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Magnesium in PDB 2wvg: Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis

Enzymatic activity of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis

All present enzymatic activity of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis:
4.1.1.1;

Protein crystallography data

The structure of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis, PDB code: 2wvg was solved by X.Y.Pei, K.Erixon, B.F.Luisi, F.J.Leeper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.04 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.277, 92.092, 98.630, 73.44, 85.76, 67.82
R / Rfree (%) 15.7 / 18.7

Other elements in 2wvg:

The structure of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis (pdb code 2wvg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis, PDB code: 2wvg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2wvg

Go back to Magnesium Binding Sites List in 2wvg
Magnesium binding site 1 out of 4 in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:14.9
occ:1.00
 O12 A:TPU600 2.2 19.0 1.0
O A:GLY469 2.2 18.4 1.0
OD1 A:ASN467 2.2 21.6 1.0
OD1 A:ASP440 2.2 22.6 1.0
O21 A:TPU600 2.3 21.9 1.0
O A:HOH2489 2.4 21.3 1.0
CG A:ASN467 3.2 27.9 1.0
P1 A:TPU600 3.4 19.8 1.0
CG A:ASP440 3.4 23.4 1.0
P2 A:TPU600 3.4 22.6 1.0
C A:GLY469 3.4 21.7 1.0
ND2 A:ASN467 3.5 23.8 1.0
O11 A:TPU600 3.7 20.0 1.0
OD2 A:ASP440 3.9 24.1 1.0
N A:ASP440 4.1 18.8 1.0
O23 A:TPU600 4.1 34.1 1.0
N A:GLY469 4.1 20.5 1.0
N A:GLY441 4.2 17.1 1.0
N A:THR471 4.2 24.9 1.0
O5G A:TPU600 4.2 18.9 1.0
O A:ILE465 4.3 23.4 1.0
CA A:GLY469 4.3 16.3 1.0
N A:TYR470 4.4 21.1 1.0
CA A:TYR470 4.5 22.1 1.0
N A:ASN467 4.5 23.3 1.0
O13 A:TPU600 4.5 17.8 1.0
O A:HOH2495 4.5 22.8 1.0
CB A:ASN467 4.6 22.2 1.0
OG1 A:THR471 4.6 30.8 1.0
CB A:ASP440 4.6 19.6 1.0
CA A:GLY439 4.7 17.5 1.0
C A:GLY439 4.7 22.3 1.0
CA A:ASP440 4.7 19.6 1.0
O22 A:TPU600 4.7 43.1 1.0
C A:ASN467 4.8 24.2 1.0
N A:TYR468 4.8 20.6 1.0
CA A:ASN467 4.8 24.8 1.0
C A:TYR470 4.9 24.5 1.0
CB A:THR471 4.9 25.2 1.0
C A:ASP440 5.0 19.7 1.0
CA A:GLY441 5.0 17.0 1.0

Magnesium binding site 2 out of 4 in 2wvg

Go back to Magnesium Binding Sites List in 2wvg
Magnesium binding site 2 out of 4 in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:15.5
occ:1.00
 OD1 B:ASP440 2.1 23.4 1.0
O12 B:TPU600 2.1 21.3 1.0
O B:GLY469 2.2 20.1 1.0
OD1 B:ASN467 2.2 23.8 1.0
O21 B:TPU600 2.3 21.2 1.0
O B:HOH2448 2.4 22.2 1.0
CG B:ASN467 3.2 23.4 1.0
CG B:ASP440 3.3 20.0 1.0
P1 B:TPU600 3.4 19.1 1.0
P2 B:TPU600 3.4 22.9 1.0
C B:GLY469 3.5 22.4 1.0
ND2 B:ASN467 3.6 26.4 1.0
O11 B:TPU600 3.7 19.7 1.0
OD2 B:ASP440 3.9 23.0 1.0
N B:ASP440 4.0 20.7 1.0
N B:GLY469 4.1 21.2 1.0
N B:GLY441 4.1 16.9 1.0
O23 B:TPU600 4.1 30.8 1.0
O5G B:TPU600 4.2 17.0 1.0
O B:ILE465 4.2 21.6 1.0
N B:THR471 4.3 20.1 1.0
CA B:GLY469 4.3 16.5 1.0
N B:TYR470 4.4 19.5 1.0
N B:ASN467 4.4 23.9 1.0
O13 B:TPU600 4.5 18.5 1.0
CB B:ASP440 4.5 22.2 1.0
CA B:TYR470 4.5 22.6 1.0
O B:HOH2450 4.6 25.1 1.0
CB B:ASN467 4.6 27.2 1.0
CA B:ASP440 4.6 16.7 1.0
CA B:GLY439 4.6 18.1 1.0
C B:GLY439 4.7 19.7 1.0
OG1 B:THR471 4.7 31.6 1.0
C B:ASN467 4.8 22.8 1.0
O22 B:TPU600 4.8 43.3 1.0
N B:TYR468 4.8 21.9 1.0
CA B:ASN467 4.8 22.2 1.0
C B:ASP440 4.9 18.2 1.0
CA B:GLY441 4.9 16.9 1.0
C B:TYR470 5.0 21.5 1.0

Magnesium binding site 3 out of 4 in 2wvg

Go back to Magnesium Binding Sites List in 2wvg
Magnesium binding site 3 out of 4 in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:10.2
occ:1.00
 O12 E:TPU600 2.2 16.0 1.0
OD1 E:ASP440 2.2 19.1 1.0
O E:GLY469 2.2 15.0 1.0
OD1 E:ASN467 2.3 18.2 1.0
O21 E:TPU600 2.3 14.8 1.0
O E:HOH2528 2.4 15.6 1.0
CG E:ASN467 3.2 19.6 1.0
P1 E:TPU600 3.4 14.2 1.0
CG E:ASP440 3.4 20.3 1.0
P2 E:TPU600 3.4 18.6 1.0
C E:GLY469 3.4 19.7 1.0
O11 E:TPU600 3.6 13.5 1.0
ND2 E:ASN467 3.6 17.0 1.0
OD2 E:ASP440 3.9 19.1 1.0
N E:ASP440 4.0 13.0 1.0
N E:GLY469 4.1 14.1 1.0
N E:GLY441 4.1 15.2 1.0
O5G E:TPU600 4.2 16.2 1.0
N E:THR471 4.2 18.6 1.0
O E:ILE465 4.3 15.8 1.0
O23 E:TPU600 4.3 34.5 1.0
CA E:GLY469 4.3 13.9 1.0
N E:TYR470 4.4 17.7 1.0
O13 E:TPU600 4.5 14.2 1.0
CA E:TYR470 4.5 19.0 1.0
N E:ASN467 4.5 18.0 1.0
O E:HOH2530 4.5 20.4 1.0
CB E:ASP440 4.6 17.3 1.0
CB E:ASN467 4.6 16.4 1.0
CA E:GLY439 4.7 11.6 1.0
OG1 E:THR471 4.7 26.5 1.0
CA E:ASP440 4.7 14.2 1.0
C E:GLY439 4.7 14.6 1.0
O22 E:TPU600 4.7 30.1 1.0
C E:ASN467 4.8 18.4 1.0
N E:TYR468 4.8 17.3 1.0
CA E:ASN467 4.9 21.1 1.0
C E:TYR470 4.9 19.8 1.0
C E:ASP440 4.9 17.1 1.0
CA E:GLY441 4.9 13.8 1.0
CB E:THR471 4.9 25.9 1.0

Magnesium binding site 4 out of 4 in 2wvg

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Magnesium binding site 4 out of 4 in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg569

b:8.6
occ:1.00
 O12 F:TPU600 2.1 16.6 1.0
OD1 F:ASP440 2.2 18.4 1.0
OD1 F:ASN467 2.2 16.2 1.0
O F:GLY469 2.2 14.2 1.0
O21 F:TPU600 2.3 16.3 1.0
O F:HOH2497 2.3 15.4 1.0
CG F:ASN467 3.2 19.0 1.0
CG F:ASP440 3.3 19.2 1.0
P2 F:TPU600 3.4 19.4 1.0
P1 F:TPU600 3.4 14.1 1.0
C F:GLY469 3.5 16.0 1.0
ND2 F:ASN467 3.5 20.8 1.0
O11 F:TPU600 3.7 13.3 1.0
OD2 F:ASP440 3.9 22.0 1.0
O23 F:TPU600 3.9 20.4 1.0
N F:ASP440 4.0 11.5 1.0
N F:GLY469 4.1 16.4 1.0
N F:GLY441 4.2 12.4 1.0
O5G F:TPU600 4.2 15.6 1.0
N F:THR471 4.2 15.1 1.0
O F:ILE465 4.3 15.7 1.0
CA F:GLY469 4.3 13.0 1.0
N F:TYR470 4.4 18.6 1.0
N F:ASN467 4.4 15.2 1.0
O13 F:TPU600 4.5 12.6 1.0
O F:HOH2499 4.5 18.5 1.0
CB F:ASN467 4.5 15.9 1.0
CA F:TYR470 4.5 19.9 1.0
CB F:ASP440 4.6 16.5 1.0
OG1 F:THR471 4.6 25.1 1.0
CA F:GLY439 4.7 12.5 1.0
CA F:ASP440 4.7 12.4 1.0
C F:ASN467 4.7 15.0 1.0
C F:GLY439 4.7 15.0 1.0
O22 F:TPU600 4.7 31.5 1.0
CA F:ASN467 4.8 18.4 1.0
N F:TYR468 4.8 13.9 1.0
C F:TYR470 4.9 17.9 1.0
CB F:THR471 4.9 21.8 1.0
C F:ASP440 5.0 13.7 1.0

Reference:

X.Y.Pei, K.Erixon, B.F.Luisi, F.J.Leeper. Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis Biochemistry V. 49 1727 2010.
ISSN: ISSN 0006-2960
PubMed: 20099870
DOI: 10.1021/BI901864J
Page generated: Mon Dec 14 07:45:31 2020

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