Calcium in PDB 3mxw: Crystal Structure Sonic Hedgehog Bound to the 5E1 Fab Fragment

The structure of Crystal Structure Sonic Hedgehog Bound to the 5E1 Fab Fragment, PDB code: 3mxw was solved by S.G.Hymowitz, H.R.Maun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.51 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.306, 90.544, 111.672, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.8

The structure of Crystal Structure Sonic Hedgehog Bound to the 5E1 Fab Fragment also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Crystal Structure Sonic Hedgehog Bound to the 5E1 Fab Fragment (pdb code 3mxw). 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 Sonic Hedgehog Bound to the 5E1 Fab Fragment, PDB code: 3mxw:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure Sonic Hedgehog Bound to the 5E1 Fab Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Sonic Hedgehog Bound to the 5E1 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:23.9 occ:1.00 OE2 A:GLU126 2.4 26.9 1.0 OE2 A:GLU89 2.4 26.9 1.0 OD2 A:ASP95 2.4 24.5 1.0 O A:THR125 2.4 23.6 1.0 OE2 A:GLU90 2.4 28.1 1.0 OE1 A:GLU89 2.4 26.4 1.0 OD1 A:ASP95 2.4 22.9 1.0 OE1 A:GLU90 2.4 25.1 1.0 CD A:GLU89 2.7 25.1 1.0 CD A:GLU90 2.7 24.9 1.0 CG A:ASP95 2.7 24.8 1.0 CD A:GLU126 3.5 30.3 1.0 C A:THR125 3.5 23.7 1.0 O A:HOH373 4.0 22.4 1.0 CA A:CA402 4.0 30.8 1.0 CA A:GLU126 4.1 24.5 1.0 CG A:GLU126 4.1 28.5 1.0 CG A:GLU89 4.2 23.3 1.0 CG A:GLU90 4.2 23.9 1.0 N A:GLU126 4.2 23.6 1.0 CB A:ASP95 4.3 25.4 1.0 O A:HOH5 4.3 21.6 1.0 N A:GLU89 4.5 23.0 1.0 OE1 A:GLU126 4.5 28.9 1.0 N A:ASP88 4.6 23.9 1.0 CB A:GLU126 4.7 23.8 1.0 CA A:THR125 4.7 23.1 1.0 CA A:ASP88 4.8 22.9 1.0 O A:HOH320 4.9 27.5 1.0 CB A:LYS87 5.0 21.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure Sonic Hedgehog Bound to the 5E1 Fab Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Sonic Hedgehog Bound to the 5E1 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:30.8 occ:1.00 O A:HOH373 2.3 22.4 1.0 OD1 A:ASP129 2.3 26.6 1.0 OD2 A:ASP131 2.3 37.6 1.0 OE2 A:GLU90 2.3 28.1 1.0 OE1 A:GLU126 2.4 28.9 1.0 OE2 A:GLU126 2.4 26.9 1.0 CD A:GLU126 2.7 30.3 1.0 O A:HOH228 3.2 29.1 1.0 CG A:ASP129 3.3 29.8 1.0 CG A:ASP131 3.5 37.5 1.0 CD A:GLU90 3.5 24.9 1.0 CB A:ASP131 3.9 35.0 1.0 CB A:ASP129 4.0 25.7 1.0 CA A:CA401 4.0 23.9 1.0 CG A:GLU90 4.1 23.9 1.0 CG A:GLU126 4.2 28.5 1.0 OD1 A:ASP95 4.2 22.9 1.0 OD2 A:ASP129 4.3 25.4 1.0 CA A:ASP129 4.3 25.6 1.0 OE2 A:GLU89 4.4 26.9 1.0 OE1 A:GLU90 4.5 25.1 1.0 OD1 A:ASP131 4.5 37.7 1.0 O A:HOH320 4.6 27.5 1.0 O A:TRP128 4.6 31.3 1.0 N A:ASP131 4.7 28.8 1.0 NE2 A:HIS134 4.8 22.9 1.0 ND1 A:HIS133 4.9 36.7 1.0 N A:GLU130 4.9 23.6 1.0 CA A:ASP131 5.0 32.7 1.0

H.R.Maun, X.Wen, A.Lingel, F.J.De Sauvage, R.A.Lazarus, S.J.Scales, S.G.Hymowitz. Hedgehog Pathway Antagonist 5E1 Binds Hedgehog at the Pseudo-Active Site. J.Biol.Chem. V. 285 26570 2010.
ISSN: ISSN 0021-9258
PubMed: 20504762
DOI: 10.1074/JBC.M110.112284