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Magnesium in PDB 2w93: Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant E477Q in Complex with the Surrogate Pyruvamide

Enzymatic activity of Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant E477Q in Complex with the Surrogate Pyruvamide

All present enzymatic activity of Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant E477Q in Complex with the Surrogate Pyruvamide:
4.1.1.1;

Protein crystallography data

The structure of Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant E477Q in Complex with the Surrogate Pyruvamide, PDB code: 2w93 was solved by S.Kutter, M.S.Weiss, S.Konig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 103.70 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 73.050, 79.220, 109.090, 89.23, 73.32, 62.43
R / Rfree (%) 18.1 / 21.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant E477Q in Complex with the Surrogate Pyruvamide (pdb code 2w93). 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 E477Q in Complex with the Surrogate Pyruvamide, PDB code: 2w93:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2w93

Go back to Magnesium Binding Sites List in 2w93
Magnesium binding site 1 out of 4 in the Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant E477Q in Complex with the Surrogate Pyruvamide


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 E477Q in Complex with the Surrogate Pyruvamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:16.3
occ:1.00
 OD1 A:ASP444 2.0 14.6 1.0
O1A A:TPP600 2.0 13.6 1.0
O3B A:TPP600 2.1 17.6 1.0
O A:HOH2351 2.1 14.8 1.0
O A:GLY473 2.1 16.3 1.0
OD1 A:ASN471 2.2 13.1 1.0
CG A:ASN471 3.1 16.1 1.0
PB A:TPP600 3.2 15.1 1.0
PA A:TPP600 3.2 14.9 1.0
CG A:ASP444 3.2 15.7 1.0
C A:GLY473 3.4 15.9 1.0
O3A A:TPP600 3.5 13.8 1.0
ND2 A:ASN471 3.5 14.9 1.0
O1B A:TPP600 3.7 14.7 1.0
OD2 A:ASP444 3.8 17.2 1.0
N A:ASP444 4.0 14.0 1.0
N A:GLY445 4.0 11.6 1.0
O A:LEU469 4.1 15.9 1.0
N A:GLY473 4.1 16.5 1.0
O7 A:TPP600 4.2 13.3 1.0
N A:THR475 4.2 16.1 1.0
CA A:GLY473 4.2 16.0 1.0
N A:TYR474 4.3 14.8 1.0
O2A A:TPP600 4.4 14.7 1.0
CA A:TYR474 4.4 15.2 1.0
CB A:ASP444 4.4 14.7 1.0
N A:ASN471 4.5 15.5 1.0
CG2 A:THR475 4.5 13.2 1.0
CB A:ASN471 4.5 16.0 1.0
O2B A:TPP600 4.5 14.2 1.0
CA A:ASP444 4.6 13.7 1.0
CA A:GLY443 4.6 14.8 1.0
C A:GLY443 4.6 14.8 1.0
O A:HOH2266 4.7 15.7 1.0
C A:ASN471 4.8 15.7 1.0
CA A:ASN471 4.8 15.1 1.0
C A:ASP444 4.8 13.8 1.0
C A:TYR474 4.8 15.8 1.0
CB A:THR475 4.8 19.6 1.0
CA A:GLY445 4.8 13.3 1.0
N A:ASP472 5.0 15.4 1.0

Magnesium binding site 2 out of 4 in 2w93

Go back to Magnesium Binding Sites List in 2w93
Magnesium binding site 2 out of 4 in the Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant E477Q in Complex with the Surrogate Pyruvamide


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 E477Q in Complex with the Surrogate Pyruvamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:14.9
occ:1.00
 O3B B:TPP600 1.9 14.1 1.0
OD1 B:ASN471 2.1 14.1 1.0
O1A B:TPP600 2.1 15.1 1.0
O B:GLY473 2.1 13.2 1.0
OD1 B:ASP444 2.1 12.3 1.0
O B:HOH2313 2.2 12.2 1.0
CG B:ASN471 3.0 15.0 1.0
PB B:TPP600 3.2 13.9 1.0
PA B:TPP600 3.3 14.9 1.0
CG B:ASP444 3.3 14.5 1.0
C B:GLY473 3.3 14.1 1.0
ND2 B:ASN471 3.4 15.1 1.0
O3A B:TPP600 3.5 14.0 1.0
O1B B:TPP600 3.7 14.8 1.0
OD2 B:ASP444 3.9 15.6 1.0
N B:THR475 4.0 14.2 1.0
N B:GLY473 4.1 15.3 1.0
N B:GLY445 4.1 11.2 1.0
N B:ASP444 4.1 13.7 1.0
O B:LEU469 4.1 14.5 1.0
N B:TYR474 4.2 14.0 1.0
O7 B:TPP600 4.2 13.6 1.0
CA B:GLY473 4.2 14.3 1.0
CA B:TYR474 4.3 13.6 1.0
O2A B:TPP600 4.4 12.8 1.0
O2B B:TPP600 4.4 12.5 1.0
CB B:ASN471 4.4 16.2 1.0
CG2 B:THR475 4.5 10.6 1.0
N B:ASN471 4.5 15.1 1.0
CB B:ASP444 4.5 12.0 1.0
O B:HOH2321 4.6 14.8 1.0
C B:TYR474 4.6 14.5 1.0
CA B:ASP444 4.7 12.8 1.0
CA B:GLY443 4.7 13.4 1.0
CB B:THR475 4.8 18.4 1.0
C B:GLY443 4.8 13.6 1.0
C B:ASN471 4.8 14.6 1.0
CA B:ASN471 4.8 14.7 1.0
C B:ASP444 4.9 12.9 1.0
CA B:GLY445 4.9 11.5 1.0

Magnesium binding site 3 out of 4 in 2w93

Go back to Magnesium Binding Sites List in 2w93
Magnesium binding site 3 out of 4 in the Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant E477Q in Complex with the Surrogate Pyruvamide


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 E477Q in Complex with the Surrogate Pyruvamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:16.6
occ:1.00
 O3B C:TPP600 2.0 17.3 1.0
O1A C:TPP600 2.1 15.2 1.0
O C:HOH2353 2.1 12.8 1.0
O C:GLY473 2.1 17.6 1.0
OD1 C:ASN471 2.1 17.6 1.0
OD1 C:ASP444 2.1 15.3 1.0
CG C:ASN471 3.1 15.6 1.0
PB C:TPP600 3.2 16.4 1.0
PA C:TPP600 3.2 16.6 1.0
CG C:ASP444 3.3 16.2 1.0
C C:GLY473 3.3 18.4 1.0
ND2 C:ASN471 3.4 15.8 1.0
O3A C:TPP600 3.5 16.3 1.0
O1B C:TPP600 3.7 17.7 1.0
OD2 C:ASP444 3.9 18.8 1.0
N C:ASP444 4.0 15.2 1.0
N C:GLY445 4.0 14.2 1.0
N C:GLY473 4.1 18.4 1.0
O C:LEU469 4.1 16.3 1.0
N C:THR475 4.2 20.3 1.0
O7 C:TPP600 4.2 16.6 1.0
CA C:GLY473 4.2 17.9 1.0
N C:TYR474 4.2 18.1 1.0
CA C:TYR474 4.3 18.4 1.0
O2A C:TPP600 4.4 16.2 1.0
CB C:ASN471 4.5 17.4 1.0
CG2 C:THR475 4.5 18.2 1.0
N C:ASN471 4.5 17.5 1.0
CB C:ASP444 4.5 14.8 1.0
O2B C:TPP600 4.5 16.3 1.0
CA C:GLY443 4.6 14.9 1.0
O C:HOH2296 4.6 18.4 1.0
CA C:ASP444 4.6 14.9 1.0
C C:GLY443 4.7 14.9 1.0
C C:ASN471 4.8 18.0 1.0
C C:TYR474 4.8 19.5 1.0
CA C:ASN471 4.8 17.5 1.0
C C:ASP444 4.8 14.9 1.0
CB C:THR475 4.9 23.0 1.0
CA C:GLY445 4.9 14.9 1.0
N C:ASP472 5.0 18.6 1.0

Magnesium binding site 4 out of 4 in 2w93

Go back to Magnesium Binding Sites List in 2w93
Magnesium binding site 4 out of 4 in the Crystal Structure of the Saccharomyces Cerevisiae Pyruvate Decarboxylase Variant E477Q in Complex with the Surrogate Pyruvamide


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 E477Q in Complex with the Surrogate Pyruvamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:17.6
occ:1.00
 O D:GLY473 2.1 15.8 1.0
OD1 D:ASP444 2.1 16.9 1.0
OD1 D:ASN471 2.1 16.2 1.0
O3B D:TPP600 2.1 17.7 1.0
O1A D:TPP600 2.1 14.3 1.0
O D:HOH2296 2.1 13.6 1.0
CG D:ASN471 3.1 18.1 1.0
CG D:ASP444 3.2 16.5 1.0
C D:GLY473 3.3 16.6 1.0
PB D:TPP600 3.3 17.5 1.0
PA D:TPP600 3.3 17.7 1.0
ND2 D:ASN471 3.5 17.7 1.0
O3A D:TPP600 3.6 17.6 1.0
O1B D:TPP600 3.8 18.3 1.0
OD2 D:ASP444 3.8 16.3 1.0
N D:GLY445 4.0 14.1 1.0
N D:ASP444 4.0 16.0 1.0
N D:GLY473 4.0 17.5 1.0
N D:THR475 4.1 19.6 1.0
O D:LEU469 4.2 17.9 1.0
CA D:GLY473 4.2 16.9 1.0
N D:TYR474 4.2 17.0 1.0
O7 D:TPP600 4.3 16.7 1.0
CA D:TYR474 4.3 17.0 1.0
CG2 D:THR475 4.4 16.9 1.0
O2A D:TPP600 4.4 16.9 1.0
CB D:ASN471 4.4 18.0 1.0
CB D:ASP444 4.5 15.6 1.0
N D:ASN471 4.5 17.9 1.0
O2B D:TPP600 4.5 17.3 1.0
CA D:ASP444 4.6 15.6 1.0
O D:HOH2219 4.7 20.1 1.0
CA D:GLY443 4.7 16.3 1.0
C D:TYR474 4.7 18.2 1.0
C D:ASN471 4.7 17.6 1.0
C D:GLY443 4.7 16.6 1.0
CA D:ASN471 4.8 17.2 1.0
CB D:THR475 4.8 22.4 1.0
C D:ASP444 4.8 14.9 1.0
CA D:GLY445 4.9 14.2 1.0
N D:ASP472 4.9 17.1 1.0
O D:ASN471 4.9 17.0 1.0

Reference:

S.Konig, M.Spinka, S.Kutter. Allosteric Activation of Pyruvate Decarboxylases. A Never-Ending Story. J.Mol.Catal., B Enzym. V. 61 100 2014.
ISSN: ISSN 1381-1177
DOI: 10.1016/J.MOLCATB.2009.02.010
Page generated: Sun Aug 10 15:37:03 2025

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