Calcium in PDB 5fm9: Human Notch 1, Egf 4-7

The structure of Human Notch 1, Egf 4-7, PDB code: 5fm9 was solved by P.C.Weisshuhn, D.Sheppard, P.Taylor, P.Whiteman, S.M.Lea, P.A.Handford, C.Redfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.73 / 2.92
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	142.260, 21.150, 83.560, 90.00, 116.27, 90.00
R / Rfree (%)	21.3 / 23.7

The binding sites of Calcium atom in the Human Notch 1, Egf 4-7 (pdb code 5fm9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Human Notch 1, Egf 4-7, PDB code: 5fm9:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human Notch 1, Egf 4-7


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, Egf 4-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1295 b:28.3 occ:1.00 OE1 A:GLU181 2.1 35.1 1.0 OD1 A:ASN197 2.3 50.4 1.0 O A:GLU198 2.4 29.0 1.0 O A:SER201 2.4 23.3 1.0 O A:HOH2001 2.5 4.4 1.0 OD1 A:ASP178 2.6 36.1 1.0 O A:VAL179 2.7 19.9 1.0 OD2 A:ASP178 3.0 32.3 1.0 CG A:ASP178 3.2 28.9 1.0 CD A:GLU181 3.2 50.8 1.0 CG A:ASN197 3.5 51.3 1.0 C A:SER201 3.5 23.9 1.0 N A:SER201 3.6 17.6 1.0 C A:GLU198 3.6 29.5 1.0 OE2 A:GLU181 3.6 54.0 1.0 N A:GLU198 3.9 26.7 1.0 C A:VAL179 3.9 19.9 1.0 N A:GLY200 3.9 14.8 1.0 CA A:SER201 4.0 17.9 1.0 ND2 A:ASN197 4.1 47.0 1.0 CA A:GLU198 4.4 27.0 1.0 C A:GLY200 4.4 18.9 1.0 N A:GLU181 4.4 20.0 1.0 CG A:GLU181 4.5 29.4 1.0 N A:VAL179 4.5 16.3 1.0 N A:VAL199 4.5 23.4 1.0 O A:SER169 4.5 15.1 1.0 CA A:GLY200 4.6 14.8 1.0 N A:TYR202 4.6 21.6 1.0 C A:VAL199 4.6 18.3 1.0 CA A:VAL199 4.6 20.8 1.0 CB A:ASP178 4.7 10.7 1.0 CA A:ASN180 4.7 18.9 1.0 CB A:ASN197 4.7 22.7 1.0 C A:ASN197 4.8 29.0 1.0 N A:ASN180 4.8 17.9 1.0 CA A:VAL179 4.8 16.1 1.0 CA A:ASN197 4.8 25.3 1.0 CB A:GLU181 5.0 21.1 1.0

Calcium binding site 2 out of 2 in the Human Notch 1, Egf 4-7


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, Egf 4-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1296 b:53.3 occ:1.00 OD1 A:ASP274 2.1 74.9 1.0 OD1 A:ASP260 2.2 69.7 1.0 O A:HOH2006 2.3 51.5 1.0 OD1 A:ASN257 2.3 79.7 1.0 O A:GLY275 2.4 59.0 1.0 O A:ILE258 2.5 61.1 1.0 CG A:ASP274 2.8 71.8 1.0 OD2 A:ASP274 2.9 73.3 1.0 CG A:ASP260 3.3 65.7 1.0 CG A:ASN257 3.5 80.0 1.0 C A:GLY275 3.6 60.9 1.0 C A:ILE258 3.7 61.2 1.0 N A:GLY275 3.7 58.7 1.0 CB A:ASP260 3.9 57.4 1.0 N A:ASP260 4.0 55.4 1.0 ND2 A:ASN257 4.1 69.9 1.0 N A:ASN277 4.2 56.1 1.0 CA A:GLY275 4.2 58.2 1.0 CB A:ASP274 4.2 60.5 1.0 CG1 A:ILE258 4.2 59.5 1.0 OD2 A:ASP260 4.2 66.6 1.0 N A:ILE258 4.3 55.7 1.0 O A:GLY248 4.3 42.5 1.0 C A:ASN257 4.3 59.2 1.0 O A:THR278 4.4 58.6 1.0 C A:ASP274 4.5 62.0 1.0 CA A:ILE258 4.5 55.7 1.0 O A:ASN257 4.5 58.7 1.0 CB A:ASN257 4.6 54.2 1.0 CA A:ASP260 4.6 55.2 1.0 CA A:ASN277 4.7 56.6 1.0 CA A:ASP274 4.7 58.2 1.0 N A:VAL276 4.7 58.0 1.0 CD1 A:ILE258 4.7 63.2 1.0 N A:ASP259 4.7 58.0 1.0 N A:THR278 4.8 56.0 1.0 CA A:ASP259 4.8 57.7 1.0 C A:ASP259 4.9 59.8 1.0 CA A:ASN257 4.9 53.8 1.0 CB A:ILE258 5.0 58.7 1.0

P.C.Weisshuhn, D.Sheppard, P.Taylor, P.Whiteman, S.M.Lea, P.A.Handford, C.Redfield. Non-Linear and Flexible Regions of the Human NOTCH1 Extracellular Domain Revealed By High-Resolution Structural Studies. Structure V. 24 555 2016.
ISSN: ISSN 0969-2126
PubMed: 26996961
DOI: 10.1016/J.STR.2016.02.010