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

The structure of Human Notch 1, Egf 4-7, PDB code: 5fma 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)	43.42 / 2.46
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.940, 86.830, 53.450, 90.00, 107.58, 90.00
R / Rfree (%)	25.9 / 26.3

The structure of Human Notch 1, Egf 4-7 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Human Notch 1, Egf 4-7 (pdb code 5fma). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Human Notch 1, Egf 4-7, PDB code: 5fma:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 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:49.1 occ:1.00 OD1 A:ASN197 2.3 38.1 1.0 OE1 A:GLU181 2.4 53.6 1.0 OD2 A:ASP178 2.5 52.2 1.0 O A:SER201 2.6 47.0 1.0 O A:GLU198 2.6 53.5 1.0 O A:VAL179 2.6 49.6 1.0 OD1 A:ASP178 2.7 57.3 1.0 CG A:ASP178 3.0 52.0 1.0 CD A:GLU181 3.4 67.2 1.0 CG A:ASN197 3.4 46.5 1.0 C A:SER201 3.5 47.4 1.0 OE2 A:GLU181 3.7 56.3 1.0 N A:SER201 3.7 46.1 1.0 C A:GLU198 3.8 54.4 1.0 C A:VAL179 3.8 50.0 1.0 ND2 A:ASN197 3.9 37.4 1.0 N A:GLU198 3.9 50.6 1.0 CA A:SER201 4.0 45.4 1.0 N A:GLY200 4.2 48.4 1.0 N A:GLU181 4.4 49.1 1.0 C A:GLY200 4.4 50.2 1.0 CB A:ASP178 4.5 44.9 1.0 CA A:ASN180 4.5 47.0 1.0 CA A:GLU198 4.5 50.7 1.0 N A:VAL179 4.5 44.9 1.0 N A:TYR202 4.6 43.4 1.0 N A:ASN180 4.6 47.5 1.0 CB A:ASN197 4.7 45.0 1.0 CG A:GLU181 4.7 56.2 1.0 O A:SER169 4.7 43.0 1.0 CA A:GLY200 4.8 47.6 1.0 CA A:VAL179 4.8 45.1 1.0 N A:VAL199 4.8 51.3 1.0 C A:ASN197 4.9 53.5 1.0 CA A:ASN197 4.9 49.2 1.0 CG2 A:VAL179 4.9 49.1 1.0 C A:VAL199 5.0 53.4 1.0

Calcium binding site 2 out of 5 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:72.2 occ:1.00 OD1 A:ASN257 2.2 85.6 1.0 OD2 A:ASP274 2.2 71.3 1.0 O A:ILE258 2.2 70.1 1.0 O A:GLY275 2.3 59.1 1.0 OD1 A:ASP274 2.6 76.2 1.0 CG A:ASP274 2.7 70.1 1.0 OD2 A:ASP260 2.7 73.6 1.0 CG A:ASN257 3.3 89.2 1.0 C A:ILE258 3.4 70.5 1.0 C A:GLY275 3.6 60.1 1.0 CG A:ASP260 3.7 71.3 1.0 ND2 A:ASN257 3.9 79.5 1.0 N A:GLY275 4.0 56.4 1.0 N A:ASP260 4.1 64.4 1.0 N A:ILE258 4.1 67.9 1.0 CB A:ASP274 4.2 58.5 1.0 N A:ASP259 4.3 66.2 1.0 CA A:ASP259 4.3 65.3 1.0 CA A:ILE258 4.3 68.0 1.0 C A:ASN257 4.4 71.0 1.0 CA A:GLY275 4.4 56.2 1.0 CB A:ASN257 4.4 67.2 1.0 OD1 A:ASP260 4.5 72.2 1.0 CB A:ASP260 4.5 66.1 1.0 N A:VAL276 4.5 57.7 1.0 C A:ASP259 4.6 68.9 1.0 O A:THR278 4.6 56.3 1.0 CA A:VAL276 4.7 58.3 1.0 C A:ASP274 4.7 59.9 1.0 N A:ASN277 4.7 58.5 1.0 O A:ASN257 4.7 70.0 1.0 CA A:ASP274 4.8 56.8 1.0 CA A:ASN257 4.9 67.7 1.0 O A:GLY248 4.9 70.8 1.0 CA A:ASP260 5.0 64.4 1.0

Calcium binding site 3 out of 5 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 3 of Human Notch 1, Egf 4-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1297 b:74.1 occ:1.00 NE2 A:GLN177 3.6 86.7 1.0 CE1 A:HIS171 3.9 50.2 1.0 O A:ASP178 3.9 47.4 1.0 CB A:GLN177 4.2 46.6 1.0 CD A:GLN177 4.5 90.2 1.0 NE2 A:HIS171 4.5 50.7 1.0 CG A:GLN177 4.6 65.3 1.0 ND1 A:HIS171 5.0 50.8 1.0

Calcium binding site 4 out of 5 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 4 of Human Notch 1, Egf 4-7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1295 b:46.9 occ:1.00 OD1 B:ASN197 2.3 43.6 1.0 OD2 B:ASP178 2.4 58.6 1.0 O B:VAL179 2.5 43.2 1.0 OE1 B:GLU181 2.5 40.8 1.0 OD1 B:ASP178 2.6 54.9 1.0 O B:GLU198 2.6 48.8 1.0 O B:SER201 2.8 47.5 1.0 CG B:ASP178 2.8 54.7 1.0 CG B:ASN197 3.3 51.7 1.0 CD B:GLU181 3.5 56.4 1.0 C B:VAL179 3.6 44.2 1.0 ND2 B:ASN197 3.7 45.4 1.0 C B:SER201 3.8 49.0 1.0 C B:GLU198 3.8 49.4 1.0 OE2 B:GLU181 3.9 52.0 1.0 N B:SER201 3.9 46.0 1.0 N B:GLU198 4.0 45.6 1.0 N B:VAL179 4.3 42.0 1.0 CA B:SER201 4.3 45.6 1.0 N B:GLY200 4.3 47.2 1.0 CB B:ASP178 4.3 45.5 1.0 CA B:ASN180 4.3 40.1 1.0 N B:ASN180 4.4 40.9 1.0 N B:GLU181 4.4 42.0 1.0 CA B:GLU198 4.5 45.5 1.0 CA B:VAL179 4.6 41.3 1.0 CB B:ASN197 4.6 43.1 1.0 C B:GLY200 4.6 50.1 1.0 O B:SER169 4.6 45.1 1.0 N B:TYR202 4.8 47.2 1.0 C B:ASP178 4.8 46.1 1.0 C B:ASN197 4.8 48.8 1.0 CA B:ASN197 4.8 44.9 1.0 N B:VAL199 4.8 46.4 1.0 CA B:GLY200 4.9 47.2 1.0 CG B:GLU181 4.9 50.0 1.0 C B:ASN180 4.9 44.9 1.0

Calcium binding site 5 out of 5 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 5 of Human Notch 1, Egf 4-7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1296 b:72.0 occ:1.00 O B:ILE258 2.3 85.0 1.0 O B:GLY275 2.3 77.5 1.0 OD1 B:ASN257 2.3 83.2 1.0 OD2 B:ASP260 2.4 99.9 1.0 OD2 B:ASP274 2.7 82.0 1.0 OD1 B:ASP274 2.9 88.4 1.0 CG B:ASP274 3.1 81.9 1.0 CG B:ASP260 3.4 93.6 1.0 CG B:ASN257 3.5 92.1 1.0 C B:ILE258 3.5 84.6 1.0 C B:GLY275 3.5 78.3 1.0 ND2 B:ASN257 4.1 82.8 1.0 OD1 B:ASP260 4.1 94.1 1.0 N B:ILE258 4.1 80.3 1.0 N B:GLY275 4.2 73.5 1.0 N B:ASN277 4.2 76.3 1.0 N B:ASP260 4.2 80.4 1.0 CB B:ASP260 4.3 83.6 1.0 CA B:ILE258 4.3 80.4 1.0 N B:VAL276 4.4 75.8 1.0 CA B:VAL276 4.4 75.9 1.0 N B:ASP259 4.5 80.6 1.0 CA B:GLY275 4.5 74.2 1.0 O B:THR278 4.5 76.4 1.0 C B:ASN257 4.5 82.4 1.0 CB B:ASP274 4.6 72.5 1.0 CA B:ASP259 4.6 80.1 1.0 CB B:ASN257 4.6 77.0 1.0 O B:GLY248 4.6 82.8 1.0 C B:ASP259 4.7 84.2 1.0 C B:VAL276 4.8 80.3 1.0 CB B:ILE258 4.8 84.8 1.0 C B:ASP274 4.9 75.9 1.0 CA B:ASP260 4.9 80.6 1.0 O B:ASN257 5.0 81.0 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