Atomistry » Magnesium » PDB 2wkp-2x0q » 2wvg
Atomistry »
  Magnesium »
    PDB 2wkp-2x0q »
      2wvg »

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

Go back to Magnesium Binding Sites List in 2wvg
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: Wed Aug 14 06:15:46 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy