Calcium in PDB 8z39: Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant L-T56A with Metals

The structure of Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant L-T56A with Metals, PDB code: 8z39 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)	48.65 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.519, 70.005, 119.974, 90, 109.24, 90
R / Rfree (%)	18 / 20.8

The structure of Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant L-T56A 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 L-T56A with Metals (pdb code 8z39). 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 L-T56A with Metals, PDB code: 8z39:
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 L-T56A 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 L-T56A with Metals within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:22.0 occ:1.00 O A:THR125 2.3 20.8 1.0 OE2 A:GLU126 2.3 27.8 1.0 OE2 A:GLU89 2.4 24.0 1.0 OE1 A:GLU89 2.4 24.3 1.0 OD2 A:ASP95 2.5 21.5 1.0 OE2 A:GLU90 2.5 30.0 1.0 OD1 A:ASP95 2.6 21.9 1.0 OE1 A:GLU90 2.6 29.2 1.0 CD A:GLU89 2.7 24.3 1.0 CG A:ASP95 2.8 22.2 1.0 CD A:GLU90 2.9 29.7 1.0 CD A:GLU126 3.5 26.5 1.0 C A:THR125 3.5 20.1 1.0 O A:HOH512 4.0 26.5 1.0 CA A:GLU126 4.1 21.2 1.0 CA A:CA402 4.1 32.5 1.0 CG A:GLU126 4.1 24.7 1.0 N A:GLU126 4.2 20.1 1.0 CG A:GLU89 4.2 26.4 1.0 O A:HOH534 4.2 42.5 0.5 CB A:ASP95 4.4 21.6 1.0 OE1 A:GLU126 4.4 31.5 1.0 CG A:GLU90 4.4 32.5 1.0 N A:ASP88 4.4 22.7 1.0 O A:HOH573 4.4 38.8 1.0 N A:GLU89 4.5 26.1 1.0 O A:HOH516 4.5 25.4 1.0 CA A:THR125 4.6 19.6 1.0 CA A:ASP88 4.7 24.8 1.0 CB A:GLU126 4.7 22.9 1.0 O A:HOH552 4.8 40.9 1.0 CB A:LYS87 4.9 20.3 1.0 N A:GLU90 5.0 30.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant L-T56A 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 L-T56A with Metals within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:32.5 occ:1.00 OD1 A:ASP129 2.3 34.7 1.0 OE2 A:GLU90 2.3 30.0 1.0 O A:HOH573 2.4 38.8 1.0 O A:HOH512 2.5 26.5 1.0 OE1 A:GLU126 2.5 31.5 1.0 OD2 A:ASP131 2.5 41.9 1.0 OE2 A:GLU126 2.7 27.8 1.0 CD A:GLU126 2.9 26.5 1.0 O A:HOH585 3.2 37.9 1.0 CG A:ASP129 3.3 34.6 1.0 CD A:GLU90 3.4 29.7 1.0 CG A:ASP131 3.7 43.9 1.0 CB A:ASP129 3.9 32.6 1.0 CG A:GLU90 3.9 32.5 1.0 CA A:CA401 4.1 22.0 1.0 CA A:ASP129 4.2 33.1 1.0 CB A:ASP131 4.3 44.4 1.0 OD2 A:ASP129 4.3 35.3 1.0 O A:HOH552 4.4 40.9 1.0 OD1 A:ASP95 4.4 21.9 1.0 OE2 A:GLU89 4.5 24.0 1.0 CG A:GLU126 4.5 24.7 1.0 OE1 A:GLU90 4.5 29.2 1.0 O A:TRP128 4.6 30.4 1.0 OD1 A:ASP131 4.7 43.8 1.0 O A:HOH534 4.8 30.7 0.5 N A:ASP131 4.8 43.6 1.0 N A:GLU130 4.8 38.7 1.0 O A:HOH534 4.9 42.5 0.5 CB A:HIS133 5.0 39.7 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.