Magnesium 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:

Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mddef in Complex with Mvapp, ADPBEF3 and Magnesium, PDB code: 6e2v:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6e2v

Go back to Magnesium Binding Sites List in 6e2v
Magnesium binding site 1 out of 2 in the Mddef in Complex with Mvapp, ADPBEF3 and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg401

b:22.4
occ:1.00
O2A A:DP6403 2.0 17.4 1.0
O1A A:ADP405 2.1 18.3 1.0
F3 A:BEF404 2.1 24.5 1.0
O1B A:ADP405 2.1 21.3 1.0
O A:HOH527 2.1 13.7 1.0
OG A:SER106 2.2 19.3 1.0
HB3 A:SER106 3.0 26.0 1.0
HG A:SER191 3.1 20.3 1.0
CB A:SER106 3.1 21.6 1.0
PA A:ADP405 3.3 22.1 1.0
PB A:ADP405 3.3 25.5 1.0
BE A:BEF404 3.3 22.8 1.0
H A:SER106 3.4 22.4 1.0
PA A:DP6403 3.5 18.7 1.0
H51 A:DP6403 3.5 20.5 1.0
O3A A:ADP405 3.6 21.7 1.0
HA A:ALA104 3.6 27.5 1.0
O2B A:ADP405 3.8 30.5 1.0
HB2 A:SER106 3.8 26.0 1.0
F2 A:BEF404 3.8 23.8 1.0
OG A:SER191 3.8 16.9 1.0
O A:HOH519 3.9 17.8 1.0
HG A:SER140 3.9 24.1 1.0
OG A:SER140 3.9 20.1 1.0
O5' A:ADP405 3.9 22.2 1.0
HB2 A:SER191 4.0 23.4 1.0
N A:SER106 4.0 18.7 1.0
CA A:SER106 4.1 18.2 1.0
MG A:MG402 4.1 39.1 1.0
H A:ALA107 4.2 28.4 1.0
HG A:SER138 4.2 23.0 1.0
O5 A:DP6403 4.2 21.3 1.0
O1A A:DP6403 4.3 16.9 1.0
C5 A:DP6403 4.3 17.1 1.0
OG A:SER138 4.3 19.1 1.0
CB A:SER191 4.4 19.5 1.0
O6 A:DP6403 4.4 16.5 1.0
HZ1 A:LYS187 4.5 32.0 1.0
O2A A:ADP405 4.5 20.6 1.0
N A:ALA107 4.6 23.7 1.0
CA A:ALA104 4.6 22.9 1.0
HB3 A:SER191 4.6 23.4 1.0
O3B A:ADP405 4.6 27.6 1.0
F1 A:BEF404 4.6 25.1 1.0
C A:SER106 4.7 22.9 1.0
HZ2 A:LYS187 4.7 32.0 1.0
H A:ALA104 4.7 29.2 1.0
H52 A:DP6403 4.7 20.5 1.0
HB2 A:ALA107 4.9 26.1 1.0
HA A:SER106 4.9 21.9 1.0
HB3 A:SER140 4.9 20.9 1.0
C A:ALA104 5.0 24.0 1.0
O2B A:DP6403 5.0 19.0 1.0
CB A:SER140 5.0 17.4 1.0

Magnesium binding site 2 out of 2 in 6e2v

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg402

b:39.1
occ:1.00
F2 A:BEF404 2.4 23.8 1.0
O A:HOH527 2.7 13.7 1.0
O A:HOH566 2.7 20.1 1.0
O2 A:DP6403 2.7 15.2 1.0
O3A A:DP6403 2.8 19.2 1.0
H51 A:DP6403 2.9 20.5 1.0
O A:HOH583 3.0 17.4 1.0
HB2 A:ALA104 3.0 25.7 1.0
HO3A A:DP6403 3.1 23.1 1.0
O A:HOH617 3.2 25.3 1.0
HA A:ALA104 3.2 27.5 1.0
F3 A:BEF404 3.4 24.5 1.0
BE A:BEF404 3.5 22.8 1.0
H52 A:DP6403 3.5 20.5 1.0
C5 A:DP6403 3.7 17.1 1.0
HB3 A:SER140 3.7 20.9 1.0
CB A:ALA104 3.7 21.4 1.0
HB1 A:ALA104 3.8 25.7 1.0
HB2 A:SER140 3.8 20.9 1.0
HH22 A:ARG143 3.9 26.5 1.0
CA A:ALA104 3.9 22.9 1.0
C1 A:DP6403 3.9 13.4 1.0
C3 A:DP6403 4.0 17.3 1.0
CB A:SER140 4.1 17.4 1.0
MG A:MG401 4.1 22.4 1.0
OG A:SER140 4.2 20.1 1.0
H A:ALA104 4.2 29.2 1.0
F1 A:BEF404 4.2 25.1 1.0
HH21 A:ARG143 4.3 26.5 1.0
HB3 A:ASP282 4.3 18.8 1.0
HB2 A:ALA107 4.4 26.1 1.0
C4 A:DP6403 4.4 15.6 1.0
N A:ALA104 4.4 24.3 1.0
NH2 A:ARG143 4.4 22.1 1.0
C2 A:DP6403 4.4 15.0 1.0
O2A A:DP6403 4.6 17.4 1.0
HB3 A:ALA104 4.6 25.7 1.0
O A:ASN11 4.6 16.2 1.0
OD1 A:ASP282 4.7 23.9 1.0
HG A:SER140 4.7 24.1 1.0
H22 A:DP6403 4.8 18.0 1.0
H42 A:DP6403 4.8 18.7 1.0
CG A:ASP282 4.8 17.7 1.0
O5 A:DP6403 4.9 21.3 1.0
O1B A:ADP405 4.9 21.3 1.0
HA A:ILE12 4.9 24.7 1.0
O1 A:DP6403 4.9 19.0 1.0
H A:ALA13 5.0 24.1 1.0

Reference:

C.V.Stauffacher, C.-L.Chen. Visualizing the Enzyme Mechanism of the Mevalonate Diphosphate Decarboxylase To Be Published.
Page generated: Mon Dec 14 22:37:52 2020

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