Magnesium in PDB 6pjv: Structure of Human Sonic Hedgehog in Complex with Zinc and Magnesium

The structure of Structure of Human Sonic Hedgehog in Complex with Zinc and Magnesium, PDB code: 6pjv was solved by R.B.Bonn-Breach, J.L.Jenkins, J.E.Wedekind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.50 / 1.43
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	118.728, 118.728, 118.728, 90.00, 90.00, 90.00
R / Rfree (%)	12.4 / 13.9

The structure of Structure of Human Sonic Hedgehog in Complex with Zinc and Magnesium also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Structure of Human Sonic Hedgehog in Complex with Zinc and Magnesium (pdb code 6pjv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Human Sonic Hedgehog in Complex with Zinc and Magnesium, PDB code: 6pjv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Human Sonic Hedgehog in Complex with Zinc and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Sonic Hedgehog in Complex with Zinc and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:15.2 occ:1.00 O A:HOH307 2.0 16.2 1.0 OE1 A:GLU126 2.0 15.1 1.0 O A:HOH315 2.0 16.2 1.0 OE2 A:GLU90 2.1 15.4 1.0 O A:HOH309 2.1 14.9 1.0 O A:HOH386 2.1 16.9 1.0 CD A:GLU126 3.0 15.0 1.0 CD A:GLU90 3.1 16.2 1.0 O A:HOH363 3.3 15.6 0.4 OE1 A:GLU90 3.4 16.6 1.0 OE2 A:GLU126 3.4 16.4 1.0 HA A:GLU126 3.9 15.6 1.0 OD1 A:ASP95 4.0 15.5 1.0 O A:HOH325 4.1 16.3 1.0 HG2 A:GLU89 4.1 28.4 1.0 OD2 A:ASP95 4.2 15.6 1.0 O A:HOH484 4.2 34.4 1.0 O A:HOH363 4.3 24.1 0.6 O A:HOH419 4.4 17.0 1.0 CG A:GLU90 4.4 17.3 1.0 CG A:GLU126 4.4 14.0 1.0 H A:GLY127 4.5 15.4 1.0 HA A:ASP129 4.5 15.4 1.0 HG2 A:GLU90 4.5 20.7 1.0 CG A:ASP95 4.5 14.9 1.0 OD1 A:ASP129 4.5 14.3 1.0 OE2 A:GLU89 4.5 25.3 1.0 HD2 A:HIS133 4.6 19.0 1.0 HB2 A:GLU126 4.6 16.0 1.0 O A:HOH438 4.7 20.7 1.0 HG3 A:GLU90 4.7 20.7 1.0 O A:THR125 4.7 14.3 1.0 CA A:GLU126 4.7 13.0 1.0 HG3 A:GLU126 4.8 16.8 1.0 CB A:GLU126 4.8 13.4 1.0 HB2 A:ASP129 4.8 16.6 1.0 CG A:GLU89 4.9 23.7 1.0 HE2 A:HIS133 4.9 19.3 1.0 HG3 A:GLU89 4.9 28.4 1.0

Magnesium binding site 2 out of 2 in the Structure of Human Sonic Hedgehog in Complex with Zinc and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Sonic Hedgehog in Complex with Zinc and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg207 b:12.1 occ:0.20 ZN A:ZN206 0.0 16.9 0.4 O A:HOH313 2.1 13.0 1.0 OD1 A:ASP147 2.1 11.6 1.0 OE1 A:GLU176 2.2 12.3 1.0 O A:HOH319 2.2 12.8 1.0 NE2 A:HIS140 2.3 12.7 1.0 ND1 A:HIS182 2.3 11.9 1.0 CG A:ASP147 3.1 11.4 1.0 CE1 A:HIS182 3.1 12.8 1.0 HB2 A:HIS182 3.1 14.4 1.0 CD A:GLU176 3.2 13.6 1.0 HE1 A:HIS182 3.2 15.4 1.0 CE1 A:HIS140 3.2 12.5 1.0 CD2 A:HIS140 3.3 12.9 1.0 HE1 A:HIS140 3.3 14.9 1.0 CG A:HIS182 3.3 12.0 1.0 HE2 A:HIS180 3.3 15.3 1.0 OD2 A:ASP147 3.4 13.1 1.0 HD2 A:HIS140 3.4 15.5 1.0 OE2 A:GLU176 3.4 14.9 1.0 CB A:HIS182 3.7 12.0 1.0 NE2 A:HIS180 4.1 12.8 1.0 HE1 A:HIS134 4.1 18.2 1.0 O A:HOH489 4.2 27.1 1.0 NE2 A:HIS182 4.3 12.3 1.0 HA A:HIS182 4.3 13.9 1.0 ND1 A:HIS140 4.3 12.7 1.0 O A:HOH332 4.3 23.2 1.0 CG A:HIS140 4.4 12.3 1.0 CD2 A:HIS182 4.4 12.9 1.0 HB3 A:HIS182 4.5 14.4 1.0 CB A:ASP147 4.5 12.2 1.0 HD2 A:HIS180 4.5 15.5 1.0 CG A:GLU176 4.5 13.0 1.0 H21 A:DMS202 4.6 88.0 1.0 HA A:ASP147 4.6 14.1 1.0 CA A:HIS182 4.6 11.6 1.0 CD2 A:HIS180 4.7 12.9 1.0 HG2 A:GLU176 4.7 15.6 1.0 CE1 A:HIS134 4.7 15.2 1.0 HB1 A:ALA145 4.8 15.3 1.0 O A:HOH361 4.8 18.0 1.0 HD1 A:HIS134 4.9 19.4 1.0 HG2 A:GLU126 4.9 16.8 1.0 HB3 A:GLU176 4.9 15.5 1.0 CA A:ASP147 4.9 11.8 1.0 HB3 A:ASP147 4.9 14.6 1.0 N A:ASP147 4.9 11.4 1.0 HB2 A:GLU176 5.0 15.5 1.0

R.Bonn-Breach, Y.Gu, J.Jenkins, R.Fasan, J.Wedekind. Structure of Sonic Hedgehog Protein in Complex with Zinc(II) and Magnesium(II) Reveals Ion-Coordination Plasticity Relevant to Peptide Drug Design. Acta Crystallogr D Struct V. 75 969 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 31692471
DOI: 10.1107/S2059798319012890