Calcium in PDB 5mwf: Human JAGGED2 C2-EGF2

The structure of Human JAGGED2 C2-EGF2, PDB code: 5mwf 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)	38.01 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	62.628, 92.929, 97.004, 71.68, 83.16, 82.68
R / Rfree (%)	21.7 / 27.5

The structure of Human JAGGED2 C2-EGF2 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Calcium atom in the Human JAGGED2 C2-EGF2 (pdb code 5mwf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 17 binding sites of Calcium where determined in the Human JAGGED2 C2-EGF2, PDB code: 5mwf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 17 in the Human JAGGED2 C2-EGF2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human JAGGED2 C2-EGF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:36.5 occ:1.00 OD1 A:ASP65 2.3 52.0 1.0 OD2 A:ASP51 2.3 48.8 1.0 O A:GLU66 2.4 37.0 1.0 OD1 A:ASP68 2.4 41.2 1.0 OD2 A:ASP68 2.6 48.1 1.0 CG A:ASP68 2.8 42.6 1.0 CG A:ASP65 3.5 47.6 1.0 CG A:ASP51 3.5 40.9 1.0 C A:GLU66 3.6 41.9 1.0 CA A:CA406 3.9 34.7 1.0 N A:GLU66 4.0 46.0 1.0 OD2 A:ASP65 4.2 48.1 1.0 CB A:ASP51 4.2 41.8 1.0 N A:ASP68 4.2 34.3 1.0 CB A:ASP68 4.2 38.6 1.0 C A:ASP65 4.2 46.9 1.0 CA A:GLU66 4.4 44.3 1.0 C A:CYS67 4.4 31.8 1.0 OD1 A:ASP51 4.5 43.4 1.0 N A:CYS67 4.6 37.5 1.0 CA A:ASP65 4.6 46.7 1.0 CB A:ASP65 4.6 42.2 1.0 CA A:CYS67 4.7 36.8 1.0 CA A:ASP68 4.7 37.1 1.0 O A:ASP65 4.7 46.3 1.0 O A:CYS67 4.9 32.8 1.0

Calcium binding site 2 out of 17 in the Human JAGGED2 C2-EGF2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human JAGGED2 C2-EGF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:34.7 occ:1.00 OD1 A:ASP152 2.2 40.5 1.0 O A:TRP151 2.4 34.6 1.0 OD2 A:ASP51 2.5 48.8 1.0 OD1 A:ASP51 2.5 43.4 1.0 OD1 A:ASP150 2.5 37.8 1.0 OD2 A:ASP68 2.5 48.1 1.0 CG A:ASP51 2.8 40.9 1.0 OD2 A:ASP150 3.0 37.2 1.0 CG A:ASP150 3.1 38.7 1.0 C A:TRP151 3.4 35.7 1.0 CG A:ASP152 3.4 42.8 1.0 CG A:ASP68 3.4 42.6 1.0 CA A:CA407 3.6 60.9 1.0 CA A:CA405 3.9 36.5 1.0 CB A:ASP68 3.9 38.6 1.0 N A:TRP151 4.0 37.8 1.0 N A:ASP152 4.1 39.4 1.0 CA A:ASP152 4.1 37.7 1.0 OD2 A:ASP152 4.3 36.3 1.0 CB A:ASP152 4.3 33.5 1.0 CB A:ASP51 4.3 41.8 1.0 N A:ASP68 4.3 34.3 1.0 CA A:TRP151 4.4 34.8 1.0 OD1 A:ASP68 4.4 41.2 1.0 CB A:ASP150 4.6 34.6 1.0 C A:ASP150 4.7 36.4 1.0 CA A:ASP68 4.8 37.1 1.0 O A:GLU66 4.8 37.0 1.0

Calcium binding site 3 out of 17 in the Human JAGGED2 C2-EGF2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human JAGGED2 C2-EGF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:60.9 occ:1.00 OD1 A:ASP51 2.4 43.4 1.0 OD2 A:ASP152 2.4 36.3 1.0 OD1 A:ASP152 2.5 40.5 1.0 OD2 A:ASP150 2.5 37.2 1.0 O A:CYS50 2.7 51.8 1.0 CG A:ASP152 2.7 42.8 1.0 O A:HOH554 3.3 50.5 1.0 CA A:CA406 3.6 34.7 1.0 CG A:ASP51 3.6 40.9 1.0 CG A:ASP150 3.7 38.7 1.0 C A:CYS50 3.7 55.6 1.0 CD2 A:LEU161 3.9 31.6 1.0 CA A:ASP51 4.1 52.0 1.0 CB A:ASP152 4.2 33.5 1.0 N A:ASP51 4.3 51.1 1.0 OD1 A:ASP150 4.3 37.8 1.0 CB A:ASP51 4.4 41.8 1.0 OD2 A:ASP51 4.5 48.8 1.0 CB A:ASP150 4.7 34.6 1.0 CA A:CYS50 4.8 47.1 1.0

Calcium binding site 4 out of 17 in the Human JAGGED2 C2-EGF2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human JAGGED2 C2-EGF2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca405 b:43.0 occ:1.00 OD1 B:ASP65 2.3 58.2 1.0 OD1 B:ASP68 2.5 46.0 1.0 OD2 B:ASP68 2.5 43.8 1.0 O B:GLU66 2.5 44.4 1.0 OD2 B:ASP51 2.5 45.5 1.0 CG B:ASP68 2.8 40.6 1.0 CG B:ASP65 3.5 51.4 1.0 CG B:ASP51 3.7 45.1 1.0 C B:GLU66 3.7 43.4 1.0 CA B:CA406 3.9 32.8 1.0 OD2 B:ASP65 4.1 42.5 1.0 CB B:ASP68 4.2 41.5 1.0 N B:ASP68 4.2 38.5 1.0 N B:GLU66 4.2 50.1 1.0 O B:HOH502 4.2 40.0 1.0 CB B:ASP51 4.2 51.1 1.0 C B:ASP65 4.4 48.4 1.0 C B:CYS67 4.5 37.6 1.0 CA B:GLU66 4.6 46.1 1.0 CB B:ASP65 4.7 55.1 1.0 N B:CYS67 4.7 39.4 1.0 OD1 B:ASP51 4.7 45.5 1.0 CA B:CYS67 4.7 42.4 1.0 CA B:ASP68 4.7 42.9 1.0 CA B:ASP65 4.8 52.8 1.0 O B:ASP65 4.8 47.5 1.0

Calcium binding site 5 out of 17 in the Human JAGGED2 C2-EGF2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human JAGGED2 C2-EGF2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca406 b:32.8 occ:1.00 OD1 B:ASP152 2.2 39.8 1.0 O B:HOH502 2.3 40.0 1.0 OD2 B:ASP51 2.5 45.5 1.0 O B:TRP151 2.5 49.5 1.0 OD1 B:ASP150 2.5 39.8 1.0 OD1 B:ASP51 2.8 45.5 1.0 OD2 B:ASP150 2.9 41.4 1.0 CG B:ASP51 3.0 45.1 1.0 CG B:ASP150 3.0 43.3 1.0 OD2 B:ASP68 3.1 43.8 1.0 C B:TRP151 3.4 43.8 1.0 CG B:ASP152 3.5 41.9 1.0 CG B:ASP68 3.8 40.6 1.0 CA B:CA407 3.9 70.3 1.0 N B:TRP151 3.9 40.1 1.0 CA B:CA405 3.9 43.0 1.0 N B:ASP152 4.1 43.1 1.0 CB B:ASP68 4.1 41.5 1.0 CA B:ASP152 4.2 44.8 1.0 OD2 B:ASP152 4.3 36.3 1.0 CA B:TRP151 4.3 39.0 1.0 N B:ASP68 4.3 38.5 1.0 CB B:ASP152 4.4 44.3 1.0 CB B:ASP150 4.4 39.2 1.0 CB B:ASP51 4.5 51.1 1.0 C B:ASP150 4.6 41.1 1.0 OD1 B:ASP68 4.7 46.0 1.0 CA B:ASP68 4.9 42.9 1.0 CA B:ASP150 4.9 38.3 1.0

Calcium binding site 6 out of 17 in the Human JAGGED2 C2-EGF2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human JAGGED2 C2-EGF2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca407 b:70.3 occ:1.00 OD1 B:ASP51 2.4 45.5 1.0 OD2 B:ASP152 2.5 36.3 1.0 OD1 B:ASP152 2.8 39.8 1.0 O B:CYS50 2.8 56.2 1.0 CG B:ASP152 2.9 41.9 1.0 OD2 B:ASP150 3.0 41.4 1.0 CG B:ASP51 3.6 45.1 1.0 CD2 B:LEU161 3.8 50.9 1.0 C B:CYS50 3.9 51.3 1.0 CA B:CA406 3.9 32.8 1.0 CA B:ASP51 4.2 53.2 1.0 CG B:ASP150 4.2 43.3 1.0 CB B:ASP152 4.4 44.3 1.0 N B:ASP51 4.5 49.9 1.0 CB B:ASP51 4.5 51.1 1.0 OD2 B:ASP51 4.5 45.5 1.0 O B:HOH502 4.8 40.0 1.0 OD1 B:ASP150 4.9 39.8 1.0 CA B:CYS50 5.0 53.0 1.0

Calcium binding site 7 out of 17 in the Human JAGGED2 C2-EGF2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Human JAGGED2 C2-EGF2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca405 b:70.5 occ:1.00 OD1 C:ASP65 2.3 75.6 1.0 OD1 C:ASP51 2.4 69.1 1.0 O C:GLU66 2.4 64.7 1.0 O C:HOH513 2.4 56.9 1.0 OD1 C:ASP68 2.5 67.7 1.0 OD2 C:ASP68 2.6 65.1 1.0 CG C:ASP68 2.8 62.5 1.0 CG C:ASP65 3.5 70.9 1.0 CA C:CA406 3.6 69.8 1.0 C C:GLU66 3.6 62.9 1.0 CG C:ASP51 3.6 71.5 1.0 OD2 C:ASP65 4.1 65.1 1.0 N C:ASP68 4.1 54.7 1.0 N C:GLU66 4.2 75.8 1.0 CB C:ASP68 4.2 62.5 1.0 C C:CYS67 4.3 55.5 1.0 CB C:ASP51 4.4 69.5 1.0 C C:ASP65 4.5 78.4 1.0 OD2 C:ASP51 4.5 77.7 1.0 CA C:GLU66 4.5 64.4 1.0 N C:CYS67 4.5 58.8 1.0 CA C:CYS67 4.6 60.7 1.0 CB C:ASP65 4.6 67.4 1.0 CA C:ASP68 4.7 58.2 1.0 O C:CYS67 4.8 55.2 1.0 CA C:ASP65 4.8 77.7 1.0 OD1 C:ASP150 5.0 62.5 1.0 O C:ASP65 5.0 72.1 1.0

Calcium binding site 8 out of 17 in the Human JAGGED2 C2-EGF2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Human JAGGED2 C2-EGF2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca406 b:69.8 occ:1.00 OD1 C:ASP152 2.3 72.1 1.0 OD2 C:ASP68 2.4 65.1 1.0 OD1 C:ASP51 2.4 69.1 1.0 OD2 C:ASP51 2.5 77.7 1.0 OD1 C:ASP150 2.5 62.5 1.0 O C:TRP151 2.6 58.9 1.0 CG C:ASP51 2.8 71.5 1.0 OD2 C:ASP150 3.2 61.7 1.0 CG C:ASP150 3.3 60.1 1.0 CG C:ASP152 3.3 62.2 1.0 CG C:ASP68 3.5 62.5 1.0 CA C:CA405 3.6 70.5 1.0 C C:TRP151 3.6 60.4 1.0 CA C:CA407 3.7 68.2 1.0 OD2 C:ASP152 3.8 59.5 1.0 CB C:ASP68 4.1 62.5 1.0 CA C:ASP152 4.2 66.6 1.0 N C:ASP68 4.2 54.7 1.0 CB C:ASP51 4.3 69.5 1.0 N C:ASP152 4.3 64.1 1.0 CB C:ASP152 4.3 54.9 1.0 N C:TRP151 4.3 60.0 1.0 OD1 C:ASP68 4.4 67.7 1.0 O C:HOH513 4.5 56.9 1.0 O C:GLU66 4.6 64.7 1.0 CA C:TRP151 4.6 57.9 1.0 CB C:ASP150 4.7 60.8 1.0 CA C:ASP68 4.8 58.2 1.0 C C:ASP150 4.9 58.5 1.0

Calcium binding site 9 out of 17 in the Human JAGGED2 C2-EGF2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Human JAGGED2 C2-EGF2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca407 b:68.2 occ:1.00 O C:CYS50 2.2 70.8 1.0 OD2 C:ASP152 2.4 59.5 1.0 OD2 C:ASP51 2.4 77.7 1.0 OD2 C:ASP150 2.5 61.7 1.0 C C:CYS50 3.1 69.5 1.0 CG C:ASP152 3.1 62.2 1.0 OD1 C:ASP152 3.2 72.1 1.0 CG C:ASP51 3.6 71.5 1.0 CA C:CA406 3.7 69.8 1.0 CG C:ASP150 3.7 60.1 1.0 N C:ASP51 3.8 73.3 1.0 CA C:ASP51 4.0 77.1 1.0 CA C:CYS50 4.0 68.5 1.0 CD2 C:LEU161 4.2 45.3 1.0 OD1 C:ASP150 4.3 62.5 1.0 CB C:ASP51 4.3 69.5 1.0 OD1 C:ASP51 4.5 69.1 1.0 CB C:CYS50 4.6 73.2 1.0 CB C:ASP152 4.6 54.9 1.0 CB C:ASP150 4.9 60.8 1.0

Calcium binding site 10 out of 17 in the Human JAGGED2 C2-EGF2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Human JAGGED2 C2-EGF2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca404 b:0.1 occ:1.00 OD2 D:ASP65 2.0 0.6 1.0 OD2 D:ASP51 2.4 95.0 1.0 OD2 D:ASP68 2.6 0.9 1.0 O D:GLU66 2.6 98.3 1.0 CG D:ASP65 2.7 0.8 1.0 OD1 D:ASP68 2.7 93.1 1.0 OD1 D:ASP65 2.8 0.5 1.0 CG D:ASP68 3.0 0.3 1.0 CG D:ASP51 3.5 99.2 1.0 C D:GLU66 3.8 99.4 1.0 C D:ASP65 4.0 0.4 1.0 CB D:ASP65 4.0 0.2 1.0 CB D:ASP51 4.0 0.3 1.0 N D:GLU66 4.0 0.0 1.0 O D:ASP65 4.1 0.2 1.0 CA D:CA405 4.1 96.7 1.0 CA D:ASP65 4.4 0.9 1.0 CB D:ASP68 4.5 93.9 1.0 OD1 D:ASP51 4.6 99.7 1.0 CA D:GLU66 4.6 99.2 1.0 N D:ASP68 4.7 91.4 1.0 C D:CYS67 4.7 96.4 1.0 N D:CYS67 4.9 96.8 1.0 CA D:CYS67 5.0 93.6 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