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Magnesium in PDB 1pvd: Crystal Structure of the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase From the Yeast Saccharomyces Cerevisiae at 2.3 Angstroms Resolution

Enzymatic activity of Crystal Structure of the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase From the Yeast Saccharomyces Cerevisiae at 2.3 Angstroms Resolution

All present enzymatic activity of Crystal Structure of the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase From the Yeast Saccharomyces Cerevisiae at 2.3 Angstroms Resolution:
4.1.1.1;

Protein crystallography data

The structure of Crystal Structure of the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase From the Yeast Saccharomyces Cerevisiae at 2.3 Angstroms Resolution, PDB code: 1pvd was solved by W.Furey, P.Arjunan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.060, 74.750, 120.320, 90.00, 116.58, 90.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase From the Yeast Saccharomyces Cerevisiae at 2.3 Angstroms Resolution (pdb code 1pvd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase From the Yeast Saccharomyces Cerevisiae at 2.3 Angstroms Resolution, PDB code: 1pvd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1pvd

Go back to Magnesium Binding Sites List in 1pvd
Magnesium binding site 1 out of 2 in the Crystal Structure of the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase From the Yeast Saccharomyces Cerevisiae at 2.3 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase From the Yeast Saccharomyces Cerevisiae at 2.3 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg558

b:19.6
occ:1.00
 OD1 A:ASN471 2.1 10.0 1.0
O A:GLY473 2.2 10.6 1.0
O A:HOH559 2.2 12.1 1.0
OD1 A:ASP444 2.3 11.3 1.0
O1A A:TPP557 2.3 8.7 1.0
O3B A:TPP557 2.3 9.1 1.0
CG A:ASN471 3.2 11.8 1.0
CG A:ASP444 3.3 7.4 1.0
C A:GLY473 3.4 8.7 1.0
PB A:TPP557 3.4 7.9 1.0
PA A:TPP557 3.5 6.7 1.0
ND2 A:ASN471 3.5 11.6 1.0
O3A A:TPP557 3.6 8.2 1.0
OD2 A:ASP444 3.6 7.0 1.0
O1B A:TPP557 4.0 6.6 1.0
O A:LEU469 4.0 10.9 1.0
N A:GLY473 4.1 10.0 1.0
N A:ASP444 4.2 5.3 1.0
N A:THR475 4.2 13.2 1.0
N A:GLY445 4.2 9.3 1.0
CG2 A:THR475 4.2 15.8 1.0
N A:TYR474 4.2 11.1 1.0
CA A:GLY473 4.3 8.0 1.0
CA A:TYR474 4.4 11.2 1.0
O7 A:TPP557 4.5 5.8 1.0
CB A:ASN471 4.5 11.3 1.0
N A:ASN471 4.5 9.9 1.0
CB A:ASP444 4.6 7.5 1.0
O2A A:TPP557 4.6 8.9 1.0
CA A:GLY443 4.7 2.5 1.0
C A:ASN471 4.7 9.8 1.0
O A:HOH834 4.7 12.5 1.0
O2B A:TPP557 4.7 11.2 1.0
CA A:ASP444 4.8 7.2 1.0
C A:GLY443 4.8 4.5 1.0
O A:ASN471 4.8 11.6 1.0
C A:TYR474 4.8 11.6 1.0
CA A:ASN471 4.9 11.1 1.0
N A:ASP472 4.9 11.2 1.0
CA A:GLY445 5.0 9.0 1.0
C A:ASP444 5.0 8.5 1.0
C A:ASP472 5.0 10.8 1.0

Magnesium binding site 2 out of 2 in 1pvd

Go back to Magnesium Binding Sites List in 1pvd
Magnesium binding site 2 out of 2 in the Crystal Structure of the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase From the Yeast Saccharomyces Cerevisiae at 2.3 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase From the Yeast Saccharomyces Cerevisiae at 2.3 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg558

b:13.6
occ:1.00
 O3B B:TPP557 2.0 7.0 1.0
O1A B:TPP557 2.1 7.0 1.0
OD1 B:ASP444 2.2 5.9 1.0
O B:HOH559 2.2 3.3 1.0
OD1 B:ASN471 2.3 14.8 1.0
O B:GLY473 2.3 8.9 1.0
PA B:TPP557 3.3 8.1 1.0
PB B:TPP557 3.3 11.1 1.0
CG B:ASP444 3.4 4.5 1.0
CG B:ASN471 3.4 16.9 1.0
C B:GLY473 3.5 10.0 1.0
O3A B:TPP557 3.7 8.4 1.0
O1B B:TPP557 3.7 10.2 1.0
OD2 B:ASP444 3.8 4.2 1.0
ND2 B:ASN471 3.8 16.3 1.0
N B:GLY473 4.1 9.0 1.0
N B:THR475 4.1 13.5 1.0
O B:LEU469 4.1 11.0 1.0
N B:ASP444 4.2 6.0 1.0
O7 B:TPP557 4.2 7.2 1.0
N B:GLY445 4.3 4.9 1.0
CA B:TYR474 4.3 12.2 1.0
N B:TYR474 4.4 11.4 1.0
CG2 B:THR475 4.4 13.9 1.0
CA B:GLY473 4.5 9.4 1.0
O B:HOH861 4.5 68.3 1.0
O2B B:TPP557 4.5 7.4 1.0
O2A B:TPP557 4.5 10.1 1.0
N B:ASN471 4.6 10.1 1.0
CB B:ASP444 4.6 4.8 1.0
CA B:GLY443 4.7 3.1 1.0
C B:ASN471 4.7 8.6 1.0
C B:TYR474 4.8 12.0 1.0
CB B:ASN471 4.8 11.9 1.0
N B:ASP472 4.8 10.0 1.0
CA B:ASP444 4.8 5.9 1.0
CA B:ASN471 4.8 11.6 1.0
C B:GLY443 4.9 5.9 1.0

Reference:

P.Arjunan, T.Umland, F.Dyda, S.Swaminathan, W.Furey, M.Sax, B.Farrenkopf, Y.Gao, D.Zhang, F.Jordan. Crystal Structure of the Thiamin Diphosphate-Dependent Enzyme Pyruvate Decarboxylase From the Yeast Saccharomyces Cerevisiae at 2.3 A Resolution. J.Mol.Biol. V. 256 590 1996.
ISSN: ISSN 0022-2836
PubMed: 8604141
DOI: 10.1006/JMBI.1996.0111
Page generated: Tue Aug 13 10:56:32 2024

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