Atomistry » Magnesium » PDB 2vfx-2vsc » 2vk4
Atomistry »
  Magnesium »
    PDB 2vfx-2vsc »
      2vk4 »

Magnesium in PDB 2vk4: Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis

Enzymatic activity of Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis

All present enzymatic activity of Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis:
4.1.1.1;

Protein crystallography data

The structure of Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis, PDB code: 2vk4 was solved by S.Kutter, S.Relle, G.Wille, M.S.Weiss, S.Konig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.45 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.709, 203.175, 79.815, 90.00, 91.81, 90.00
R / Rfree (%) 17.8 / 23

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis (pdb code 2vk4). 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 Pyruvate Decarboxylase From Kluyveromyces Lactis, PDB code: 2vk4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2vk4

Go back to Magnesium Binding Sites List in 2vk4
Magnesium binding site 1 out of 4 in the Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis


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 Pyruvate Decarboxylase From Kluyveromyces Lactis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:15.7
occ:1.00
 O3B A:TPP600 1.9 16.7 1.0
O A:GLY473 2.0 13.1 1.0
O A:HOH2238 2.1 20.8 1.0
O1A A:TPP600 2.1 12.1 1.0
OD2 A:ASP444 2.1 15.7 1.0
OD1 A:ASN471 2.2 18.5 1.0
PB A:TPP600 3.1 13.7 1.0
CG A:ASN471 3.1 17.7 1.0
PA A:TPP600 3.2 12.6 1.0
C A:GLY473 3.2 12.9 1.0
CG A:ASP444 3.3 14.3 1.0
ND2 A:ASN471 3.5 14.5 1.0
O3A A:TPP600 3.5 13.1 1.0
O1B A:TPP600 3.6 12.5 1.0
OD1 A:ASP444 3.9 19.6 1.0
N A:THR475 3.9 14.2 1.0
N A:GLY445 4.1 13.2 1.0
O7 A:TPP600 4.1 14.6 1.0
N A:TYR474 4.1 12.9 1.0
O A:LEU469 4.2 16.3 1.0
CA A:GLY473 4.2 13.2 1.0
N A:GLY473 4.2 15.4 1.0
CA A:TYR474 4.2 13.5 1.0
N A:ASP444 4.2 13.2 1.0
O2A A:TPP600 4.3 10.3 1.0
O2B A:TPP600 4.3 12.3 1.0
OG1 A:THR475 4.4 16.4 1.0
CB A:ASN471 4.5 15.9 1.0
C A:TYR474 4.6 13.3 1.0
CB A:ASP444 4.6 12.3 1.0
CA A:GLY443 4.6 12.9 1.0
N A:ASN471 4.6 15.1 1.0
C A:GLY443 4.7 13.1 1.0
CA A:ASP444 4.8 13.1 1.0
CB A:THR475 4.8 15.7 1.0
C A:ASN471 4.8 15.1 1.0
CA A:GLY445 4.9 13.0 1.0
C A:ASP444 4.9 12.2 1.0
CA A:ASN471 4.9 15.5 1.0
CA A:THR475 5.0 15.7 1.0

Magnesium binding site 2 out of 4 in 2vk4

Go back to Magnesium Binding Sites List in 2vk4
Magnesium binding site 2 out of 4 in the Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis


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 Pyruvate Decarboxylase From Kluyveromyces Lactis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:17.1
occ:1.00
 O B:GLY473 2.0 12.3 1.0
OD1 B:ASN471 2.1 13.9 1.0
O B:HOH2256 2.1 11.8 1.0
OD2 B:ASP444 2.1 11.6 1.0
O1A B:TPP600 2.1 9.6 1.0
O3B B:TPP600 2.2 12.8 1.0
CG B:ASN471 3.1 13.5 1.0
C B:GLY473 3.2 12.2 1.0
PB B:TPP600 3.3 12.7 1.0
CG B:ASP444 3.3 14.3 1.0
PA B:TPP600 3.3 11.4 1.0
O3A B:TPP600 3.5 13.7 1.0
ND2 B:ASN471 3.6 13.8 1.0
OD1 B:ASP444 3.8 12.1 1.0
O1B B:TPP600 3.9 12.8 1.0
N B:GLY473 3.9 12.3 1.0
N B:GLY445 4.0 14.6 1.0
CA B:GLY473 4.1 11.1 1.0
O B:LEU469 4.1 12.8 1.0
N B:THR475 4.1 14.0 1.0
N B:TYR474 4.1 12.1 1.0
O7 B:TPP600 4.2 11.9 1.0
N B:ASP444 4.2 15.3 1.0
CA B:TYR474 4.3 13.1 1.0
N B:ASN471 4.4 13.0 1.0
O2A B:TPP600 4.5 14.7 1.0
CB B:ASN471 4.5 12.9 1.0
OG1 B:THR475 4.5 11.9 1.0
O2B B:TPP600 4.5 12.5 1.0
CB B:ASP444 4.6 14.7 1.0
O B:HOH2262 4.6 10.3 1.0
CA B:GLY443 4.6 14.9 1.0
C B:TYR474 4.7 13.1 1.0
CA B:ASP444 4.7 14.7 1.0
C B:ASN471 4.7 12.4 1.0
CA B:ASN471 4.7 12.7 1.0
C B:GLY443 4.8 16.0 1.0
CA B:GLY445 4.8 14.2 1.0
C B:ASP444 4.8 14.1 1.0
CB B:THR475 4.8 12.8 1.0
N B:ASP472 4.9 13.0 1.0

Magnesium binding site 3 out of 4 in 2vk4

Go back to Magnesium Binding Sites List in 2vk4
Magnesium binding site 3 out of 4 in the Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis


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 Pyruvate Decarboxylase From Kluyveromyces Lactis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:12.4
occ:1.00
 OD1 C:ASN471 2.0 12.1 1.0
O3B C:TPP600 2.0 8.3 1.0
OD2 C:ASP444 2.1 9.1 1.0
O C:HOH2374 2.1 6.7 1.0
O C:GLY473 2.1 11.2 1.0
O1A C:TPP600 2.2 11.0 1.0
CG C:ASN471 3.0 10.9 1.0
PB C:TPP600 3.2 12.6 1.0
CG C:ASP444 3.3 11.3 1.0
PA C:TPP600 3.3 13.0 1.0
ND2 C:ASN471 3.3 12.2 1.0
C C:GLY473 3.3 11.8 1.0
O3A C:TPP600 3.5 10.8 1.0
O1B C:TPP600 3.5 11.7 1.0
OD1 C:ASP444 3.8 12.6 1.0
O C:LEU469 4.0 12.6 1.0
N C:THR475 4.0 12.0 1.0
N C:GLY445 4.1 9.1 1.0
N C:ASP444 4.1 8.3 1.0
O7 C:TPP600 4.1 14.9 1.0
N C:GLY473 4.2 14.6 1.0
CA C:GLY473 4.2 12.6 1.0
N C:TYR474 4.3 11.5 1.0
CA C:TYR474 4.4 11.4 1.0
OG1 C:THR475 4.4 10.7 1.0
CB C:ASN471 4.4 9.5 1.0
O2A C:TPP600 4.4 11.4 1.0
N C:ASN471 4.5 9.2 1.0
O2B C:TPP600 4.5 7.2 1.0
CB C:ASP444 4.5 10.5 1.0
CA C:GLY443 4.5 8.1 1.0
O C:HOH2302 4.6 8.9 1.0
C C:GLY443 4.6 8.2 1.0
CA C:ASP444 4.7 8.9 1.0
CB C:THR475 4.7 11.9 1.0
C C:TYR474 4.7 11.7 1.0
C C:ASN471 4.7 11.5 1.0
CA C:ASN471 4.8 9.6 1.0
C C:ASP444 4.9 9.5 1.0
CA C:GLY445 4.9 10.0 1.0
O C:ASN471 5.0 11.5 1.0
CA C:THR475 5.0 10.9 1.0

Magnesium binding site 4 out of 4 in 2vk4

Go back to Magnesium Binding Sites List in 2vk4
Magnesium binding site 4 out of 4 in the Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis


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 Pyruvate Decarboxylase From Kluyveromyces Lactis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:20.7
occ:1.00
 OD2 D:ASP444 1.9 17.4 1.0
OD1 D:ASN471 1.9 21.4 1.0
O D:GLY473 2.1 14.5 1.0
O D:HOH2237 2.1 11.4 1.0
O1A D:TPP600 2.2 17.1 1.0
O3B D:TPP600 2.2 19.0 1.0
CG D:ASN471 3.0 19.6 1.0
CG D:ASP444 3.1 16.6 1.0
C D:GLY473 3.3 15.1 1.0
ND2 D:ASN471 3.3 15.4 1.0
PB D:TPP600 3.4 15.9 1.0
PA D:TPP600 3.5 14.5 1.0
OD1 D:ASP444 3.6 18.9 1.0
O3A D:TPP600 3.7 15.4 1.0
O1B D:TPP600 3.8 18.4 1.0
N D:ASP444 3.9 13.7 1.0
O D:LEU469 3.9 16.2 1.0
N D:GLY445 4.0 14.0 1.0
N D:GLY473 4.0 16.3 1.0
CA D:GLY473 4.2 15.8 1.0
N D:THR475 4.2 17.1 1.0
N D:TYR474 4.3 15.5 1.0
CB D:ASN471 4.3 19.5 1.0
N D:ASN471 4.4 19.6 1.0
CB D:ASP444 4.4 15.1 1.0
O7 D:TPP600 4.5 14.2 1.0
CA D:TYR474 4.5 15.7 1.0
CA D:GLY443 4.5 14.5 1.0
O2A D:TPP600 4.5 15.0 1.0
OG1 D:THR475 4.5 14.0 1.0
CA D:ASP444 4.5 14.7 1.0
C D:GLY443 4.6 13.9 1.0
O2B D:TPP600 4.7 16.0 1.0
CA D:ASN471 4.7 19.1 1.0
C D:ASN471 4.7 19.0 1.0
C D:ASP444 4.8 14.2 1.0
CA D:GLY445 4.8 11.7 1.0
C D:TYR474 4.9 16.3 1.0
CB D:THR475 4.9 16.9 1.0
N D:ASP472 4.9 19.2 1.0
O D:ASN471 5.0 18.8 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: Wed Aug 14 05:15:07 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