Atomistry » Magnesium » PDB 2vfx-2vsc » 2vk1
Atomistry »
  Magnesium »
    PDB 2vfx-2vsc »
      2vk1 »

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

Go back to Magnesium Binding Sites List in 2vk1
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

Go back to Magnesium Binding Sites List in 2vk1
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

Go back to Magnesium Binding Sites List in 2vk1
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy