4.8 62.5 1.0 CB A:THR491 4.9 61.2 1.0 CB A:ASN490 4.9 42.0 1.0 O A:GLY481 5.0 60.5 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