Magnesium in PDB 4k9q: The Crystal Structure of Benzoylformate Decarboxylase From Polynucleobacter Necessarius

All present enzymatic activity of The Crystal Structure of Benzoylformate Decarboxylase From Polynucleobacter Necessarius:
4.1.1.7;

The structure of The Crystal Structure of Benzoylformate Decarboxylase From Polynucleobacter Necessarius, PDB code: 4k9q was solved by H.R.Brodkin, W.R.P.Novak, M.J.Mcleish, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.82 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.737, 104.953, 158.731, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 18.9

The binding sites of Magnesium atom in the The Crystal Structure of Benzoylformate Decarboxylase From Polynucleobacter Necessarius (pdb code 4k9q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Crystal Structure of Benzoylformate Decarboxylase From Polynucleobacter Necessarius, PDB code: 4k9q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Crystal Structure of Benzoylformate Decarboxylase From Polynucleobacter Necessarius


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Benzoylformate Decarboxylase From Polynucleobacter Necessarius within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:10.3 occ:1.00 O2A A:TPP602 2.2 14.5 1.0 OD1 A:ASN456 2.2 11.8 1.0 OD1 A:ASP429 2.2 13.1 1.0 O3B A:TPP602 2.2 12.2 1.0 O A:GLU458 2.3 10.8 1.0 O A:HOH753 2.3 13.8 1.0 CG A:ASN456 3.2 14.6 1.0 PA A:TPP602 3.3 14.8 1.0 PB A:TPP602 3.3 14.5 1.0 CG A:ASP429 3.4 14.3 1.0 C A:GLU458 3.5 11.8 1.0 O3A A:TPP602 3.5 13.6 1.0 ND2 A:ASN456 3.5 12.0 1.0 N A:ASP429 4.0 10.4 1.0 OD2 A:ASP429 4.0 16.8 1.0 O2B A:TPP602 4.0 18.6 1.0 N A:GLU458 4.0 12.7 1.0 N A:GLY460 4.1 13.4 1.0 N A:GLY430 4.1 11.2 1.0 O7 A:TPP602 4.2 16.4 1.0 O A:PHE454 4.3 12.3 1.0 CA A:GLU458 4.4 9.3 1.0 N A:ASN456 4.4 11.3 1.0 N A:TYR459 4.4 11.2 1.0 O1A A:TPP602 4.4 14.0 1.0 CA A:TYR459 4.5 11.9 1.0 CB A:ASN456 4.5 12.2 1.0 CG A:GLU458 4.5 15.5 1.0 O1B A:TPP602 4.5 17.4 1.0 CB A:ASP429 4.6 12.0 1.0 CA A:ASP429 4.6 10.4 1.0 N A:GLU457 4.8 9.8 1.0 C A:GLY428 4.8 10.4 1.0 CA A:GLY428 4.8 10.6 1.0 CA A:ASN456 4.8 11.8 1.0 C A:TYR459 4.9 12.4 1.0 C A:ASN456 4.9 13.6 1.0 C A:ASP429 4.9 11.2 1.0

Magnesium binding site 2 out of 2 in the The Crystal Structure of Benzoylformate Decarboxylase From Polynucleobacter Necessarius


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Benzoylformate Decarboxylase From Polynucleobacter Necessarius within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:14.3 occ:1.00 O1A B:TPP602 2.2 18.0 1.0 O1B B:TPP602 2.2 17.3 1.0 OD1 B:ASN456 2.2 13.5 1.0 OD1 B:ASP429 2.3 17.0 1.0 O B:GLU458 2.3 14.2 1.0 O B:HOH1182 2.4 18.0 1.0 CG B:ASN456 3.2 19.1 1.0 PA B:TPP602 3.3 15.1 0.8 PB B:TPP602 3.3 18.8 1.0 CG B:ASP429 3.4 16.6 1.0 ND2 B:ASN456 3.5 16.5 1.0 C B:GLU458 3.5 18.7 1.0 O3A B:TPP602 3.5 18.1 1.0 OD2 B:ASP429 4.0 21.0 1.0 N B:ASP429 4.0 13.6 1.0 O2B B:TPP602 4.0 23.6 1.0 N B:GLU458 4.1 15.2 1.0 N B:GLY460 4.1 15.3 1.0 O7 B:TPP602 4.1 19.7 1.0 N B:GLY430 4.2 14.7 1.0 O B:PHE454 4.3 17.7 1.0 CA B:GLU458 4.4 16.2 1.0 N B:TYR459 4.4 15.3 1.0 O2A B:TPP602 4.4 14.6 0.8 CA B:TYR459 4.5 14.3 1.0 N B:ASN456 4.5 14.7 1.0 CG B:GLU458 4.5 17.1 1.0 O3B B:TPP602 4.5 24.1 1.0 CB B:ASN456 4.6 16.0 1.0 CB B:ASP429 4.6 16.5 1.0 CA B:ASP429 4.7 12.7 1.0 CA B:GLY428 4.7 15.3 1.0 C B:GLY428 4.8 15.3 1.0 N B:GLU457 4.8 13.3 1.0 C B:TYR459 4.8 16.6 1.0 CA B:ASN456 4.9 11.8 1.0 C B:ASN456 4.9 14.2 1.0 CA B:GLY460 5.0 17.3 1.0 C B:ASP429 5.0 15.8 1.0

H.R.Brodkin, F.H.Andrews, W.R.P.Novak, G.A.Petsko, D.Ringe, M.J.Mcleish. The Crystal Structure of Benzoylformate Decarboxylase From Polynucleobacter Necessarius To Be Published.