Calcium in PDB 8z2v: Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A with Metals

The structure of Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A with Metals, PDB code: 8z2v was solved by J.M.M.Caaveiro, I.Kaneda, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.48 / 1.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.641, 69.752, 119.27, 90, 108.73, 90
R / Rfree (%)	18.6 / 22.5

The structure of Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A with Metals also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A with Metals (pdb code 8z2v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A with Metals, PDB code: 8z2v:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A with Metals


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 Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A with Metals within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:23.5 occ:1.00 O A:THR125 2.3 20.3 1.0 OE2 A:GLU126 2.4 24.6 1.0 OE2 A:GLU89 2.4 22.2 1.0 OE2 A:GLU90 2.4 23.6 1.0 OE1 A:GLU89 2.4 21.6 1.0 OD1 A:ASP95 2.5 22.3 1.0 OD2 A:ASP95 2.5 21.4 1.0 OE1 A:GLU90 2.6 22.8 1.0 CD A:GLU89 2.7 22.0 1.0 CD A:GLU90 2.9 23.8 1.0 CG A:ASP95 2.9 22.6 1.0 CD A:GLU126 3.5 24.9 1.0 C A:THR125 3.5 20.4 1.0 CA A:CA204 4.0 31.0 1.0 O A:HOH304 4.0 25.5 1.0 CG A:GLU126 4.1 23.4 1.0 CA A:GLU126 4.1 22.7 1.0 CG A:GLU89 4.2 22.6 1.0 O A:HOH302 4.2 40.2 1.0 O A:HOH355 4.2 41.5 1.0 N A:GLU126 4.2 21.2 1.0 CG A:GLU90 4.3 25.2 1.0 O A:HOH322 4.4 24.0 1.0 CB A:ASP95 4.4 22.6 1.0 N A:ASP88 4.5 22.1 1.0 N A:GLU89 4.5 22.7 1.0 OE1 A:GLU126 4.5 27.7 1.0 CA A:THR125 4.6 20.3 1.0 CA A:ASP88 4.7 23.7 1.0 CB A:GLU126 4.7 23.1 1.0 O A:HOH353 4.8 34.8 1.0 CB A:LYS87 5.0 20.5 1.0 N A:GLU90 5.0 24.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A with Metals


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 Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A with Metals within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:31.0 occ:1.00 OD1 A:ASP129 2.2 30.4 1.0 OD2 A:ASP131 2.3 36.8 1.0 OE2 A:GLU90 2.3 23.6 1.0 OE2 A:GLU126 2.4 24.6 1.0 OE1 A:GLU126 2.4 27.7 1.0 O A:HOH353 2.5 34.8 1.0 O A:HOH304 2.6 25.5 1.0 CD A:GLU126 2.8 24.9 1.0 O A:HOH334 3.1 32.3 1.0 CG A:ASP129 3.3 31.4 1.0 CD A:GLU90 3.4 23.8 1.0 CG A:ASP131 3.5 38.0 1.0 CB A:ASP129 3.9 30.8 1.0 CA A:CA203 4.0 23.5 1.0 CG A:GLU90 4.0 25.2 1.0 O A:HOH302 4.0 40.2 1.0 CB A:ASP131 4.1 38.1 1.0 OD1 A:ASP95 4.3 22.3 1.0 CA A:ASP129 4.3 30.7 1.0 CG A:GLU126 4.3 23.4 1.0 OD2 A:ASP129 4.3 31.6 1.0 OE2 A:GLU89 4.4 22.2 1.0 O A:HOH367 4.4 46.0 1.0 OE1 A:GLU90 4.5 22.8 1.0 OD1 A:ASP131 4.6 38.9 1.0 O A:TRP128 4.7 28.6 1.0 N A:ASP131 4.8 37.8 1.0 N A:GLU130 5.0 33.8 1.0

I.Kaneda, R.Matsunaga, S.Nagatoishi, A.Senoo, J.M.M.Caaveiro, D.Kuroda, K.Tsumoto. Biophysical Insights to Improve Affinity of Antibodies to Fluctuated Epitope of Antigen: A Case of Anti-Shh Antibody 5E1 Against Shh Antigen. To Be Published.