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Magnesium in PDB 3oab: Mint Deletion Mutant of Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Ligands

Enzymatic activity of Mint Deletion Mutant of Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Ligands

All present enzymatic activity of Mint Deletion Mutant of Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Ligands:
2.5.1.1;

Protein crystallography data

The structure of Mint Deletion Mutant of Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Ligands, PDB code: 3oab was solved by F.-L.Hsieh, T.-H.Chang, T.-P.Ko, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.96 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.274, 109.258, 182.727, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 27.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mint Deletion Mutant of Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Ligands (pdb code 3oab). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mint Deletion Mutant of Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Ligands, PDB code: 3oab:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3oab

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Magnesium binding site 1 out of 4 in the Mint Deletion Mutant of Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Ligands


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mint Deletion Mutant of Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Ligands within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:32.3
occ:1.00
 O7 A:DST804 2.0 47.9 1.0
O A:HOH393 2.1 53.8 1.0
OD1 A:ASP83 2.2 29.0 1.0
OD2 A:ASP89 2.2 34.7 1.0
O A:HOH400 2.4 32.1 1.0
CG A:ASP83 2.9 29.2 1.0
P3 A:DST804 3.0 46.7 1.0
OD2 A:ASP83 3.0 33.0 1.0
CG A:ASP89 3.0 35.0 1.0
OD1 A:ASP89 3.1 33.8 1.0
O8 A:DST804 3.4 48.3 1.0
MG A:MG904 3.6 33.6 1.0
S9 A:DST804 3.7 57.0 1.0
O A:HOH423 4.0 22.8 1.0
C10 A:DST804 4.0 49.9 1.0
O2 A:DST804 4.2 49.7 1.0
CB A:ASP83 4.4 26.6 1.0
OD2 A:ASP159 4.4 43.0 1.0
NE2 A:GLN156 4.4 33.1 1.0
CB A:ASP89 4.5 36.0 1.0
OE1 A:GLN156 4.6 37.4 1.0
O4 A:DST804 4.8 52.1 1.0
C11 A:DST804 4.8 50.5 1.0
CD A:GLN156 4.9 35.6 1.0
O A:ASP83 4.9 27.3 1.0
P1 A:DST804 5.0 51.3 1.0

Magnesium binding site 2 out of 4 in 3oab

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Magnesium binding site 2 out of 4 in the Mint Deletion Mutant of Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Ligands


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mint Deletion Mutant of Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Ligands within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg904

b:33.6
occ:1.00
 O4 A:DST804 2.1 52.1 1.0
OD2 A:ASP83 2.2 33.0 1.0
O A:HOH423 2.3 22.8 1.0
OD2 A:ASP89 2.3 34.7 1.0
O7 A:DST804 2.4 47.9 1.0
CG A:ASP89 3.3 35.0 1.0
P1 A:DST804 3.3 51.3 1.0
CG A:ASP83 3.4 29.2 1.0
CB A:ASP89 3.5 36.0 1.0
O2 A:DST804 3.6 49.7 1.0
MG A:MG903 3.6 32.3 1.0
OD1 A:ASP84 3.7 37.7 1.0
P3 A:DST804 3.7 46.7 1.0
NH1 A:ARG94 3.7 28.8 1.0
OD1 A:ASP91 3.8 43.0 1.0
OD1 A:ASP83 4.0 29.0 1.0
O6 A:DST804 4.2 53.2 1.0
O A:ASP83 4.3 27.3 1.0
O5 A:DST804 4.4 51.9 1.0
OD1 A:ASP89 4.4 33.8 1.0
CB A:ASP83 4.5 26.6 1.0
C A:ASP83 4.6 28.6 1.0
CZ A:ARG94 4.8 31.3 1.0
C10 A:DST804 4.8 49.9 1.0
CG A:ASP84 4.8 34.7 1.0
O8 A:DST804 4.9 48.3 1.0
CG A:ASP91 4.9 42.1 1.0
O A:HOH400 5.0 32.1 1.0
S9 A:DST804 5.0 57.0 1.0
N A:ASP84 5.0 28.7 1.0

Magnesium binding site 3 out of 4 in 3oab

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Magnesium binding site 3 out of 4 in the Mint Deletion Mutant of Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Ligands


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mint Deletion Mutant of Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Ligands within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg901

b:58.9
occ:1.00
 OD2 D:ASP221 2.5 46.4 1.0
O8 D:DST802 2.7 57.4 1.0
O6 D:DST802 2.8 51.0 1.0
CG D:ASP221 3.3 42.4 1.0
O2 D:DST802 3.3 53.8 1.0
OD1 D:ASP221 3.5 39.8 1.0
P3 D:DST802 3.5 56.8 1.0
P1 D:DST802 3.6 47.1 1.0
OD1 D:ASP225 3.7 58.7 1.0
OD2 D:ASP240 3.9 85.3 1.0
O D:HOH297 4.0 38.6 1.0
O7 D:DST802 4.2 57.1 1.0
CG D:ASP225 4.2 57.3 1.0
O D:ASP221 4.2 43.5 1.0
NZ D:LYS235 4.3 26.4 1.0
CB D:ASP225 4.3 54.1 1.0
O5 D:DST802 4.4 49.2 1.0
CG D:ASP240 4.5 84.9 1.0
NE2 D:GLN218 4.5 40.2 1.0
OD1 D:ASP240 4.5 85.3 1.0
C D:ASP221 4.6 43.4 1.0
CB D:ASP221 4.6 40.5 1.0
OD1 D:ASP222 4.7 55.9 1.0
O4 D:DST802 4.7 50.5 1.0

Magnesium binding site 4 out of 4 in 3oab

Go back to Magnesium Binding Sites List in 3oab
Magnesium binding site 4 out of 4 in the Mint Deletion Mutant of Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Ligands


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mint Deletion Mutant of Heterotetrameric Geranyl Pyrophosphate Synthase in Complex with Ligands within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg902

b:54.4
occ:1.00
 O D:HOH402 1.9 37.5 1.0
O7 D:DST802 2.0 57.1 1.0
O D:HOH297 2.3 38.6 1.0
O4 D:DST802 2.3 50.5 1.0
OD2 D:ASP89 2.3 48.5 1.0
OD2 D:ASP83 2.4 38.2 1.0
P1 D:DST802 3.3 47.1 1.0
CG D:ASP89 3.4 48.4 1.0
CG D:ASP83 3.5 38.1 1.0
P3 D:DST802 3.5 56.8 1.0
O6 D:DST802 3.5 51.0 1.0
OD1 D:ASP91 3.6 47.2 1.0
O D:HOH298 3.8 35.8 1.0
O2 D:DST802 3.8 53.8 1.0
CB D:ASP89 3.9 47.7 1.0
OD1 D:ASP83 4.0 37.7 1.0
NH1 D:ARG94 4.4 25.6 1.0
OD1 D:ASP89 4.5 49.4 1.0
OD1 D:ASP84 4.5 29.5 1.0
O D:ASP83 4.5 35.3 1.0
NZ D:LYS245 4.6 89.3 1.0
O5 D:DST802 4.6 49.2 1.0
O8 D:DST802 4.7 57.4 1.0
CG D:ASP91 4.7 43.5 1.0
S9 D:DST802 4.7 60.2 1.0
CB D:ASP83 4.8 37.1 1.0
O D:HOH299 4.8 42.7 1.0
C10 D:DST802 4.8 58.6 1.0

Reference:

F.-L.Hsieh, T.-H.Chang, T.-P.Ko, A.H.-J.Wang. Enhanced Specificity of Mint Geranyl Pyrophosphate Synthase By Modifying the R-Loop Interactions J.Mol.Biol. V. 404 859 2010.
ISSN: ISSN 0022-2836
PubMed: 20965200
DOI: 10.1016/J.JMB.2010.10.011
Page generated: Thu Aug 15 08:13:49 2024

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