Calcium in PDB 5mwb: Human Notch-2 EGF11-13

The structure of Human Notch-2 EGF11-13, PDB code: 5mwb was solved by R.J.Suckling, P.A.Handford, S.M.Lea, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.00 / 1.86
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	20.160, 49.790, 125.500, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 26.4

The binding sites of Calcium atom in the Human Notch-2 EGF11-13 (pdb code 5mwb). 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 Notch-2 EGF11-13, PDB code: 5mwb:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human Notch-2 EGF11-13


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Notch-2 EGF11-13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:25.9 occ:1.00 O A:LYS512 2.2 27.6 1.0 OE1 A:GLU497 2.2 25.1 1.0 O A:ILE495 2.3 26.2 1.0 OD1 A:ASP511 2.3 26.5 1.0 OE2 A:GLU494 2.4 32.8 1.0 O A:HOH726 2.5 25.6 1.0 CG A:ASP511 3.0 29.3 1.0 OD2 A:ASP511 3.1 36.9 1.0 CD A:GLU497 3.3 26.7 1.0 CD A:GLU494 3.4 35.5 1.0 C A:LYS512 3.4 29.4 1.0 C A:ILE495 3.5 29.7 1.0 CG A:GLU494 3.5 29.4 1.0 OE2 A:GLU497 3.7 27.7 1.0 N A:GLU497 4.0 24.4 1.0 N A:LYS512 4.1 28.3 1.0 CA A:VAL513 4.1 26.6 1.0 CA A:ASN496 4.2 26.8 1.0 N A:VAL513 4.2 29.6 1.0 N A:ASN514 4.2 26.7 1.0 N A:ASN496 4.3 27.9 1.0 CA A:LYS512 4.4 29.7 1.0 O A:ARG515 4.4 25.4 1.0 C A:ASP511 4.4 28.7 1.0 CB A:ASP511 4.4 27.4 1.0 O A:HOH729 4.4 34.4 1.0 OE1 A:GLU494 4.5 34.4 1.0 CA A:ILE495 4.6 26.9 1.0 N A:ILE495 4.6 28.1 1.0 CG A:GLU497 4.6 28.7 1.0 C A:VAL513 4.6 26.9 1.0 C A:ASN496 4.7 26.0 1.0 O A:HOH748 4.7 34.0 1.0 CA A:ASP511 4.8 25.8 1.0 CB A:GLU494 4.8 33.3 1.0 CB A:GLU497 4.8 25.0 1.0 O A:GLY485 4.8 25.0 1.0 O A:ASP511 4.9 31.9 1.0 C A:GLU494 4.9 30.8 1.0 CB A:ILE495 5.0 27.3 1.0

Calcium binding site 2 out of 3 in the Human Notch-2 EGF11-13


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Notch-2 EGF11-13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:35.2 occ:1.00 O A:VAL416 2.2 38.5 1.0 OD1 A:ASP415 2.3 38.9 1.0 OD1 A:ASN435 2.4 32.5 1.0 O A:HOH703 2.4 37.5 1.0 O A:THR436 2.4 29.8 1.0 OE1 A:GLU418 2.5 36.1 1.0 O A:ALA439 2.5 34.4 1.0 OD2 A:ASP415 2.9 39.2 1.0 CG A:ASP415 2.9 39.2 1.0 CD A:GLU418 3.4 37.7 1.0 CG A:ASN435 3.4 34.9 1.0 C A:VAL416 3.4 40.7 1.0 OE2 A:GLU418 3.5 42.8 1.0 C A:THR436 3.6 33.4 1.0 C A:ALA439 3.6 34.6 1.0 N A:ALA439 3.7 34.8 1.0 ND2 A:ASN435 3.9 34.1 1.0 N A:THR436 4.0 27.7 1.0 N A:GLY438 4.1 35.9 1.0 N A:VAL416 4.1 42.9 1.0 CA A:ALA439 4.1 37.2 1.0 CA A:VAL416 4.4 42.2 1.0 N A:ASP417 4.4 42.3 1.0 C A:GLY438 4.4 37.3 1.0 CA A:ASP417 4.4 40.8 1.0 N A:GLU418 4.4 39.6 1.0 CB A:ASP415 4.4 44.3 1.0 CA A:THR436 4.5 31.1 1.0 N A:ASP437 4.6 35.5 1.0 CA A:ASP437 4.6 35.3 0.4 CA A:ASP437 4.6 35.1 0.6 O A:HOH779 4.6 42.1 1.0 C A:ASP437 4.7 36.8 1.0 CB A:ASN435 4.7 30.6 1.0 CA A:GLY438 4.7 37.8 1.0 N A:PHE440 4.7 34.3 1.0 CG A:GLU418 4.8 38.2 1.0 C A:ASP415 4.8 42.6 1.0 C A:ASN435 4.8 28.1 1.0 CA A:ASN435 4.9 32.4 1.0 CB A:VAL416 4.9 43.4 1.0 OG1 A:THR436 5.0 34.9 1.0 C A:ASP417 5.0 43.0 1.0

Calcium binding site 3 out of 3 in the Human Notch-2 EGF11-13


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Notch-2 EGF11-13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca607 b:35.6 occ:1.00 O A:ILE457 2.2 39.0 1.0 OD1 A:ASP473 2.3 34.4 1.0 OD1 A:ASP456 2.4 40.0 1.0 O A:HOH725 2.4 39.9 1.0 O A:LYS474 2.4 30.8 1.0 OE1 A:GLU459 2.4 39.3 1.0 O A:HOH720 2.5 36.9 1.0 CG A:ASP473 2.9 38.2 1.0 OD2 A:ASP473 2.9 45.1 1.0 CG A:ASP456 3.4 41.2 1.0 C A:LYS474 3.4 31.6 1.0 C A:ILE457 3.4 39.2 1.0 CD A:GLU459 3.5 39.7 1.0 OD2 A:ASP456 3.7 42.8 1.0 OE2 A:GLU459 3.8 39.6 1.0 N A:LYS474 4.0 33.4 1.0 N A:GLY476 4.2 30.6 1.0 N A:ILE475 4.2 35.0 1.0 N A:ILE457 4.2 37.7 1.0 CA A:ILE475 4.3 32.5 1.0 CA A:LYS474 4.3 35.3 1.0 N A:GLU459 4.3 37.6 1.0 O A:GLY477 4.3 34.9 1.0 CB A:ASP473 4.3 37.5 1.0 N A:ASN458 4.3 39.4 1.0 O A:HOH713 4.3 41.0 1.0 CA A:ASN458 4.4 38.7 1.0 CA A:ILE457 4.4 36.9 1.0 C A:ASP473 4.4 36.5 1.0 C A:ASP456 4.5 41.2 1.0 C A:ILE475 4.7 28.4 1.0 CB A:ASP456 4.7 42.6 1.0 O A:GLY447 4.7 33.8 1.0 CA A:ASP473 4.8 33.2 1.0 CG A:GLU459 4.8 39.8 1.0 O A:ASP456 4.8 42.2 1.0 N A:GLY477 4.9 36.3 1.0 C A:ASN458 4.9 36.5 1.0 CB A:ILE457 4.9 38.5 1.0

R.J.Suckling, B.Korona, P.Whiteman, C.Chillakuri, L.Holt, P.A.Handford, S.M.Lea. Structural and Functional Dissection of the Interplay Between Lipid and Notch Binding By Human Notch Ligands. Embo J. V. 36 2204 2017.
ISSN: ESSN 1460-2075
PubMed: 28572448
DOI: 10.15252/EMBJ.201796632