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Magnesium in PDB 7pco: Burg E232Q Mutant (Holo) in Complex with 2R,3R-2,3-Dihydroxy-6-Methyl- Heptanoate (12): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins

Enzymatic activity of Burg E232Q Mutant (Holo) in Complex with 2R,3R-2,3-Dihydroxy-6-Methyl- Heptanoate (12): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins

All present enzymatic activity of Burg E232Q Mutant (Holo) in Complex with 2R,3R-2,3-Dihydroxy-6-Methyl- Heptanoate (12): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins:
1.1.1.86;

Protein crystallography data

The structure of Burg E232Q Mutant (Holo) in Complex with 2R,3R-2,3-Dihydroxy-6-Methyl- Heptanoate (12): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins, PDB code: 7pco was solved by F.Trottmann, K.Ishida, M.Ishida, H.Kries, M.Groll, C.Hertweck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.73, 83.4, 104.78, 90, 90, 90
R / Rfree (%) 17.6 / 19.9

Other elements in 7pco:

The structure of Burg E232Q Mutant (Holo) in Complex with 2R,3R-2,3-Dihydroxy-6-Methyl- Heptanoate (12): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Burg E232Q Mutant (Holo) in Complex with 2R,3R-2,3-Dihydroxy-6-Methyl- Heptanoate (12): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins (pdb code 7pco). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Burg E232Q Mutant (Holo) in Complex with 2R,3R-2,3-Dihydroxy-6-Methyl- Heptanoate (12): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins, PDB code: 7pco:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7pco

Go back to Magnesium Binding Sites List in 7pco
Magnesium binding site 1 out of 4 in the Burg E232Q Mutant (Holo) in Complex with 2R,3R-2,3-Dihydroxy-6-Methyl- Heptanoate (12): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Burg E232Q Mutant (Holo) in Complex with 2R,3R-2,3-Dihydroxy-6-Methyl- Heptanoate (12): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:33.3
occ:1.00
 O A:HOH1031 1.9 27.0 1.0
O5 B:7FI401 2.0 17.3 1.0
O A:HOH955 2.1 20.0 1.0
OD1 A:ASP191 2.1 17.8 1.0
O7 B:7FI401 2.2 29.6 1.0
O A:HOH901 2.4 16.5 1.0
C6 B:7FI401 2.9 23.9 1.0
C4 B:7FI401 2.9 17.6 1.0
CG A:ASP191 3.1 14.9 1.0
C8 B:7FI401 3.3 24.5 1.0
OD2 A:ASP191 3.5 14.5 1.0
MG A:MG803 3.6 13.0 1.0
OE1 A:GLN194 3.7 25.6 1.0
NH2 A:ARG131 3.8 18.7 1.0
OE2 A:GLU195 3.8 17.3 1.0
OE1 B:GLN232 3.9 33.4 1.0
O A:HOH932 4.2 13.6 1.0
CZ A:ARG131 4.3 15.1 1.0
O A:HOH990 4.3 14.9 1.0
C2 B:7FI401 4.3 16.8 1.0
CB A:ASP191 4.4 15.0 1.0
O A:PRO130 4.5 15.5 1.0
C5N A:NAD801 4.5 14.9 1.0
C4N A:NAD801 4.5 16.3 1.0
O1 B:7FI401 4.6 15.4 1.0
NE2 B:GLN232 4.7 25.5 1.0
NH1 A:ARG131 4.7 16.7 1.0
OE1 B:GLU226 4.7 20.1 1.0
CD B:GLN232 4.7 21.0 1.0
C9 B:7FI401 4.7 28.5 1.0
CD A:GLN194 4.8 17.4 1.0
CD A:GLU195 4.9 15.6 1.0
CA A:ASP191 4.9 15.8 1.0
NE A:ARG131 4.9 13.7 1.0

Magnesium binding site 2 out of 4 in 7pco

Go back to Magnesium Binding Sites List in 7pco
Magnesium binding site 2 out of 4 in the Burg E232Q Mutant (Holo) in Complex with 2R,3R-2,3-Dihydroxy-6-Methyl- Heptanoate (12): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Burg E232Q Mutant (Holo) in Complex with 2R,3R-2,3-Dihydroxy-6-Methyl- Heptanoate (12): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:13.0
occ:1.00
 OD2 A:ASP191 2.0 14.5 1.0
O A:HOH990 2.0 14.9 1.0
OE2 A:GLU195 2.0 17.3 1.0
O5 B:7FI401 2.0 17.3 1.0
O A:HOH967 2.1 14.8 1.0
O1 B:7FI401 2.1 15.4 1.0
C2 B:7FI401 2.9 16.8 1.0
C4 B:7FI401 2.9 17.6 1.0
CG A:ASP191 3.0 14.9 1.0
CD A:GLU195 3.1 15.6 1.0
OD1 A:ASP191 3.4 17.8 1.0
OE1 A:GLU195 3.5 15.0 1.0
MG A:MG802 3.6 33.3 1.0
O A:HOH901 3.6 16.5 1.0
O3 B:7FI401 4.1 14.9 1.0
C6 B:7FI401 4.1 23.9 1.0
O A:HOH932 4.1 13.6 1.0
C8 B:7FI401 4.3 24.5 1.0
CB A:ASP191 4.3 15.0 1.0
O A:HOH955 4.3 20.0 1.0
O2D A:NAD801 4.3 14.1 1.0
OG B:SER254 4.4 14.3 1.0
CG A:GLU195 4.4 14.7 1.0
CE1 A:HIS108 4.4 14.0 1.0
NE2 A:HIS108 4.4 13.2 1.0
ND1 A:HIS108 4.5 14.0 1.0
CD2 A:HIS108 4.6 13.9 1.0
CB B:CYS257 4.6 14.3 1.0
O7 B:7FI401 4.7 29.6 1.0
CG A:HIS108 4.7 13.6 1.0
O A:ASP191 4.9 15.4 1.0

Magnesium binding site 3 out of 4 in 7pco

Go back to Magnesium Binding Sites List in 7pco
Magnesium binding site 3 out of 4 in the Burg E232Q Mutant (Holo) in Complex with 2R,3R-2,3-Dihydroxy-6-Methyl- Heptanoate (12): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Burg E232Q Mutant (Holo) in Complex with 2R,3R-2,3-Dihydroxy-6-Methyl- Heptanoate (12): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:29.0
occ:1.00
 O B:HOH570 2.0 20.3 1.0
OD1 B:ASP191 2.0 15.4 1.0
O5 A:7FI804 2.0 16.5 1.0
O B:HOH563 2.1 22.5 1.0
O B:HOH501 2.2 16.7 1.0
O7 A:7FI804 2.3 31.5 1.0
C4 A:7FI804 3.0 19.9 1.0
C6 A:7FI804 3.0 25.3 1.0
CG B:ASP191 3.0 13.8 1.0
OD2 B:ASP191 3.4 14.0 1.0
C8 A:7FI804 3.4 27.7 1.0
MG B:MG404 3.6 15.2 1.0
OE1 B:GLN194 3.7 23.4 1.0
NH2 B:ARG131 3.7 18.5 1.0
OE2 B:GLU195 3.8 16.3 1.0
OE1 A:GLN232 4.0 35.6 1.0
O B:HOH532 4.1 14.2 1.0
CZ B:ARG131 4.2 15.4 1.0
C2 A:7FI804 4.3 17.9 1.0
CB B:ASP191 4.3 15.0 1.0
O B:HOH613 4.4 15.4 1.0
O B:PRO130 4.4 13.9 1.0
C5N B:NAD402 4.5 16.3 1.0
C4N B:NAD402 4.5 16.5 1.0
NE2 A:GLN232 4.5 28.2 1.0
O1 A:7FI804 4.6 15.9 1.0
NH1 B:ARG131 4.7 15.8 1.0
OE1 A:GLU226 4.7 20.5 1.0
CD A:GLN232 4.7 22.0 1.0
CD B:GLN194 4.8 17.6 1.0
NE B:ARG131 4.9 13.6 1.0
CA B:ASP191 4.9 14.9 1.0
C9 A:7FI804 4.9 31.2 1.0
CD B:GLU195 4.9 14.5 1.0

Magnesium binding site 4 out of 4 in 7pco

Go back to Magnesium Binding Sites List in 7pco
Magnesium binding site 4 out of 4 in the Burg E232Q Mutant (Holo) in Complex with 2R,3R-2,3-Dihydroxy-6-Methyl- Heptanoate (12): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Burg E232Q Mutant (Holo) in Complex with 2R,3R-2,3-Dihydroxy-6-Methyl- Heptanoate (12): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:15.2
occ:1.00
 OD2 B:ASP191 2.0 14.0 1.0
OE2 B:GLU195 2.0 16.3 1.0
O B:HOH613 2.0 15.4 1.0
O5 A:7FI804 2.0 16.5 1.0
O B:HOH600 2.0 15.8 1.0
O1 A:7FI804 2.1 15.9 1.0
C2 A:7FI804 2.8 17.9 1.0
C4 A:7FI804 2.9 19.9 1.0
CD B:GLU195 3.0 14.5 1.0
CG B:ASP191 3.1 13.8 1.0
OE1 B:GLU195 3.4 14.9 1.0
OD1 B:ASP191 3.5 15.4 1.0
MG B:MG403 3.6 29.0 1.0
O B:HOH501 3.6 16.7 1.0
O3 A:7FI804 4.0 15.5 1.0
C6 A:7FI804 4.1 25.3 1.0
O B:HOH532 4.2 14.2 1.0
OG A:SER254 4.3 13.2 1.0
C8 A:7FI804 4.3 27.7 1.0
CB B:ASP191 4.3 15.0 1.0
CG B:GLU195 4.4 14.3 1.0
O2D B:NAD402 4.4 13.2 1.0
NE2 B:HIS108 4.4 11.9 1.0
O B:HOH570 4.4 20.3 1.0
CD2 B:HIS108 4.5 12.2 1.0
CE1 B:HIS108 4.5 13.3 1.0
O7 A:7FI804 4.7 31.5 1.0
CB A:CYS257 4.7 14.8 1.0
ND1 B:HIS108 4.7 12.9 1.0
CG B:HIS108 4.7 12.7 1.0
C6N B:NAD402 4.9 15.9 1.0
O B:ASP191 5.0 14.7 1.0
N1N B:NAD402 5.0 14.1 1.0

Reference:

F.Trottmann, K.Ishida, M.Ishida-Ito, H.Kries, M.Groll, C.Hertweck. Pathogenic Bacteria Remodel Central Metabolic Enzyme to Build A Cyclopropanol Warhead. Nat.Chem. V. 14 884 2022.
ISSN: ESSN 1755-4349
PubMed: 35906404
DOI: 10.1038/S41557-022-01005-Z
Page generated: Thu Oct 3 04:08:17 2024

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