Calcium in PDB 7ona: Crystal Structure of the Computationally Designed SAKE6AC Protein

The structure of Crystal Structure of the Computationally Designed SAKE6AC Protein, PDB code: 7ona was solved by S.M.L.Wouters, H.Noguchi, G.Velpula, D.E.Clarke, A.R.D.Voet, S.De Feyter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.77 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.38, 74.873, 46.938, 90, 122.08, 90
R / Rfree (%)	17 / 18.5

The binding sites of Calcium atom in the Crystal Structure of the Computationally Designed SAKE6AC Protein (pdb code 7ona). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Computationally Designed SAKE6AC Protein, PDB code: 7ona:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Computationally Designed SAKE6AC Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Computationally Designed SAKE6AC Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:20.0 occ:0.41 O A:HOH691 2.3 26.1 0.5 OE2 A:GLU33 2.4 23.4 1.0 O A:HOH609 2.5 20.4 1.0 O A:HOH569 2.5 24.2 1.0 CD A:GLU33 3.3 23.9 1.0 OE1 A:GLU33 4.0 27.0 1.0 CG A:GLU33 4.0 23.2 1.0 NH1 A:ARG7 4.1 20.1 1.0 OD1 A:ASP31 4.6 19.9 1.0 OD2 A:ASP31 4.8 21.4 1.0 CB A:GLU33 4.9 21.7 1.0 O A:HOH578 5.0 20.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Computationally Designed SAKE6AC Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Computationally Designed SAKE6AC Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:20.0 occ:0.42 O A:HOH692 2.3 25.2 0.5 OE2 A:GLU186 2.4 24.3 1.0 O A:HOH605 2.4 20.4 1.0 O A:HOH577 2.6 22.0 1.0 CD A:GLU186 3.3 24.1 1.0 CG A:GLU186 4.0 23.3 1.0 NH1 A:ARG160 4.0 19.4 1.0 OE1 A:GLU186 4.2 26.9 1.0 O A:HOH548 4.2 31.7 1.0 OD1 A:ASP184 4.6 19.2 1.0 O A:HOH585 4.9 19.2 1.0 OD2 A:ASP184 4.9 19.6 1.0 CB A:GLU186 4.9 21.2 1.0 O A:GLY159 4.9 16.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Computationally Designed SAKE6AC Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Computationally Designed SAKE6AC Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:21.9 occ:0.74 OE2 A:GLU84 2.2 28.7 1.0 O A:HOH677 2.4 40.4 1.0 O A:HOH689 2.4 24.6 1.0 O A:HOH571 2.5 22.7 1.0 CD A:GLU84 3.2 28.1 1.0 CG A:GLU84 4.0 26.0 1.0 OE1 A:GLU84 4.0 30.2 1.0 NH1 A:ARG58 4.1 24.1 1.0 O A:HOH539 4.1 31.4 1.0 OD1 A:ASP82 4.5 23.3 1.0 OD2 A:ASP82 4.7 24.3 1.0 CB A:GLU84 4.7 23.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Computationally Designed SAKE6AC Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Computationally Designed SAKE6AC Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:21.9 occ:0.76 OE2 A:GLU135 2.4 28.3 1.0 O A:HOH599 2.4 27.4 1.0 O A:HOH641 2.4 23.9 1.0 O A:HOH693 2.5 25.3 1.0 CD A:GLU135 3.3 28.9 1.0 CG A:GLU135 4.0 28.9 1.0 NH1 A:ARG109 4.1 23.0 1.0 OE1 A:GLU135 4.1 30.2 1.0 OD1 A:ASP133 4.6 24.9 1.0 OD2 A:ASP133 4.9 27.1 1.0 CB A:GLU135 4.9 27.4 1.0 O A:HOH598 5.0 22.1 1.0

S.M.L.Wouters, D.E.Clarke, H.Noguchi, G.Velpula, A.R.D.Voet, S.De Feyter. Sake: Computationally Designed Modular Protein Building Blocks For Macromolecular Assemblies To Be Published.