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Magnesium in PDB 2vbi: Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus

Enzymatic activity of Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus

All present enzymatic activity of Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus:
4.1.1.1;

Protein crystallography data

The structure of Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus, PDB code: 2vbi was solved by D.Gocke, C.L.Berthold, G.Schneider, M.Pohl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 179.619, 162.434, 169.331, 90.00, 102.71, 90.00
R / Rfree (%) 22.4 / 24.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus (pdb code 2vbi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus, PDB code: 2vbi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2vbi

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Magnesium binding site 1 out of 8 in the Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1000

b:42.1
occ:1.00
 OD1 A:ASP436 1.9 41.3 1.0
O1A A:TPP2000 2.0 55.3 1.0
O3B A:TPP2000 2.2 57.3 1.0
O A:GLY465 2.3 41.9 1.0
OD1 A:ASN463 2.4 42.4 1.0
O A:HOH2006 2.5 22.0 1.0
CG A:ASP436 3.1 42.0 1.0
PA A:TPP2000 3.3 54.5 1.0
PB A:TPP2000 3.3 58.0 1.0
CG A:ASN463 3.4 42.1 1.0
C A:GLY465 3.4 42.1 1.0
O3A A:TPP2000 3.5 55.0 1.0
N A:ASP436 3.6 41.9 1.0
OD2 A:ASP436 3.8 42.1 1.0
N A:GLY437 3.9 42.1 1.0
ND2 A:ASN463 3.9 42.0 1.0
N A:GLY465 4.0 42.3 1.0
O A:ILE461 4.1 41.6 1.0
O2B A:TPP2000 4.2 58.3 1.0
CB A:ASP436 4.2 42.0 1.0
CA A:GLY465 4.2 42.1 1.0
O7 A:TPP2000 4.2 53.8 1.0
O2A A:TPP2000 4.2 54.4 1.0
CA A:ASP436 4.3 42.0 1.0
CA A:GLY435 4.3 41.8 1.0
C A:GLY435 4.3 41.8 1.0
N A:TYR466 4.4 42.2 1.0
O1B A:TPP2000 4.4 57.7 1.0
N A:VAL467 4.5 42.4 1.0
N A:ASN463 4.5 41.9 1.0
C A:ASP436 4.6 42.1 1.0
CA A:TYR466 4.6 42.2 1.0
CB A:ASN463 4.7 42.1 1.0
CA A:GLY437 4.8 42.2 1.0
N A:ARG464 4.8 42.1 1.0
CG2 A:VAL467 4.9 42.3 1.0
CA A:ASN463 4.9 42.0 1.0
C A:ASN463 4.9 42.0 1.0

Magnesium binding site 2 out of 8 in 2vbi

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Magnesium binding site 2 out of 8 in the Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1000

b:40.5
occ:1.00
 O B:HOH2005 1.9 29.1 1.0
O1A B:TPP2000 2.0 58.3 1.0
O B:GLY465 2.2 42.0 1.0
OD1 B:ASN463 2.3 42.3 1.0
O3B B:TPP2000 2.4 58.2 1.0
O2B B:TPP2000 2.5 59.3 1.0
OD1 B:ASP436 2.5 41.3 1.0
PB B:TPP2000 2.9 59.7 1.0
CG B:ASN463 3.2 42.1 1.0
PA B:TPP2000 3.2 57.7 1.0
O3A B:TPP2000 3.4 57.9 1.0
C B:GLY465 3.4 42.1 1.0
ND2 B:ASN463 3.4 42.0 1.0
CG B:ASP436 3.8 41.9 1.0
N B:VAL467 4.0 42.4 1.0
N B:ASP436 4.1 41.9 1.0
O7 B:TPP2000 4.2 57.0 1.0
N B:GLY465 4.3 42.3 1.0
O1B B:TPP2000 4.3 59.0 1.0
O2A B:TPP2000 4.3 58.3 1.0
N B:TYR466 4.3 42.2 1.0
O B:ILE461 4.4 41.6 1.0
CG2 B:VAL467 4.4 42.3 1.0
OD2 B:ASP436 4.4 42.1 1.0
CA B:GLY465 4.4 42.1 1.0
CA B:TYR466 4.4 42.2 1.0
N B:GLY437 4.4 42.2 1.0
CB B:VAL467 4.5 42.4 1.0
CA B:GLY435 4.6 41.9 1.0
CB B:ASN463 4.6 42.1 1.0
N B:ASN463 4.7 41.9 1.0
C B:TYR466 4.7 42.2 1.0
C B:GLY435 4.8 41.8 1.0
CA B:VAL467 4.9 42.4 1.0
CB B:ASP436 4.9 42.0 1.0
CA B:ASP436 4.9 42.0 1.0
CA B:ASN463 5.0 42.0 1.0

Magnesium binding site 3 out of 8 in 2vbi

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Magnesium binding site 3 out of 8 in the Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1000

b:33.3
occ:1.00
 O1A C:TPP2000 1.9 30.6 1.0
OD1 C:ASP436 2.0 41.2 1.0
O3B C:TPP2000 2.1 30.3 1.0
OD1 C:ASN463 2.3 42.3 1.0
O C:HOH2013 2.3 31.0 1.0
O C:GLY465 2.4 42.0 1.0
PA C:TPP2000 3.2 31.9 1.0
PB C:TPP2000 3.2 30.6 1.0
CG C:ASP436 3.2 42.0 1.0
CG C:ASN463 3.3 42.1 1.0
O3A C:TPP2000 3.5 31.3 1.0
C C:GLY465 3.5 42.1 1.0
N C:ASP436 3.6 41.9 1.0
ND2 C:ASN463 3.7 42.0 1.0
O2B C:TPP2000 3.8 31.6 1.0
OD2 C:ASP436 3.9 42.2 1.0
N C:GLY437 4.0 42.1 1.0
O C:ILE461 4.0 41.6 1.0
N C:GLY465 4.1 42.2 1.0
O7 C:TPP2000 4.2 32.9 1.0
O2A C:TPP2000 4.2 31.1 1.0
CA C:GLY435 4.3 41.8 1.0
CB C:ASP436 4.4 42.1 1.0
CA C:GLY465 4.4 42.1 1.0
C C:GLY435 4.4 41.8 1.0
CA C:ASP436 4.4 42.0 1.0
O1B C:TPP2000 4.4 28.4 1.0
N C:VAL467 4.4 42.4 1.0
N C:ASN463 4.5 41.9 1.0
N C:TYR466 4.5 42.2 1.0
CB C:ASN463 4.7 42.1 1.0
CA C:TYR466 4.7 42.2 1.0
C C:ASP436 4.8 42.1 1.0
CG2 C:VAL467 4.8 42.3 1.0
N C:ARG464 4.9 42.1 1.0
CA C:ASN463 4.9 42.0 1.0
CA C:GLY437 4.9 42.1 1.0
C C:ASN463 4.9 42.0 1.0
CB C:VAL467 5.0 42.4 1.0

Magnesium binding site 4 out of 8 in 2vbi

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Magnesium binding site 4 out of 8 in the Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1000

b:21.5
occ:1.00
 OD1 D:ASP436 2.0 41.3 1.0
O D:GLY465 2.0 41.9 1.0
O1A D:TPP2000 2.1 28.2 1.0
O D:HOH2015 2.2 37.7 1.0
O3B D:TPP2000 2.3 27.1 1.0
OD1 D:ASN463 2.3 42.3 1.0
C D:GLY465 3.2 42.1 1.0
CG D:ASP436 3.2 41.9 1.0
PB D:TPP2000 3.3 27.3 1.0
PA D:TPP2000 3.3 27.3 1.0
CG D:ASN463 3.4 42.1 1.0
O3A D:TPP2000 3.6 27.6 1.0
O2B D:TPP2000 3.6 26.7 1.0
OD2 D:ASP436 3.8 42.1 1.0
N D:GLY465 3.8 42.3 1.0
N D:ASP436 3.9 42.0 1.0
ND2 D:ASN463 3.9 42.0 1.0
CA D:GLY465 4.0 42.1 1.0
N D:GLY437 4.0 42.2 1.0
N D:TYR466 4.1 42.2 1.0
O7 D:TPP2000 4.2 25.7 1.0
N D:VAL467 4.2 42.4 1.0
O D:ILE461 4.3 41.6 1.0
CB D:ASP436 4.4 42.0 1.0
CA D:TYR466 4.4 42.2 1.0
O2A D:TPP2000 4.4 26.6 1.0
N D:ASN463 4.5 41.8 1.0
CA D:ASP436 4.5 42.0 1.0
CA D:GLY435 4.6 41.8 1.0
C D:GLY435 4.6 41.8 1.0
O1B D:TPP2000 4.6 27.0 1.0
CG2 D:VAL467 4.7 42.3 1.0
CB D:ASN463 4.7 42.0 1.0
N D:ARG464 4.7 42.1 1.0
C D:ASP436 4.8 42.2 1.0
C D:ASN463 4.8 42.0 1.0
CA D:GLY437 4.9 42.2 1.0
CA D:ASN463 4.9 42.0 1.0
C D:TYR466 4.9 42.2 1.0
CB D:VAL467 4.9 42.4 1.0
C D:ARG464 5.0 42.3 1.0

Magnesium binding site 5 out of 8 in 2vbi

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Magnesium binding site 5 out of 8 in the Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1000

b:32.4
occ:1.00
 O1A E:TPP2000 1.9 36.8 1.0
O3B E:TPP2000 2.0 35.7 1.0
OD1 E:ASP436 2.0 41.3 1.0
O E:HOH2020 2.1 33.2 1.0
OD1 E:ASN463 2.2 42.3 1.0
O E:GLY465 2.4 41.9 1.0
PA E:TPP2000 3.1 35.9 1.0
PB E:TPP2000 3.2 36.0 1.0
CG E:ASN463 3.2 42.0 1.0
CG E:ASP436 3.3 41.9 1.0
O3A E:TPP2000 3.3 36.6 1.0
C E:GLY465 3.5 42.1 1.0
ND2 E:ASN463 3.6 42.0 1.0
N E:ASP436 3.7 41.9 1.0
OD2 E:ASP436 4.0 42.0 1.0
O2A E:TPP2000 4.0 37.9 1.0
O E:ILE461 4.0 41.8 1.0
N E:GLY437 4.1 42.1 1.0
N E:GLY465 4.1 42.3 1.0
O1B E:TPP2000 4.2 36.3 1.0
O2B E:TPP2000 4.2 34.6 1.0
O7 E:TPP2000 4.2 37.0 1.0
CA E:GLY465 4.3 42.1 1.0
CA E:GLY435 4.4 41.9 1.0
CB E:ASP436 4.4 42.0 1.0
N E:VAL467 4.4 42.4 1.0
N E:ASN463 4.4 41.8 1.0
C E:GLY435 4.4 41.8 1.0
CA E:ASP436 4.5 41.9 1.0
N E:TYR466 4.5 42.2 1.0
CB E:ASN463 4.6 42.0 1.0
CA E:TYR466 4.7 42.2 1.0
CG2 E:VAL467 4.7 42.2 1.0
C E:ASP436 4.8 42.1 1.0
CA E:ASN463 4.8 41.9 1.0
N E:ARG464 4.8 42.1 1.0
C E:ASN463 4.9 42.0 1.0
CB E:VAL467 4.9 42.4 1.0
CA E:GLY437 5.0 42.1 1.0

Magnesium binding site 6 out of 8 in 2vbi

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Magnesium binding site 6 out of 8 in the Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1000

b:28.6
occ:1.00
 OD1 F:ASP436 2.1 41.2 1.0
O F:GLY465 2.1 41.9 1.0
O1A F:TPP2000 2.1 32.9 1.0
OD1 F:ASN463 2.1 42.3 1.0
O3B F:TPP2000 2.3 34.8 1.0
O F:HOH2007 2.4 25.2 1.0
CG F:ASN463 3.2 42.1 1.0
C F:GLY465 3.2 42.1 1.0
CG F:ASP436 3.3 41.9 1.0
PB F:TPP2000 3.4 34.4 1.0
PA F:TPP2000 3.5 33.0 1.0
ND2 F:ASN463 3.6 42.0 1.0
O2B F:TPP2000 3.7 36.7 1.0
N F:GLY465 3.8 42.2 1.0
OD2 F:ASP436 3.8 42.1 1.0
O3A F:TPP2000 3.9 33.9 1.0
N F:ASP436 3.9 41.9 1.0
CA F:GLY465 4.1 42.1 1.0
N F:GLY437 4.2 42.1 1.0
N F:VAL467 4.2 42.4 1.0
N F:TYR466 4.2 42.3 1.0
O F:ILE461 4.2 41.6 1.0
O2A F:TPP2000 4.4 33.8 1.0
N F:ASN463 4.4 41.9 1.0
CB F:ASP436 4.4 42.0 1.0
O7 F:TPP2000 4.5 31.4 1.0
CA F:TYR466 4.5 42.2 1.0
CB F:ASN463 4.5 42.1 1.0
CG2 F:VAL467 4.5 42.2 1.0
CA F:ASP436 4.6 42.0 1.0
CA F:GLY435 4.6 41.9 1.0
N F:ARG464 4.7 42.2 1.0
C F:ASN463 4.7 42.0 1.0
C F:GLY435 4.7 41.8 1.0
O1B F:TPP2000 4.7 34.9 1.0
CA F:ASN463 4.7 42.0 1.0
CB F:VAL467 4.8 42.4 1.0
C F:TYR466 4.9 42.2 1.0
C F:ASP436 4.9 42.1 1.0
C F:ARG464 5.0 42.3 1.0

Magnesium binding site 7 out of 8 in 2vbi

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Magnesium binding site 7 out of 8 in the Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1000

b:37.2
occ:1.00
 O G:HOH2011 1.9 46.9 1.0
O3A G:TPP2000 2.1 41.9 1.0
O G:GLY465 2.1 42.0 1.0
OD1 G:ASN463 2.3 42.3 1.0
OD1 G:ASP436 2.3 41.3 1.0
PB G:TPP2000 3.0 43.0 1.0
O1A G:TPP2000 3.0 40.1 1.0
PA G:TPP2000 3.2 40.8 1.0
O3B G:TPP2000 3.2 43.3 1.0
O2B G:TPP2000 3.2 44.2 1.0
C G:GLY465 3.3 42.2 1.0
CG G:ASN463 3.3 42.1 1.0
CG G:ASP436 3.5 42.0 1.0
ND2 G:ASN463 3.6 42.0 1.0
N G:ASP436 4.0 41.9 1.0
N G:VAL467 4.0 42.4 1.0
N G:GLY465 4.1 42.3 1.0
O7 G:TPP2000 4.1 41.4 1.0
OD2 G:ASP436 4.2 42.1 1.0
N G:TYR466 4.2 42.2 1.0
CA G:GLY465 4.2 42.1 1.0
N G:GLY437 4.2 42.1 1.0
O2A G:TPP2000 4.3 41.3 1.0
CA G:TYR466 4.3 42.2 1.0
O G:ILE461 4.4 41.6 1.0
O1B G:TPP2000 4.4 41.2 1.0
CG2 G:VAL467 4.5 42.3 1.0
CA G:GLY435 4.6 41.8 1.0
CB G:ASN463 4.6 42.1 1.0
CB G:VAL467 4.7 42.4 1.0
N G:ASN463 4.7 41.8 1.0
CB G:ASP436 4.7 42.0 1.0
C G:GLY435 4.7 41.8 1.0
C G:TYR466 4.8 42.2 1.0
CA G:ASP436 4.8 42.0 1.0
C G:ASN463 4.9 42.0 1.0
CA G:ASN463 5.0 42.0 1.0
N G:ARG464 5.0 42.1 1.0

Magnesium binding site 8 out of 8 in 2vbi

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Magnesium binding site 8 out of 8 in the Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Holostructure of Pyruvate Decarboxylase From Acetobacter Pasteurianus within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1000

b:41.8
occ:1.00
 O1A H:TPP2000 2.0 33.8 1.0
O H:HOH2013 2.0 40.7 1.0
OD1 H:ASN463 2.0 42.2 1.0
O H:GLY465 2.1 42.1 1.0
OD1 H:ASP436 2.2 41.4 1.0
O3B H:TPP2000 2.6 39.2 1.0
CG H:ASN463 3.1 42.1 1.0
C H:GLY465 3.3 42.2 1.0
PA H:TPP2000 3.3 36.8 1.0
O2B H:TPP2000 3.3 38.5 1.0
CG H:ASP436 3.4 41.9 1.0
PB H:TPP2000 3.4 39.2 1.0
ND2 H:ASN463 3.5 41.9 1.0
O3A H:TPP2000 3.8 37.9 1.0
N H:GLY465 3.9 42.2 1.0
OD2 H:ASP436 4.0 42.2 1.0
N H:ASP436 4.0 41.9 1.0
CA H:GLY465 4.1 42.1 1.0
N H:VAL467 4.2 42.4 1.0
O H:ILE461 4.2 41.7 1.0
O2A H:TPP2000 4.2 37.7 1.0
N H:GLY437 4.3 42.1 1.0
N H:TYR466 4.3 42.2 1.0
N H:ASN463 4.4 41.8 1.0
O7 H:TPP2000 4.4 36.7 1.0
CB H:ASN463 4.4 42.1 1.0
CG2 H:VAL467 4.5 42.3 1.0
CA H:TYR466 4.5 42.2 1.0
CB H:ASP436 4.5 42.0 1.0
N H:ARG464 4.7 42.1 1.0
C H:ASN463 4.7 42.0 1.0
CA H:GLY435 4.7 41.8 1.0
CA H:ASN463 4.7 42.0 1.0
CA H:ASP436 4.7 42.0 1.0
CB H:VAL467 4.7 42.4 1.0
C H:GLY435 4.8 41.8 1.0
O1B H:TPP2000 4.8 39.1 1.0
C H:TYR466 4.9 42.2 1.0

Reference:

D.Gocke, C.L.Berthold, G.Schneider, M.Pohl. N/A N/A.
Page generated: Sun Aug 10 15:00:11 2025

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