Magnesium in PDB 1pyd: Catalytic Centers in the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase at 2.4 Angstroms Resolution

All present enzymatic activity of Catalytic Centers in the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase at 2.4 Angstroms Resolution:
4.1.1.1;

The structure of Catalytic Centers in the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase at 2.4 Angstroms Resolution, PDB code: 1pyd was solved by W.Furey, F.Dyda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	141.950, 74.670, 119.950, 90.00, 116.39, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Catalytic Centers in the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase at 2.4 Angstroms Resolution (pdb code 1pyd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Catalytic Centers in the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase at 2.4 Angstroms Resolution, PDB code: 1pyd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Catalytic Centers in the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase at 2.4 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Catalytic Centers in the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase at 2.4 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg559 b:16.3 occ:1.00 O A:HOH560 2.0 4.0 1.0 OD1 A:ASP444 2.0 10.5 1.0 OD1 A:ASN471 2.0 7.9 1.0 O23 A:TDP557 2.2 5.7 1.0 O12 A:TDP557 2.2 5.8 1.0 O A:GLY473 2.2 5.7 1.0 CG A:ASP444 3.1 7.8 1.0 CG A:ASN471 3.1 8.0 1.0 P2 A:TDP557 3.3 4.7 1.0 P1 A:TDP557 3.4 5.2 1.0 C A:GLY473 3.4 5.1 1.0 ND2 A:ASN471 3.5 8.1 1.0 O11 A:TDP557 3.6 8.2 1.0 O21 A:TDP557 3.7 5.7 1.0 OD2 A:ASP444 3.8 7.7 1.0 N A:ASP444 3.9 6.6 1.0 O A:LEU469 3.9 8.3 1.0 N A:GLY445 4.1 3.3 1.0 CB A:ASP444 4.2 6.7 1.0 N A:TYR474 4.2 4.2 1.0 N A:THR475 4.3 3.2 1.0 N A:GLY473 4.3 6.6 1.0 O13 A:TDP557 4.4 9.9 1.0 CG2 A:THR475 4.4 5.4 1.0 CB A:ASN471 4.4 6.9 1.0 CA A:ASP444 4.5 7.2 1.0 CA A:GLY443 4.5 5.8 1.0 CA A:TYR474 4.5 3.6 1.0 O5G A:TDP557 4.5 8.2 1.0 CA A:GLY473 4.5 5.2 1.0 N A:ASN471 4.5 7.7 1.0 C A:GLY443 4.5 7.0 1.0 O22 A:TDP557 4.5 6.3 1.0 CA A:ASN471 4.8 7.5 1.0 C A:ASN471 4.8 7.7 1.0 C A:ASP444 4.8 5.9 1.0 N A:ASP472 4.9 8.1 1.0 C A:TYR474 4.9 2.4 1.0

Magnesium binding site 2 out of 2 in the Catalytic Centers in the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase at 2.4 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Catalytic Centers in the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase at 2.4 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg559 b:2.0 occ:1.00 OD1 B:ASN471 1.9 13.2 1.0 O B:GLY473 2.1 7.7 1.0 O23 B:TDP557 2.2 7.0 1.0 O B:HOH560 2.3 4.0 1.0 OD1 B:ASP444 2.3 2.0 1.0 O12 B:TDP557 2.4 5.6 1.0 CG B:ASN471 3.0 13.2 1.0 C B:GLY473 3.3 7.1 1.0 P2 B:TDP557 3.4 5.2 1.0 CG B:ASP444 3.5 3.4 1.0 ND2 B:ASN471 3.5 14.6 1.0 P1 B:TDP557 3.6 5.7 1.0 O11 B:TDP557 3.8 7.0 1.0 N B:GLY473 3.9 11.4 1.0 OD2 B:ASP444 4.0 2.0 1.0 O21 B:TDP557 4.0 9.3 1.0 N B:ASP444 4.2 2.5 1.0 N B:THR475 4.2 7.4 1.0 N B:TYR474 4.2 8.1 1.0 CA B:GLY473 4.2 8.2 1.0 O B:LEU469 4.2 6.8 1.0 N B:GLY445 4.3 2.3 1.0 CG2 B:THR475 4.3 8.4 1.0 CB B:ASN471 4.4 10.2 1.0 CA B:TYR474 4.4 7.4 1.0 N B:ASN471 4.4 8.9 1.0 O5G B:TDP557 4.6 6.0 1.0 C B:ASN471 4.7 8.1 1.0 O22 B:TDP557 4.7 7.3 1.0 CA B:ASN471 4.7 9.1 1.0 O13 B:TDP557 4.7 7.5 1.0 CB B:ASP444 4.8 2.0 1.0 CA B:GLY443 4.8 2.0 1.0 N B:ASP472 4.8 9.0 1.0 C B:TYR474 4.8 7.5 1.0 CA B:ASP444 4.8 4.2 1.0 C B:GLY443 4.9 3.3 1.0

F.Dyda, W.Furey, S.Swaminathan, M.Sax, B.Farrenkopf, F.Jordan. Catalytic Centers in the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase at 2.4-A Resolution. Biochemistry V. 32 6165 1993.
ISSN: ISSN 0006-2960
PubMed: 8512926
DOI: 10.1021/BI00075A008