Fluorine in PDB 6e2v: Mddef in Complex with Mvapp, ADPBEF3 and Magnesium

Enzymatic activity of Mddef in Complex with Mvapp, ADPBEF3 and Magnesium

All present enzymatic activity of Mddef in Complex with Mvapp, ADPBEF3 and Magnesium:
4.1.1.33;

Protein crystallography data

The structure of Mddef in Complex with Mvapp, ADPBEF3 and Magnesium, PDB code: 6e2v was solved by C.V.Stauffacher, C.-L.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.70 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.636, 98.599, 45.632, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.3

Other elements in 6e2v:

The structure of Mddef in Complex with Mvapp, ADPBEF3 and Magnesium also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Mddef in Complex with Mvapp, ADPBEF3 and Magnesium (pdb code 6e2v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Mddef in Complex with Mvapp, ADPBEF3 and Magnesium, PDB code: 6e2v:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6e2v

Go back to Fluorine Binding Sites List in 6e2v
Fluorine binding site 1 out of 3 in the Mddef in Complex with Mvapp, ADPBEF3 and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Mddef in Complex with Mvapp, ADPBEF3 and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:25.1
occ:1.00
F1 A:BEF404 0.0 25.1 1.0
BE A:BEF404 1.5 22.8 1.0
H A:ALA283 2.2 22.1 1.0
HA2 A:GLY102 2.4 21.8 1.0
HB3 A:ALA283 2.5 26.0 1.0
F2 A:BEF404 2.5 23.8 1.0
F3 A:BEF404 2.5 24.5 1.0
HO3A A:DP6403 2.6 23.1 1.0
HZ1 A:LYS187 2.7 32.0 1.0
HB3 A:ASP282 2.8 18.8 1.0
HZ3 A:LYS187 2.9 32.0 1.0
N A:ALA283 3.0 18.4 1.0
O2B A:ADP405 3.0 30.5 1.0
HG A:SER191 3.1 20.3 1.0
NZ A:LYS187 3.2 26.6 1.0
CB A:ALA283 3.3 21.7 1.0
CA A:GLY102 3.4 18.2 1.0
OG A:SER191 3.4 16.9 1.0
O3A A:DP6403 3.4 19.2 1.0
CA A:ALA283 3.5 18.7 1.0
H3A1 A:DP6403 3.6 18.6 1.0
HZ2 A:LYS187 3.6 32.0 1.0
HB2 A:ALA283 3.6 26.0 1.0
CB A:ASP282 3.6 15.7 1.0
HB2 A:ASP282 3.6 18.8 1.0
HA3 A:GLY102 3.7 21.8 1.0
O A:ALA283 3.8 20.4 1.0
C A:ALA283 3.9 19.5 1.0
C A:GLY102 3.9 22.2 1.0
H51 A:DP6403 4.0 20.5 1.0
HB1 A:ALA283 4.0 26.0 1.0
C A:ASP282 4.1 18.9 1.0
H A:ALA104 4.1 29.2 1.0
H42 A:DP6403 4.2 18.7 1.0
O A:GLY102 4.2 16.9 1.0
H A:GLY102 4.2 26.3 1.0
MG A:MG402 4.2 39.1 1.0
C3A A:DP6403 4.3 15.5 1.0
PB A:ADP405 4.3 25.5 1.0
N A:GLY102 4.3 21.9 1.0
C3 A:DP6403 4.4 17.3 1.0
CA A:ASP282 4.4 20.0 1.0
HA A:ALA283 4.4 22.5 1.0
O A:HOH617 4.5 25.3 1.0
HE2 A:LYS187 4.5 31.4 1.0
CE A:LYS187 4.5 26.2 1.0
H3A2 A:DP6403 4.5 18.6 1.0
C4 A:DP6403 4.6 15.6 1.0
MG A:MG401 4.6 22.4 1.0
CB A:SER191 4.7 19.5 1.0
O1B A:ADP405 4.7 21.3 1.0
HB3 A:SER191 4.7 23.4 1.0
N A:LEU103 4.7 21.5 1.0
CG A:ASP282 4.7 17.7 1.0
C5 A:DP6403 4.8 17.1 1.0
HA A:ASP282 4.8 24.0 1.0
O3A A:ADP405 4.8 21.7 1.0
H A:LEU103 4.9 25.8 1.0
N A:GLY284 4.9 13.4 1.0
N A:ALA104 4.9 24.3 1.0
HA A:ALA104 4.9 27.5 1.0

Fluorine binding site 2 out of 3 in 6e2v

Go back to Fluorine Binding Sites List in 6e2v
Fluorine binding site 2 out of 3 in the Mddef in Complex with Mvapp, ADPBEF3 and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Mddef in Complex with Mvapp, ADPBEF3 and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:23.8
occ:1.00
F2 A:BEF404 0.0 23.8 1.0
BE A:BEF404 1.6 22.8 1.0
H A:ALA104 2.4 29.2 1.0
MG A:MG402 2.4 39.1 1.0
F1 A:BEF404 2.5 25.1 1.0
F3 A:BEF404 2.5 24.5 1.0
HA A:ALA104 2.6 27.5 1.0
O A:HOH617 2.8 25.3 1.0
O2B A:ADP405 2.9 30.5 1.0
N A:ALA104 2.9 24.3 1.0
HO3A A:DP6403 3.1 23.1 1.0
CA A:ALA104 3.1 22.9 1.0
HB2 A:ALA104 3.2 25.7 1.0
O A:HOH527 3.4 13.7 1.0
O3A A:DP6403 3.4 19.2 1.0
HA2 A:GLY102 3.5 21.8 1.0
HB3 A:ASP282 3.5 18.8 1.0
O1B A:ADP405 3.7 21.3 1.0
CB A:ALA104 3.7 21.4 1.0
C A:GLY102 3.8 22.2 1.0
MG A:MG401 3.8 22.4 1.0
PB A:ADP405 3.8 25.5 1.0
H51 A:DP6403 3.9 20.5 1.0
N A:LEU103 4.0 21.5 1.0
C A:LEU103 4.0 27.7 1.0
O A:GLY102 4.0 16.9 1.0
HB2 A:ASP282 4.1 18.8 1.0
CA A:GLY102 4.1 18.2 1.0
HZ1 A:LYS187 4.2 32.0 1.0
CB A:ASP282 4.2 15.7 1.0
HG A:SER191 4.2 20.3 1.0
H A:LEU103 4.2 25.8 1.0
HB1 A:ALA104 4.3 25.7 1.0
H A:ALA283 4.3 22.1 1.0
CA A:LEU103 4.4 22.3 1.0
HB3 A:ALA104 4.4 25.7 1.0
HA A:LEU103 4.4 26.8 1.0
O A:HOH583 4.5 17.4 1.0
C A:ALA104 4.5 24.0 1.0
CG A:ASP282 4.7 17.7 1.0
H A:GLY102 4.7 26.3 1.0
HZ1 A:LYS288 4.7 30.0 1.0
H A:SER105 4.7 26.3 1.0
O A:HOH566 4.8 20.1 1.0
C5 A:DP6403 4.8 17.1 1.0
HA3 A:GLY102 4.8 21.8 1.0
O3B A:ADP405 4.8 27.6 1.0
C3 A:DP6403 4.8 17.3 1.0
O2 A:DP6403 4.8 15.2 1.0
OG A:SER191 4.9 16.9 1.0
N A:GLY102 4.9 21.9 1.0
HB3 A:ALA283 5.0 26.0 1.0
NZ A:LYS187 5.0 26.6 1.0
O2A A:DP6403 5.0 17.4 1.0
O A:LEU103 5.0 20.5 1.0
HZ3 A:LYS187 5.0 32.0 1.0
N A:SER105 5.0 21.9 1.0

Fluorine binding site 3 out of 3 in 6e2v

Go back to Fluorine Binding Sites List in 6e2v
Fluorine binding site 3 out of 3 in the Mddef in Complex with Mvapp, ADPBEF3 and Magnesium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Mddef in Complex with Mvapp, ADPBEF3 and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:24.5
occ:1.00
F3 A:BEF404 0.0 24.5 1.0
BE A:BEF404 1.5 22.8 1.0
HG A:SER191 1.9 20.3 1.0
MG A:MG401 2.1 22.4 1.0
F2 A:BEF404 2.5 23.8 1.0
F1 A:BEF404 2.5 25.1 1.0
H51 A:DP6403 2.7 20.5 1.0
OG A:SER191 2.7 16.9 1.0
O2A A:DP6403 2.9 17.4 1.0
O2B A:ADP405 2.9 30.5 1.0
O1B A:ADP405 2.9 21.3 1.0
O1A A:ADP405 2.9 18.3 1.0
O A:HOH527 3.0 13.7 1.0
HO3A A:DP6403 3.2 23.1 1.0
HZ1 A:LYS187 3.2 32.0 1.0
PB A:ADP405 3.3 25.5 1.0
MG A:MG402 3.4 39.1 1.0
C5 A:DP6403 3.6 17.1 1.0
HZ2 A:LYS187 3.6 32.0 1.0
O3A A:DP6403 3.7 19.2 1.0
CB A:SER191 3.7 19.5 1.0
HB3 A:SER191 3.8 23.4 1.0
NZ A:LYS187 3.8 26.6 1.0
O3A A:ADP405 3.8 21.7 1.0
HB2 A:SER191 3.8 23.4 1.0
PA A:ADP405 3.8 22.1 1.0
HA A:ALA104 3.8 27.5 1.0
HZ3 A:LYS187 3.9 32.0 1.0
H42 A:DP6403 3.9 18.7 1.0
O5 A:DP6403 4.0 21.3 1.0
HB3 A:ALA283 4.0 26.0 1.0
PA A:DP6403 4.1 18.7 1.0
H A:ALA104 4.1 29.2 1.0
C4 A:DP6403 4.2 15.6 1.0
H52 A:DP6403 4.2 20.5 1.0
HA2 A:GLY102 4.2 21.8 1.0
OG A:SER106 4.3 19.3 1.0
H A:ALA283 4.6 22.1 1.0
C3 A:DP6403 4.6 17.3 1.0
O2A A:ADP405 4.7 20.6 1.0
CA A:ALA104 4.7 22.9 1.0
H3A1 A:DP6403 4.7 18.6 1.0
HB3 A:ASP282 4.8 18.8 1.0
N A:ALA104 4.8 24.3 1.0
O3B A:ADP405 4.8 27.6 1.0
H A:SER106 4.8 22.4 1.0
CB A:ALA283 4.9 21.7 1.0
HB3 A:SER106 4.9 26.0 1.0
H A:SER191 5.0 23.5 1.0
HB2 A:ALA283 5.0 26.0 1.0

Reference:

C.V.Stauffacher, C.-L.Chen. Visualizing the Enzyme Mechanism of the Mevalonate Diphosphate Decarboxylase To Be Published.
Page generated: Sun Dec 13 12:48:42 2020

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