Calcium in PDB 2vj3: Human Notch-1 Egfs 11-13

The structure of Human Notch-1 Egfs 11-13, PDB code: 2vj3 was solved by S.Johnson, J.Cordle, J.Z.Tay, P.Roversi, S.M.Lea, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.40 / 2.60
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	28.000, 28.000, 281.700, 90.00, 90.00, 120.00
R / Rfree (%)	23.9 / 24.4

The structure of Human Notch-1 Egfs 11-13 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the Human Notch-1 Egfs 11-13 (pdb code 2vj3). 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 Notch-1 Egfs 11-13, PDB code: 2vj3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Human Notch-1 Egfs 11-13


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Notch-1 Egfs 11-13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1531 b:31.9 occ:1.00 O A:VAL453 2.3 30.1 1.0 O A:GLN470 2.4 26.9 1.0 O A:HOH2007 2.4 40.1 1.0 O A:HOH2009 2.4 33.5 1.0 OE1 A:GLU455 2.6 29.6 1.0 OD1 A:ASP469 2.7 35.5 1.0 OD1 A:ASP452 2.9 37.5 1.0 C A:GLN470 3.4 28.2 1.0 C A:VAL453 3.5 31.0 1.0 CG A:ASP469 3.6 36.4 1.0 CG A:ASP452 3.6 35.7 1.0 CD A:GLU455 3.7 41.5 1.0 OD2 A:ASP452 3.8 42.0 1.0 OE2 A:GLU455 4.0 28.2 1.0 OD2 A:ASP469 4.0 40.5 1.0 N A:GLN470 4.0 25.7 1.0 C A:ASP469 4.2 29.4 1.0 N A:VAL453 4.3 25.0 1.0 N A:ILE471 4.3 23.7 1.0 CA A:GLN470 4.3 24.1 1.0 C A:ASP452 4.3 29.5 1.0 O A:HOH2013 4.4 0.6 1.0 CA A:ILE471 4.4 23.3 1.0 CA A:VAL453 4.4 25.8 1.0 N A:ASN454 4.4 29.3 1.0 O A:ASP452 4.5 29.1 1.0 N A:GLY472 4.5 23.5 1.0 CA A:ASN454 4.5 28.8 1.0 N A:GLU455 4.5 29.7 1.0 O A:ASP469 4.5 29.7 1.0 O A:GLY443 4.7 26.7 1.0 CB A:ASP469 4.7 28.1 1.0 CA A:ASP469 4.7 25.8 1.0 CB A:ASP452 4.8 27.2 1.0 O A:GLU473 4.8 24.6 1.0 CB A:VAL453 4.9 29.5 1.0 C A:ILE471 5.0 26.5 1.0 CA A:ASP452 5.0 25.5 1.0

Calcium binding site 2 out of 4 in the Human Notch-1 Egfs 11-13


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Notch-1 Egfs 11-13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1532 b:37.5 occ:1.00 O A:SER435 2.4 26.4 1.0 OD1 A:ASN431 2.4 25.4 1.0 O A:HOH2002 2.5 60.0 1.0 OE1 A:GLU415 2.6 37.8 1.0 O A:VAL413 2.6 40.0 1.0 O A:THR432 2.6 29.9 1.0 OD1 A:ASP412 2.8 61.2 1.0 OD2 A:ASP412 3.3 66.6 1.0 CG A:ASP412 3.4 61.4 1.0 C A:SER435 3.5 28.1 1.0 CG A:ASN431 3.6 35.4 1.0 CD A:GLU415 3.6 47.6 1.0 C A:VAL413 3.7 40.5 1.0 C A:THR432 3.8 30.0 1.0 N A:SER435 3.8 26.7 1.0 OE2 A:GLU415 3.9 37.1 1.0 CA A:SER435 4.1 26.1 1.0 ND2 A:ASN431 4.1 27.9 1.0 N A:THR432 4.2 23.9 1.0 N A:GLY434 4.2 29.2 1.0 N A:GLU415 4.4 28.9 1.0 CA A:ASP414 4.4 32.6 1.0 C A:GLY434 4.4 31.8 1.0 N A:ASP414 4.4 34.2 1.0 N A:VAL413 4.4 43.2 1.0 N A:PHE436 4.6 22.9 1.0 CA A:THR432 4.6 24.4 1.0 CA A:VAL413 4.7 41.0 1.0 N A:LEU433 4.8 28.4 1.0 CA A:GLY434 4.8 28.3 1.0 CB A:ASN431 4.8 23.5 1.0 CA A:LEU433 4.8 28.4 1.0 CB A:PHE436 4.9 23.5 1.0 CB A:ASP412 4.9 50.3 1.0 C A:LEU433 4.9 32.4 1.0 CG A:GLU415 4.9 37.0 1.0 C A:ASP414 4.9 34.4 1.0 CA A:PHE436 5.0 21.6 1.0 OG1 A:THR432 5.0 28.6 1.0 C A:ASN431 5.0 28.1 1.0 O A:GLY434 5.0 32.0 1.0 CA A:ASN431 5.0 23.8 1.0

Calcium binding site 3 out of 4 in the Human Notch-1 Egfs 11-13


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Notch-1 Egfs 11-13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1533 b:29.7 occ:1.00 O A:LYS508 2.2 30.3 1.0 O A:THR491 2.2 33.6 1.0 O A:HOH2015 2.5 56.6 1.0 OD1 A:ASN490 2.6 35.5 1.0 OE1 A:GLU493 2.6 29.4 1.0 OD1 A:ASP507 2.8 43.0 1.0 OD2 A:ASP507 3.0 48.8 1.0 CG A:ASP507 3.3 43.7 1.0 C A:LYS508 3.4 30.9 1.0 C A:THR491 3.4 32.6 1.0 CD A:GLU493 3.7 39.6 1.0 CG A:ASN490 3.7 41.7 1.0 OE2 A:GLU493 4.0 30.4 1.0 N A:THR491 4.0 26.8 1.0 CA A:ILE509 4.1 26.8 1.0 C A:ASN490 4.1 29.8 1.0 CA A:THR491 4.2 26.9 1.0 N A:ILE509 4.2 26.9 1.0 O A:ASN490 4.2 29.6 1.0 N A:LYS508 4.2 29.2 1.0 N A:ASN510 4.2 26.3 1.0 O A:GLY481 4.4 28.8 1.0 N A:ASP492 4.4 30.2 1.0 CA A:LYS508 4.5 28.6 1.0 ND2 A:ASN490 4.5 32.0 1.0 N A:GLU493 4.6 30.3 1.0 CB A:THR491 4.6 30.4 1.0 CA A:ASP492 4.6 30.3 1.0 O A:GLU511 4.7 30.6 1.0 C A:ILE509 4.7 29.4 1.0 CB A:ASN490 4.7 24.5 1.0 CB A:ASP507 4.7 34.2 1.0 CA A:ASN490 4.8 23.0 1.0 O A:HOH2019 4.9 32.8 1.0 C A:ASP507 4.9 34.9 1.0 CG A:GLU493 5.0 36.3 1.0

Calcium binding site 4 out of 4 in the Human Notch-1 Egfs 11-13


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Notch-1 Egfs 11-13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1534 b:12.0 occ:0.50 OE2 A:GLU511 2.3 22.8 1.0 NE2 A:HIS523 2.5 39.8 1.0 CE1 A:HIS523 3.3 39.8 1.0 CD A:GLU511 3.4 47.1 1.0 CD2 A:HIS523 3.6 39.7 1.0 OE1 A:GLU511 3.7 54.3 1.0 CE2 A:PHE512 4.3 34.5 1.0 ND1 A:HIS523 4.4 40.7 1.0 CZ A:PHE512 4.5 32.5 1.0 CG A:HIS523 4.6 38.8 1.0 CG A:GLU511 4.7 37.2 1.0 CD2 A:PHE512 4.8 31.9 1.0 O A:PHE512 5.0 30.7 1.0

J.Cordle, S.Johnson, J.Z.Tay, P.Roversi, M.B.Wilkin, B.H.De Madrid, H.Shimizu, S.Jensen, P.Whiteman, B.Jin, C.Redfield, M.Baron, S.M.Lea, P.A.Handford. A Conserved Face of the Jagged/Serrate Dsl Domain Is Involved in Notch Trans-Activation and Cis-Inhibition. Nat.Struct.Mol.Biol. V. 15 849 2008.
ISSN: ISSN 1545-9993
PubMed: 18660822
DOI: 10.1038/NSMB.1457