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Magnesium in PDB 2vjy: Pyruvate Decarboxylase From Kluyveromyces Lactis in Complex with the Substrate Analogue Methyl Acetylphosphonate

Enzymatic activity of Pyruvate Decarboxylase From Kluyveromyces Lactis in Complex with the Substrate Analogue Methyl Acetylphosphonate

All present enzymatic activity of Pyruvate Decarboxylase From Kluyveromyces Lactis in Complex with the Substrate Analogue Methyl Acetylphosphonate:
4.1.1.1;

Protein crystallography data

The structure of Pyruvate Decarboxylase From Kluyveromyces Lactis in Complex with the Substrate Analogue Methyl Acetylphosphonate, PDB code: 2vjy was solved by S.Kutter, 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) 20.19 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.760, 135.770, 107.260, 90.00, 103.88, 90.00
R / Rfree (%) 15.4 / 22.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyruvate Decarboxylase From Kluyveromyces Lactis in Complex with the Substrate Analogue Methyl Acetylphosphonate (pdb code 2vjy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pyruvate Decarboxylase From Kluyveromyces Lactis in Complex with the Substrate Analogue Methyl Acetylphosphonate, PDB code: 2vjy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2vjy

Go back to Magnesium Binding Sites List in 2vjy
Magnesium binding site 1 out of 4 in the Pyruvate Decarboxylase From Kluyveromyces Lactis in Complex with the Substrate Analogue Methyl Acetylphosphonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyruvate Decarboxylase From Kluyveromyces Lactis in Complex with the Substrate Analogue Methyl Acetylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:20.1
occ:1.00
 O A:GLY473 1.9 14.9 1.0
OD1 A:ASN471 2.0 18.1 1.0
OD1 A:ASP444 2.1 13.4 1.0
O3B A:TPP600 2.2 20.5 1.0
O2A A:TPP600 2.2 15.3 1.0
O A:HOH2238 2.3 9.5 1.0
CG A:ASN471 3.0 17.8 1.0
CG A:ASP444 3.2 15.1 1.0
C A:GLY473 3.2 14.8 1.0
PB A:TPP600 3.3 15.8 1.0
PA A:TPP600 3.4 18.7 1.0
ND2 A:ASN471 3.4 17.3 1.0
OD2 A:ASP444 3.6 18.2 1.0
O3A A:TPP600 3.7 18.2 1.0
O2B A:TPP600 3.8 14.8 1.0
N A:THR475 3.9 16.8 1.0
N A:GLY473 4.0 13.2 1.0
O A:LEU469 4.1 17.3 1.0
N A:ASP444 4.1 15.7 1.0
N A:TYR474 4.1 14.6 1.0
CA A:GLY473 4.2 13.3 1.0
N A:GLY445 4.2 17.5 1.0
CA A:TYR474 4.2 14.6 1.0
O7 A:TPP600 4.3 19.2 1.0
CB A:ASN471 4.4 18.0 1.0
OG1 A:THR475 4.4 16.4 1.0
N A:ASN471 4.4 19.5 1.0
CB A:ASP444 4.5 16.6 1.0
O1A A:TPP600 4.5 17.7 1.0
O1B A:TPP600 4.6 11.4 1.0
O A:HOH2244 4.6 22.5 1.0
C A:TYR474 4.6 16.1 1.0
CA A:GLY443 4.6 14.4 1.0
C A:ASN471 4.6 18.6 1.0
CA A:ASP444 4.7 16.4 1.0
CA A:ASN471 4.7 18.5 1.0
C A:GLY443 4.7 15.2 1.0
CB A:THR475 4.8 16.3 1.0
O A:ASN471 4.9 18.2 1.0
N A:ASP472 4.9 18.8 1.0
C A:ASP444 4.9 18.1 1.0

Magnesium binding site 2 out of 4 in 2vjy

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Magnesium binding site 2 out of 4 in the Pyruvate Decarboxylase From Kluyveromyces Lactis in Complex with the Substrate Analogue Methyl Acetylphosphonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyruvate Decarboxylase From Kluyveromyces Lactis in Complex with the Substrate Analogue Methyl Acetylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:15.3
occ:1.00
 O B:GLY473 1.9 17.3 1.0
OD1 B:ASP444 2.0 19.6 1.0
OD1 B:ASN471 2.1 18.4 1.0
O3B B:TPP600 2.1 12.9 1.0
O2A B:TPP600 2.1 13.8 1.0
O B:HOH2300 2.2 14.5 1.0
C B:GLY473 3.1 18.5 1.0
CG B:ASN471 3.1 19.7 1.0
CG B:ASP444 3.2 16.6 1.0
PA B:TPP600 3.3 14.8 1.0
PB B:TPP600 3.4 14.3 1.0
ND2 B:ASN471 3.5 16.8 1.0
O3A B:TPP600 3.7 16.9 1.0
OD2 B:ASP444 3.7 20.8 1.0
O2B B:TPP600 3.9 14.2 1.0
N B:GLY473 3.9 20.1 1.0
CA B:GLY473 4.0 18.5 1.0
N B:TYR474 4.0 18.2 1.0
N B:GLY445 4.1 15.3 1.0
N B:THR475 4.1 19.7 1.0
N B:ASP444 4.1 14.7 1.0
O B:LEU469 4.1 19.4 1.0
CA B:TYR474 4.2 18.6 1.0
O7 B:TPP600 4.2 16.5 1.0
OG1 B:THR475 4.3 20.5 1.0
N B:ASN471 4.4 18.8 1.0
CB B:ASN471 4.4 17.8 1.0
CB B:ASP444 4.5 14.7 1.0
O B:HOH2248 4.5 15.4 1.0
O1A B:TPP600 4.5 19.1 1.0
O1B B:TPP600 4.6 11.2 1.0
CA B:ASP444 4.7 14.4 1.0
C B:ASN471 4.7 17.8 1.0
C B:TYR474 4.7 19.5 1.0
CA B:ASN471 4.7 18.6 1.0
CA B:GLY443 4.8 12.4 1.0
N B:ASP472 4.8 19.7 1.0
C B:GLY443 4.8 13.7 1.0
CB B:THR475 4.8 19.4 1.0
C B:ASP444 4.9 15.5 1.0
CA B:GLY445 4.9 15.2 1.0
O B:ASN471 5.0 18.0 1.0

Magnesium binding site 3 out of 4 in 2vjy

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Magnesium binding site 3 out of 4 in the Pyruvate Decarboxylase From Kluyveromyces Lactis in Complex with the Substrate Analogue Methyl Acetylphosphonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyruvate Decarboxylase From Kluyveromyces Lactis in Complex with the Substrate Analogue Methyl Acetylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:30.7
occ:1.00
 OD1 C:ASP444 1.9 25.4 1.0
O C:GLY473 2.1 26.1 1.0
O1A C:TPP600 2.1 18.5 1.0
O C:HOH2220 2.2 25.6 1.0
OD1 C:ASN471 2.3 23.3 1.0
O3B C:TPP600 2.3 22.0 1.0
CG C:ASP444 3.1 24.7 1.0
C C:GLY473 3.3 26.2 1.0
PA C:TPP600 3.3 22.7 1.0
CG C:ASN471 3.4 27.3 1.0
PB C:TPP600 3.5 23.0 1.0
OD2 C:ASP444 3.6 26.2 1.0
O3A C:TPP600 3.8 24.3 1.0
N C:ASP444 3.8 24.0 1.0
N C:GLY445 3.9 24.0 1.0
ND2 C:ASN471 3.9 22.9 1.0
O C:LEU469 3.9 29.9 1.0
N C:GLY473 4.0 27.4 1.0
CA C:GLY473 4.1 25.9 1.0
O1B C:TPP600 4.1 23.4 1.0
N C:THR475 4.2 28.9 1.0
O7 C:TPP600 4.2 24.4 1.0
N C:TYR474 4.3 27.0 1.0
CB C:ASP444 4.3 23.7 1.0
O2A C:TPP600 4.3 19.7 1.0
CA C:ASP444 4.4 24.2 1.0
CA C:TYR474 4.4 27.4 1.0
N C:ASN471 4.4 29.3 1.0
CA C:GLY443 4.5 21.9 1.0
C C:GLY443 4.5 23.7 1.0
C C:ASP444 4.6 24.1 1.0
OG1 C:THR475 4.6 27.4 1.0
O C:HOH2194 4.7 29.1 1.0
CB C:ASN471 4.7 28.8 1.0
CA C:GLY445 4.7 23.5 1.0
O2B C:TPP600 4.8 23.0 1.0
C C:ASN471 4.8 29.0 1.0
C C:TYR474 4.8 28.6 1.0
CA C:ASN471 4.9 28.9 1.0
CB C:THR475 4.9 28.7 1.0
N C:ASP472 5.0 29.4 1.0

Magnesium binding site 4 out of 4 in 2vjy

Go back to Magnesium Binding Sites List in 2vjy
Magnesium binding site 4 out of 4 in the Pyruvate Decarboxylase From Kluyveromyces Lactis in Complex with the Substrate Analogue Methyl Acetylphosphonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyruvate Decarboxylase From Kluyveromyces Lactis in Complex with the Substrate Analogue Methyl Acetylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:20.3
occ:1.00
 O D:GLY473 2.1 22.2 1.0
OD1 D:ASP444 2.1 25.7 1.0
OD1 D:ASN471 2.1 29.0 1.0
O1B D:TPP600 2.1 19.7 1.0
O1A D:TPP600 2.2 23.9 1.0
O D:HOH2184 2.2 19.6 1.0
CG D:ASN471 3.1 26.1 1.0
CG D:ASP444 3.2 23.3 1.0
C D:GLY473 3.3 23.9 1.0
PB D:TPP600 3.4 24.0 1.0
PA D:TPP600 3.4 23.3 1.0
ND2 D:ASN471 3.6 22.5 1.0
O3A D:TPP600 3.7 26.8 1.0
OD2 D:ASP444 3.7 21.9 1.0
O3B D:TPP600 3.9 23.1 1.0
N D:GLY473 4.0 25.3 1.0
O D:LEU469 4.0 23.6 1.0
N D:GLY445 4.1 23.0 1.0
N D:THR475 4.1 22.0 1.0
N D:ASP444 4.1 22.6 1.0
CA D:GLY473 4.2 24.2 1.0
OG1 D:THR475 4.2 20.6 1.0
N D:TYR474 4.2 23.8 1.0
O7 D:TPP600 4.3 25.7 1.0
CA D:TYR474 4.4 23.6 1.0
N D:ASN471 4.5 24.5 1.0
CB D:ASP444 4.5 23.3 1.0
O2A D:TPP600 4.5 22.6 1.0
CB D:ASN471 4.5 24.5 1.0
O2B D:TPP600 4.6 22.1 1.0
O D:HOH2190 4.6 25.4 1.0
CA D:GLY443 4.6 21.8 1.0
CA D:ASP444 4.6 23.5 1.0
C D:GLY443 4.7 22.6 1.0
C D:ASN471 4.7 24.9 1.0
C D:TYR474 4.8 22.7 1.0
CA D:ASN471 4.8 24.5 1.0
CB D:THR475 4.8 23.2 1.0
C D:ASP444 4.9 23.0 1.0
N D:ASP472 4.9 24.9 1.0
CA D:GLY445 4.9 21.8 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: Mon Dec 14 07:42:15 2020

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