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Magnesium in PDB 2vk1: Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant D28A in Complex with Its Substrate

Enzymatic activity of Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant D28A in Complex with Its Substrate

All present enzymatic activity of Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant D28A in Complex with Its Substrate:
4.1.1.1;

Protein crystallography data

The structure of Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant D28A in Complex with Its Substrate, PDB code: 2vk1 was solved by S.Kutter, M.Weik, M.S.Weiss, S.Konig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 109.11 / 1.71
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.880, 141.310, 114.410, 90.00, 107.19, 90.00
R / Rfree (%) 19.1 / 22

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant D28A in Complex with Its Substrate (pdb code 2vk1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant D28A in Complex with Its Substrate, PDB code: 2vk1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2vk1

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant D28A in Complex with Its Substrate


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 Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant D28A in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:15.1
occ:1.00
 OD1 A:ASP444 2.0 12.2 1.0
O1A A:TPP600 2.1 12.1 1.0
O A:GLY473 2.1 12.3 1.0
OD1 A:ASN471 2.1 13.1 1.0
O A:HOH2435 2.2 12.2 1.0
O3B A:TPP600 2.2 14.9 1.0
CG A:ASN471 3.1 14.1 1.0
CG A:ASP444 3.2 14.5 1.0
PB A:TPP600 3.2 14.2 1.0
PA A:TPP600 3.3 14.7 1.0
C A:GLY473 3.3 13.9 1.0
ND2 A:ASN471 3.5 12.9 1.0
O3A A:TPP600 3.5 13.6 1.0
O1B A:TPP600 3.7 15.0 1.0
OD2 A:ASP444 3.8 16.8 1.0
N A:GLY445 4.0 13.4 1.0
N A:ASP444 4.0 12.5 1.0
N A:THR475 4.1 14.9 1.0
O A:LEU469 4.1 13.9 1.0
N A:GLY473 4.1 15.6 1.0
N A:TYR474 4.2 14.0 1.0
CA A:TYR474 4.2 15.2 1.0
CA A:GLY473 4.2 14.7 1.0
O7 A:TPP600 4.2 15.5 1.0
O2A A:TPP600 4.3 11.1 1.0
CG2 A:THR475 4.4 12.3 1.0
CB A:ASP444 4.5 13.7 1.0
CB A:ASN471 4.5 14.0 1.0
O2B A:TPP600 4.5 11.7 1.0
N A:ASN471 4.5 15.6 1.0
CA A:GLY443 4.6 12.6 1.0
CA A:ASP444 4.6 13.5 1.0
C A:GLY443 4.7 13.1 1.0
C A:TYR474 4.7 15.1 1.0
O A:HOH2357 4.7 16.0 1.0
C A:ASN471 4.8 15.6 1.0
CA A:ASN471 4.8 14.5 1.0
C A:ASP444 4.8 13.5 1.0
CA A:GLY445 4.8 13.3 1.0
CB A:THR475 5.0 17.7 1.0

Magnesium binding site 2 out of 4 in 2vk1

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Magnesium binding site 2 out of 4 in the Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant D28A in Complex with Its Substrate


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 Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant D28A in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:15.7
occ:1.00
 O B:GLY473 2.0 15.7 1.0
OD1 B:ASP444 2.0 13.5 1.0
O3B B:TPP600 2.1 15.8 1.0
O1A B:TPP600 2.1 13.3 1.0
OD1 B:ASN471 2.2 15.8 1.0
O B:HOH2306 2.2 16.1 1.0
CG B:ASN471 3.2 17.9 1.0
CG B:ASP444 3.2 17.4 1.0
C B:GLY473 3.2 17.8 1.0
PB B:TPP600 3.2 14.7 1.0
PA B:TPP600 3.3 15.5 1.0
O3A B:TPP600 3.6 14.6 1.0
ND2 B:ASN471 3.6 15.2 1.0
O1B B:TPP600 3.7 14.2 1.0
OD2 B:ASP444 3.8 19.5 1.0
N B:ASP444 4.0 15.5 1.0
N B:THR475 4.1 16.1 1.0
N B:GLY445 4.1 14.1 1.0
N B:GLY473 4.1 17.5 1.0
N B:TYR474 4.1 16.7 1.0
CA B:GLY473 4.2 17.4 1.0
O B:LEU469 4.2 15.5 1.0
O7 B:TPP600 4.3 14.9 1.0
CA B:TYR474 4.3 16.6 1.0
O2A B:TPP600 4.4 13.4 1.0
CG2 B:THR475 4.4 10.9 1.0
CB B:ASP444 4.4 15.7 1.0
O2B B:TPP600 4.5 12.5 1.0
N B:ASN471 4.5 16.2 1.0
CB B:ASN471 4.5 16.3 1.0
O B:HOH2309 4.6 16.5 1.0
CA B:ASP444 4.6 15.4 1.0
CA B:GLY443 4.6 13.4 1.0
C B:GLY443 4.7 14.6 1.0
C B:TYR474 4.7 16.2 1.0
C B:ASN471 4.7 16.3 1.0
CA B:ASN471 4.8 15.6 1.0
CB B:THR475 4.8 18.4 1.0
C B:ASP444 4.8 14.7 1.0
CA B:GLY445 4.9 14.6 1.0
N B:ASP472 5.0 17.1 1.0

Magnesium binding site 3 out of 4 in 2vk1

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Magnesium binding site 3 out of 4 in the Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant D28A in Complex with Its Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant D28A in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:17.9
occ:1.00
 O C:HOH2407 2.0 14.1 1.0
OD1 C:ASP444 2.0 17.2 1.0
O C:GLY473 2.1 18.3 1.0
O1A C:TPP600 2.1 14.5 1.0
OD1 C:ASN471 2.2 14.7 1.0
O3B C:TPP600 2.2 18.4 1.0
CG C:ASN471 3.2 17.8 1.0
CG C:ASP444 3.2 17.2 1.0
C C:GLY473 3.3 18.2 1.0
PB C:TPP600 3.3 17.6 1.0
PA C:TPP600 3.3 17.5 1.0
O3A C:TPP600 3.6 15.4 1.0
ND2 C:ASN471 3.6 17.5 1.0
O1B C:TPP600 3.7 14.7 1.0
OD2 C:ASP444 3.8 17.6 1.0
N C:GLY445 4.0 15.4 1.0
N C:ASP444 4.0 16.5 1.0
N C:GLY473 4.0 19.4 1.0
O C:LEU469 4.1 16.3 1.0
N C:THR475 4.2 18.6 1.0
N C:TYR474 4.2 18.3 1.0
CA C:GLY473 4.2 19.1 1.0
O7 C:TPP600 4.3 15.9 1.0
CA C:TYR474 4.3 18.5 1.0
O2A C:TPP600 4.3 13.8 1.0
CG2 C:THR475 4.4 14.7 1.0
CB C:ASP444 4.5 16.2 1.0
N C:ASN471 4.5 18.3 1.0
CB C:ASN471 4.5 17.4 1.0
O C:HOH2334 4.6 19.2 1.0
CA C:ASP444 4.6 16.3 1.0
O2B C:TPP600 4.6 15.6 1.0
CA C:GLY443 4.6 15.3 1.0
C C:GLY443 4.7 15.8 1.0
C C:ASN471 4.8 17.8 1.0
C C:ASP444 4.8 16.1 1.0
C C:TYR474 4.8 18.2 1.0
CA C:GLY445 4.8 15.5 1.0
CA C:ASN471 4.8 17.6 1.0
CB C:THR475 4.9 19.7 1.0
N C:ASP472 5.0 18.3 1.0

Magnesium binding site 4 out of 4 in 2vk1

Go back to Magnesium Binding Sites List in 2vk1
Magnesium binding site 4 out of 4 in the Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant D28A in Complex with Its Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant D28A in Complex with Its Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:19.2
occ:1.00
 OD1 D:ASP444 2.1 15.4 1.0
O D:GLY473 2.1 14.6 1.0
O1A D:TPP600 2.1 14.8 1.0
OD1 D:ASN471 2.1 15.3 1.0
O D:HOH2336 2.2 13.5 1.0
O3B D:TPP600 2.2 16.8 1.0
CG D:ASN471 3.1 18.4 1.0
CG D:ASP444 3.3 17.1 1.0
C D:GLY473 3.3 16.4 1.0
PB D:TPP600 3.3 16.3 1.0
PA D:TPP600 3.3 15.6 1.0
ND2 D:ASN471 3.5 16.7 1.0
O3A D:TPP600 3.6 15.9 1.0
O1B D:TPP600 3.7 17.7 1.0
OD2 D:ASP444 3.8 17.8 1.0
N D:ASP444 3.9 16.0 1.0
N D:GLY445 4.0 16.1 1.0
N D:GLY473 4.1 17.9 1.0
O D:LEU469 4.1 18.3 1.0
N D:THR475 4.2 17.1 1.0
N D:TYR474 4.2 16.2 1.0
CA D:GLY473 4.2 17.1 1.0
CA D:TYR474 4.3 16.5 1.0
O7 D:TPP600 4.3 15.6 1.0
O2A D:TPP600 4.4 15.0 1.0
CB D:ASP444 4.5 16.6 1.0
N D:ASN471 4.5 18.8 1.0
CB D:ASN471 4.5 17.3 1.0
CG2 D:THR475 4.5 15.2 1.0
CA D:ASP444 4.6 15.8 1.0
O2B D:TPP600 4.6 17.0 1.0
CA D:GLY443 4.6 15.0 1.0
C D:GLY443 4.6 14.8 1.0
O D:HOH2265 4.7 17.1 1.0
C D:ASN471 4.8 18.0 1.0
C D:TYR474 4.8 16.6 1.0
C D:ASP444 4.8 16.6 1.0
CA D:ASN471 4.8 17.4 1.0
CA D:GLY445 4.8 16.3 1.0
N D:ASP472 4.9 18.6 1.0
CB D:THR475 4.9 20.5 1.0

Reference:

S.Kutter, M.S.Weiss, G.Wille, R.Golbik, M.Spinka, S.Konig. Covalently Bound Substrate at the Regulatory Site of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation. J.Biol.Chem. V. 284 12136 2009.
ISSN: ISSN 0021-9258
PubMed: 19246454
DOI: 10.1074/JBC.M806228200
Page generated: Wed Aug 14 05:14:37 2024

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