Magnesium in PDB 4ak5: Native Crystal Structure of BPGH117

The structure of Native Crystal Structure of BPGH117, PDB code: 4ak5 was solved by J.H.Hehemann, L.Smyth, A.Yadav, D.J.Vocadlo, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	105.54 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.990, 93.000, 105.540, 90.00, 90.00, 90.00
R / Rfree (%)	17.372 / 20.653

The structure of Native Crystal Structure of BPGH117 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Native Crystal Structure of BPGH117 (pdb code 4ak5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Native Crystal Structure of BPGH117, PDB code: 4ak5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Native Crystal Structure of BPGH117


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Native Crystal Structure of BPGH117 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1405 b:15.4 occ:1.00 O A:HOH2089 2.1 13.7 1.0 O A:HOH2085 2.1 13.9 1.0 O A:HOH2086 2.1 14.1 1.0 O A:HOH2293 2.1 15.9 1.0 O A:HOH2087 2.2 15.0 1.0 O A:HOH2371 2.2 13.1 1.0 O A:PRO91 3.7 12.3 1.0 O A:HOH2178 3.9 14.9 1.0 O A:ILE349 4.1 15.1 1.0 O A:ALA348 4.1 17.1 1.0 O A:HOH2175 4.2 12.2 1.0 OE2 A:GLU167 4.3 13.7 1.0 OD1 A:ASP245 4.4 17.5 1.0 O A:PRO166 4.4 13.5 1.0 O A:ASP90 4.4 12.3 1.0 C A:ALA348 4.4 16.2 1.0 OD1 A:ASP90 4.4 17.3 1.0 C A:ASP90 4.5 11.9 1.0 CA A:ALA348 4.5 12.8 1.0 CG2 A:THR165 4.6 14.6 1.0 C A:PRO91 4.6 11.1 1.0 O A:VAL304 4.6 13.9 1.0 CB A:ALA348 4.6 13.1 1.0 CA A:ASP90 4.7 12.9 1.0 CB A:ASP90 4.7 11.7 1.0 CG A:GLU167 4.8 14.0 1.0 CD A:GLU167 4.9 12.3 1.0 C A:ILE349 4.9 16.4 1.0

Magnesium binding site 2 out of 2 in the Native Crystal Structure of BPGH117


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Native Crystal Structure of BPGH117 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1405 b:13.7 occ:1.00 O B:HOH2302 2.0 14.5 1.0 O B:HOH2071 2.1 15.5 1.0 O B:HOH2069 2.1 15.3 1.0 O B:HOH2073 2.1 13.2 1.0 O B:HOH2070 2.1 12.5 1.0 O B:HOH2240 2.2 16.2 1.0 O B:PRO91 3.7 12.0 1.0 O B:HOH2146 4.0 14.7 1.0 O B:HOH2143 4.2 13.5 1.0 O B:ALA348 4.2 13.4 1.0 O B:ILE349 4.2 12.6 1.0 OD1 B:ASP245 4.3 18.3 1.0 OD1 B:ASP90 4.3 14.8 1.0 OE2 B:GLU167 4.4 11.8 1.0 O B:ASP90 4.4 12.1 1.0 O B:PRO166 4.4 12.9 1.0 C B:ALA348 4.5 11.6 1.0 C B:ASP90 4.5 11.9 1.0 CG2 B:THR165 4.5 11.5 1.0 CA B:ALA348 4.6 13.1 1.0 CB B:ASP90 4.6 12.7 1.0 C B:PRO91 4.6 11.3 1.0 CA B:ASP90 4.7 12.1 1.0 O B:VAL304 4.7 14.1 1.0 CB B:ALA348 4.7 12.2 1.0 CG B:GLU167 4.7 10.7 1.0 CD B:GLU167 4.9 10.8 1.0 C B:ILE349 5.0 13.4 1.0

J.H.Hehemann, L.Smyth, A.Yadav, D.J.Vocadlo, A.B.Boraston. Analysis of Keystone Enzyme in Agar Hydrolysis Provides Insight Into the Degradation (of A Polysaccharide From) Red Seaweeds. J.Biol.Chem. V. 287 13985 2012.
ISSN: ISSN 0021-9258
PubMed: 22393053
DOI: 10.1074/JBC.M112.345645