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Fluorine 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:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis, PDB code: 2wvg:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 2wvg

Go back to Fluorine Binding Sites List in 2wvg
Fluorine 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 Fluorine with other atoms in the F 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:F569

b:37.1
occ:1.00
 N A:ASP27 2.8 17.5 1.0
OG1 A:THR72 2.8 19.7 1.0
OD1 A:ASP27 2.9 23.2 1.0
NE2 A:HIS114 2.9 22.6 1.0
CA A:GLY26 3.1 14.5 1.0
C A:GLY26 3.2 21.3 1.0
CD2 A:HIS114 3.3 20.9 1.0
O B:HOH2455 3.3 38.6 1.0
CB A:THR72 3.6 20.6 1.0
CG2 A:THR72 3.6 18.3 1.0
N A:TYR28 3.8 15.4 1.0
CG A:ASP27 3.9 28.8 1.0
CA A:ASP27 3.9 16.1 1.0
C35 B:TPU600 3.9 14.1 1.0
CE1 A:HIS114 4.1 19.9 1.0
O A:GLY26 4.2 17.2 1.0
O B:HOH2329 4.3 48.8 1.0
CB A:ASP27 4.4 17.8 1.0
CD2 A:TYR28 4.4 14.8 1.0
C A:ASP27 4.4 19.3 1.0
C5' B:TPU600 4.4 14.7 1.0
N A:GLY26 4.5 16.7 1.0
CG A:HIS114 4.6 15.8 1.0
OE1 B:GLU473 4.7 44.2 1.0
N4' B:TPU600 4.8 14.2 1.0
NE2 A:HIS113 4.8 21.7 1.0
C4' B:TPU600 4.8 15.4 1.0
OD2 A:ASP27 4.9 25.9 1.0
CB A:TYR28 4.9 11.8 1.0
CG A:TYR28 5.0 12.6 1.0
CA A:TYR28 5.0 11.7 1.0
ND1 A:HIS114 5.0 16.2 1.0

Fluorine binding site 2 out of 4 in 2wvg

Go back to Fluorine Binding Sites List in 2wvg
Fluorine 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 Fluorine with other atoms in the F 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:F569

b:37.6
occ:1.00
 NE2 B:HIS114 2.8 22.1 1.0
OG1 B:THR72 2.9 19.7 1.0
N B:ASP27 2.9 17.8 1.0
OD1 B:ASP27 2.9 23.0 1.0
CD2 B:HIS114 3.2 21.3 1.0
CA B:GLY26 3.2 16.6 1.0
O A:HOH2496 3.3 35.9 1.0
C B:GLY26 3.3 20.8 1.0
CG2 B:THR72 3.6 14.4 1.0
CB B:THR72 3.6 21.5 1.0
C35 A:TPU600 3.9 12.3 1.0
CG B:ASP27 3.9 28.5 1.0
N B:TYR28 3.9 15.1 1.0
CA B:ASP27 4.0 18.6 1.0
CE1 B:HIS114 4.0 21.8 1.0
O B:GLY26 4.3 18.0 1.0
C5' A:TPU600 4.4 16.5 1.0
CD2 B:TYR28 4.4 16.0 1.0
CB B:ASP27 4.4 18.8 1.0
O A:HOH2573 4.4 44.6 1.0
CG B:HIS114 4.5 17.9 1.0
C B:ASP27 4.5 19.1 1.0
N B:GLY26 4.6 15.9 1.0
NE2 B:HIS113 4.7 20.9 1.0
N4' A:TPU600 4.8 14.6 1.0
C4' A:TPU600 4.8 13.9 1.0
OE1 A:GLU473 4.8 43.7 1.0
ND1 B:HIS114 4.9 19.4 1.0
OD2 B:ASP27 4.9 26.7 1.0
CB B:TYR28 4.9 12.5 1.0
CG B:TYR28 5.0 14.2 1.0
C6' A:TPU600 5.0 17.4 1.0

Fluorine binding site 3 out of 4 in 2wvg

Go back to Fluorine Binding Sites List in 2wvg
Fluorine 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 Fluorine with other atoms in the F 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:F569

b:35.7
occ:1.00
 OG1 E:THR72 2.8 15.1 1.0
N E:ASP27 2.8 14.4 1.0
OD1 E:ASP27 2.8 20.2 1.0
NE2 E:HIS114 2.9 18.8 1.0
CD2 E:HIS114 3.2 20.2 1.0
CA E:GLY26 3.2 13.7 1.0
C E:GLY26 3.2 17.5 1.0
O F:HOH2503 3.3 42.9 1.0
CB E:THR72 3.5 18.0 1.0
CG2 E:THR72 3.6 15.7 1.0
N E:TYR28 3.7 16.1 1.0
CG E:ASP27 3.8 28.9 1.0
CA E:ASP27 3.9 12.1 1.0
C35 F:TPU600 4.0 12.0 1.0
CE1 E:HIS114 4.2 18.1 1.0
O E:GLY26 4.2 15.7 1.0
CD2 E:TYR28 4.2 12.8 1.0
C E:ASP27 4.3 17.8 1.0
CB E:ASP27 4.3 16.0 1.0
C5' F:TPU600 4.5 12.6 1.0
CG E:HIS114 4.5 18.2 1.0
N E:GLY26 4.6 13.7 1.0
NE2 E:HIS113 4.7 19.3 1.0
CB E:TYR28 4.7 11.9 1.0
CG E:TYR28 4.8 10.4 1.0
OE1 F:GLU473 4.8 44.1 1.0
CA E:TYR28 4.8 9.6 1.0
OD2 E:ASP27 4.8 23.1 1.0
N4' F:TPU600 4.9 10.2 1.0
CE2 E:TYR28 4.9 13.7 1.0
C4' F:TPU600 4.9 11.6 1.0
ND1 E:HIS114 5.0 15.2 1.0
CA E:THR72 5.0 13.1 1.0

Fluorine binding site 4 out of 4 in 2wvg

Go back to Fluorine Binding Sites List in 2wvg
Fluorine 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 Fluorine with other atoms in the F 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:F570

b:34.2
occ:1.00
 NE2 F:HIS114 2.8 20.9 1.0
OG1 F:THR72 2.9 16.5 1.0
N F:ASP27 2.9 14.4 1.0
OD1 F:ASP27 2.9 19.5 1.0
CD2 F:HIS114 3.2 19.3 1.0
CA F:GLY26 3.2 12.4 1.0
C F:GLY26 3.3 16.8 1.0
O E:HOH2535 3.4 44.1 1.0
CG2 F:THR72 3.6 14.0 1.0
CB F:THR72 3.6 20.4 1.0
C35 E:TPU600 3.9 11.7 1.0
CG F:ASP27 3.9 21.7 1.0
N F:TYR28 4.0 13.9 1.0
CA F:ASP27 4.0 14.5 1.0
CE1 F:HIS114 4.0 18.1 1.0
O F:GLY26 4.3 12.9 1.0
CD2 F:TYR28 4.4 13.0 1.0
C5' E:TPU600 4.4 11.7 1.0
CB F:ASP27 4.4 20.0 1.0
CG F:HIS114 4.5 18.7 1.0
C F:ASP27 4.5 14.7 1.0
N F:GLY26 4.6 11.2 1.0
N4' E:TPU600 4.7 10.5 1.0
NE2 F:HIS113 4.8 20.5 1.0
C4' E:TPU600 4.8 10.7 1.0
ND1 F:HIS114 4.9 13.9 1.0
OE1 E:GLU473 4.9 40.0 1.0
O E:HOH2628 4.9 60.0 1.0
OD2 F:ASP27 4.9 24.7 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: Sun Dec 13 11:41:14 2020

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