Magnesium in PDB 6a50: Structure of Benzoylformate Decarboxylases in Complex with Cofactor Tpp

All present enzymatic activity of Structure of Benzoylformate Decarboxylases in Complex with Cofactor Tpp:
4.1.1.7;

The structure of Structure of Benzoylformate Decarboxylases in Complex with Cofactor Tpp, PDB code: 6a50 was solved by Y.Guo, S.Wang, Y.Nie, S.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.59 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.889, 124.392, 97.758, 90.00, 122.35, 90.00
R / Rfree (%)	15.9 / 17.7

The binding sites of Magnesium atom in the Structure of Benzoylformate Decarboxylases in Complex with Cofactor Tpp (pdb code 6a50). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Benzoylformate Decarboxylases in Complex with Cofactor Tpp, PDB code: 6a50:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of Benzoylformate Decarboxylases in Complex with Cofactor Tpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Benzoylformate Decarboxylases in Complex with Cofactor Tpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:13.8 occ:1.00 O2A A:TPP602 2.0 24.4 1.0 O A:THR457 2.2 21.6 1.0 OD1 A:ASN455 2.2 21.4 1.0 O A:HOH786 2.2 23.7 1.0 O3B A:TPP602 2.2 24.4 1.0 OD1 A:ASP428 2.2 19.5 1.0 CG A:ASN455 3.2 21.6 1.0 PA A:TPP602 3.2 24.5 1.0 CG A:ASP428 3.3 19.4 1.0 C A:THR457 3.4 21.7 1.0 PB A:TPP602 3.4 24.8 1.0 O3A A:TPP602 3.5 24.5 1.0 ND2 A:ASN455 3.6 21.9 1.0 OD2 A:ASP428 3.9 19.8 1.0 N A:THR457 4.0 21.2 1.0 O7 A:TPP602 4.0 25.2 1.0 N A:ASP428 4.1 18.3 1.0 N A:GLY459 4.2 22.9 1.0 CA A:THR457 4.3 21.4 1.0 N A:GLY429 4.3 18.0 1.0 O A:MET453 4.3 19.7 1.0 O1B A:TPP602 4.3 25.0 1.0 N A:TYR458 4.4 21.7 1.0 O1A A:TPP602 4.4 24.5 1.0 N A:ASN455 4.4 20.9 1.0 CB A:ASN455 4.5 21.6 1.0 O2B A:TPP602 4.5 24.8 1.0 CA A:TYR458 4.5 21.9 1.0 CB A:ASP428 4.6 19.0 1.0 O A:HOH714 4.6 24.0 1.0 N A:GLY456 4.7 21.2 1.0 CA A:GLY427 4.7 17.9 1.0 CA A:ASP428 4.7 18.5 1.0 CA A:ASN455 4.8 21.3 1.0 C A:GLY427 4.8 18.1 1.0 CG2 A:THR457 4.8 21.4 1.0 C A:ASN455 4.8 21.5 1.0 C A:TYR458 4.9 22.3 1.0

Magnesium binding site 2 out of 3 in the Structure of Benzoylformate Decarboxylases in Complex with Cofactor Tpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Benzoylformate Decarboxylases in Complex with Cofactor Tpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:10.3 occ:1.00 O A:ARG120 2.4 13.0 1.0 O B:ARG120 2.4 13.1 1.0 O A:LEU118 2.5 12.1 1.0 O B:LEU118 2.5 12.0 1.0 O A:ASN117 2.7 12.1 1.0 O B:ASN117 2.7 12.1 1.0 C A:LEU118 3.3 12.1 1.0 C B:LEU118 3.3 12.0 1.0 O B:HOH1033 3.4 16.4 1.0 C A:ARG120 3.5 13.1 1.0 C B:ARG120 3.6 13.3 1.0 C A:ASN117 3.8 12.3 1.0 CA A:LEU118 3.8 12.0 1.0 CA B:LEU118 3.8 12.0 1.0 C B:ASN117 3.8 12.3 1.0 N A:ARG120 3.9 13.0 1.0 N B:ARG120 3.9 13.2 1.0 CA A:ARG120 4.2 13.4 1.0 CA B:ARG120 4.2 13.6 1.0 N A:PRO119 4.3 12.3 1.0 N A:LEU118 4.3 12.0 1.0 C A:PRO119 4.3 12.8 1.0 N B:PRO119 4.3 12.3 1.0 N B:LEU118 4.3 11.9 1.0 C B:PRO119 4.3 12.9 1.0 CB A:ARG120 4.5 14.1 1.0 CB B:ARG120 4.5 14.3 1.0 CE A:MET79 4.5 12.7 0.5 CE B:MET79 4.6 12.9 0.6 CA A:PRO119 4.6 12.6 1.0 N A:PRO121 4.6 13.1 1.0 N B:PRO121 4.7 13.3 1.0 CA B:PRO119 4.7 12.6 1.0 CD B:PRO121 4.9 13.4 1.0 CD A:PRO121 4.9 13.2 1.0 CE A:MET79 4.9 12.6 0.5 CE B:MET79 4.9 12.2 0.4 O A:PRO119 5.0 12.9 1.0

Magnesium binding site 3 out of 3 in the Structure of Benzoylformate Decarboxylases in Complex with Cofactor Tpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Benzoylformate Decarboxylases in Complex with Cofactor Tpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:14.1 occ:1.00 O2A B:TPP602 2.0 24.1 1.0 O B:HOH772 2.1 23.2 1.0 OD1 B:ASN455 2.2 21.5 1.0 O B:THR457 2.2 21.0 1.0 O2B B:TPP602 2.2 24.0 1.0 OD1 B:ASP428 2.2 19.3 1.0 CG B:ASN455 3.2 21.7 1.0 PA B:TPP602 3.2 24.1 1.0 CG B:ASP428 3.3 19.2 1.0 PB B:TPP602 3.4 24.2 1.0 C B:THR457 3.4 21.0 1.0 O3A B:TPP602 3.5 24.1 1.0 ND2 B:ASN455 3.6 22.0 1.0 OD2 B:ASP428 3.9 19.6 1.0 N B:THR457 4.0 20.7 1.0 N B:ASP428 4.0 18.1 1.0 O7 B:TPP602 4.0 24.8 1.0 N B:GLY459 4.2 22.1 1.0 N B:GLY429 4.3 17.8 1.0 O B:MET453 4.3 19.7 1.0 O3B B:TPP602 4.3 24.5 1.0 CA B:THR457 4.3 20.8 1.0 N B:TYR458 4.4 21.0 1.0 N B:ASN455 4.4 20.8 1.0 O1A B:TPP602 4.4 24.0 1.0 CB B:ASN455 4.5 21.5 1.0 O1B B:TPP602 4.5 24.1 1.0 O B:HOH712 4.5 24.2 1.0 CB B:ASP428 4.5 18.8 1.0 CA B:TYR458 4.6 21.3 1.0 CA B:GLY427 4.7 17.7 1.0 N B:GLY456 4.7 21.0 1.0 CA B:ASP428 4.7 18.4 1.0 CG2 B:THR457 4.7 20.8 1.0 CA B:ASN455 4.8 21.3 1.0 C B:GLY427 4.8 17.9 1.0 C B:ASN455 4.8 21.2 1.0 C B:TYR458 4.9 21.7 1.0

X.Lu, Y.Liu, Y.Yang, S.Wang, Q.Wang, X.Wang, Z.Yan, J.Cheng, C.Liu, X.Yang, H.Luo, S.Yang, J.Gou, L.Ye, L.Lu, Z.Zhang, Y.Guo, Y.Nie, J.Lin, S.Li, T.Cai, H.Ma, W.Wang, Y.Liu, Y.Li, H.Jiang, C.Tian. A Synthetic Pathway For Acetyl-Coenzyme A Biosynthesis Nat Commun 2019.
ISSN: ESSN 2041-1723