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Magnesium in PDB 7pcm: Burg (Holo) in Complex with (Z)-2,3-Dihydroxy-6-Methyl-Hept-2-Enoate (13): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins

Enzymatic activity of Burg (Holo) in Complex with (Z)-2,3-Dihydroxy-6-Methyl-Hept-2-Enoate (13): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins

All present enzymatic activity of Burg (Holo) in Complex with (Z)-2,3-Dihydroxy-6-Methyl-Hept-2-Enoate (13): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins:
1.1.1.86;

Protein crystallography data

The structure of Burg (Holo) in Complex with (Z)-2,3-Dihydroxy-6-Methyl-Hept-2-Enoate (13): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins, PDB code: 7pcm 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 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.81, 83.61, 100.73, 90, 90, 90
R / Rfree (%) 20.3 / 23.9

Other elements in 7pcm:

The structure of Burg (Holo) in Complex with (Z)-2,3-Dihydroxy-6-Methyl-Hept-2-Enoate (13): 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 (Holo) in Complex with (Z)-2,3-Dihydroxy-6-Methyl-Hept-2-Enoate (13): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins (pdb code 7pcm). 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 (Holo) in Complex with (Z)-2,3-Dihydroxy-6-Methyl-Hept-2-Enoate (13): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins, PDB code: 7pcm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7pcm

Go back to Magnesium Binding Sites List in 7pcm
Magnesium binding site 1 out of 4 in the Burg (Holo) in Complex with (Z)-2,3-Dihydroxy-6-Methyl-Hept-2-Enoate (13): 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 (Holo) in Complex with (Z)-2,3-Dihydroxy-6-Methyl-Hept-2-Enoate (13): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:27.2
occ:1.00
 O B:HOH506 2.0 28.2 1.0
O7 B:7I3401 2.0 35.5 1.0
O A:HOH922 2.1 23.9 1.0
OD1 A:ASP191 2.1 23.0 1.0
O A:HOH902 2.3 23.8 1.0
O5 B:7I3401 2.4 28.9 1.0
C6 B:7I3401 2.8 33.4 1.0
C4 B:7I3401 3.0 30.8 1.0
CG A:ASP191 3.1 24.7 1.0
OD2 A:ASP191 3.6 27.4 1.0
NH2 A:ARG131 3.8 26.1 1.0
OE1 B:GLU232 3.9 31.6 1.0
MG A:MG803 3.9 25.5 1.0
OE2 A:GLU195 4.0 23.5 1.0
OE1 A:GLN194 4.1 27.7 1.0
OE2 B:GLU232 4.2 30.9 1.0
C8 B:7I3401 4.3 34.7 1.0
C5N A:NAI801 4.4 27.5 1.0
CZ A:ARG131 4.4 26.6 1.0
CB A:ASP191 4.4 24.5 1.0
O A:HOH915 4.4 24.7 1.0
CD B:GLU232 4.5 29.6 1.0
O A:PRO130 4.5 30.6 1.0
C2 B:7I3401 4.5 29.7 1.0
OE1 B:GLU226 4.5 30.1 1.0
C4N A:NAI801 4.5 27.7 1.0
O B:HOH530 4.6 25.0 1.0
C9 B:7I3401 4.7 37.1 1.0
NH1 A:ARG131 4.9 26.4 1.0
CD A:GLN194 4.9 24.8 1.0
CA A:ASP191 4.9 23.6 1.0
C6N A:NAI801 5.0 28.3 1.0
NE A:ARG131 5.0 25.7 1.0

Magnesium binding site 2 out of 4 in 7pcm

Go back to Magnesium Binding Sites List in 7pcm
Magnesium binding site 2 out of 4 in the Burg (Holo) in Complex with (Z)-2,3-Dihydroxy-6-Methyl-Hept-2-Enoate (13): 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 (Holo) in Complex with (Z)-2,3-Dihydroxy-6-Methyl-Hept-2-Enoate (13): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:25.5
occ:1.00
 OD2 A:ASP191 2.0 27.4 1.0
O5 B:7I3401 2.0 28.9 1.0
OE2 A:GLU195 2.0 23.5 1.0
O A:HOH921 2.0 20.2 1.0
O B:HOH530 2.2 25.0 1.0
O1 B:7I3401 2.5 34.0 1.0
C4 B:7I3401 2.8 30.8 1.0
C2 B:7I3401 3.0 29.7 1.0
CD A:GLU195 3.1 24.4 1.0
CG A:ASP191 3.1 24.7 1.0
OE1 A:GLU195 3.5 24.3 1.0
OD1 A:ASP191 3.6 23.0 1.0
O A:HOH902 3.9 23.8 1.0
MG A:MG802 3.9 27.2 1.0
O3 B:7I3401 4.1 29.3 1.0
C6 B:7I3401 4.2 33.4 1.0
O A:HOH915 4.2 24.7 1.0
NE2 A:HIS108 4.3 26.1 1.0
CE1 A:HIS108 4.3 26.2 1.0
O2D A:NAI801 4.3 28.3 1.0
CB A:ASP191 4.3 24.5 1.0
OG B:SER254 4.4 22.6 1.0
CG A:GLU195 4.4 23.5 1.0
ND1 A:HIS108 4.4 25.4 1.0
CD2 A:HIS108 4.4 25.9 1.0
CG A:HIS108 4.6 25.4 1.0
C6N A:NAI801 4.6 28.3 1.0
O A:HOH922 4.6 23.9 1.0
CB B:CYS257 4.7 23.6 1.0
O7 B:7I3401 4.7 35.5 1.0
N1N A:NAI801 5.0 28.5 1.0
O A:ASP191 5.0 24.4 1.0

Magnesium binding site 3 out of 4 in 7pcm

Go back to Magnesium Binding Sites List in 7pcm
Magnesium binding site 3 out of 4 in the Burg (Holo) in Complex with (Z)-2,3-Dihydroxy-6-Methyl-Hept-2-Enoate (13): 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 (Holo) in Complex with (Z)-2,3-Dihydroxy-6-Methyl-Hept-2-Enoate (13): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:27.6
occ:1.00
 OD1 B:ASP191 1.9 23.3 1.0
O A:HOH913 2.1 30.0 1.0
O B:HOH509 2.1 21.3 1.0
O5 A:7I3804 2.3 33.2 1.0
O B:HOH521 2.3 26.4 1.0
O7 A:7I3804 2.4 35.7 1.0
CG B:ASP191 3.0 25.5 1.0
C4 A:7I3804 3.0 32.4 1.0
C6 A:7I3804 3.0 34.3 1.0
OD2 B:ASP191 3.5 27.0 1.0
MG B:MG404 3.7 23.9 1.0
NH2 B:ARG131 3.7 29.3 1.0
OE2 B:GLU195 4.0 26.3 1.0
O B:HOH532 4.0 26.6 1.0
OE1 A:GLU232 4.0 29.9 1.0
CB B:ASP191 4.2 24.1 1.0
CZ B:ARG131 4.3 27.1 1.0
OE1 B:GLN194 4.3 28.1 1.0
O B:PRO130 4.4 24.3 1.0
OE1 A:GLU226 4.4 26.4 1.0
C2 A:7I3804 4.4 30.1 1.0
O B:HOH534 4.5 22.0 1.0
C8 A:7I3804 4.5 35.0 1.0
OE2 A:GLU232 4.5 26.7 1.0
C5N B:NAI402 4.6 29.4 1.0
NH1 B:ARG131 4.7 25.9 1.0
CA B:ASP191 4.7 24.7 1.0
CD A:GLU232 4.7 26.7 1.0
C4N B:NAI402 4.8 29.6 1.0
O1 A:7I3804 4.9 29.9 1.0
NE B:ARG131 4.9 28.3 1.0
O B:ASP191 4.9 23.2 1.0
C6N B:NAI402 5.0 28.7 1.0
C9 A:7I3804 5.0 34.9 1.0
CD B:GLU195 5.0 26.2 1.0

Magnesium binding site 4 out of 4 in 7pcm

Go back to Magnesium Binding Sites List in 7pcm
Magnesium binding site 4 out of 4 in the Burg (Holo) in Complex with (Z)-2,3-Dihydroxy-6-Methyl-Hept-2-Enoate (13): 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 (Holo) in Complex with (Z)-2,3-Dihydroxy-6-Methyl-Hept-2-Enoate (13): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:23.9
occ:1.00
 O5 A:7I3804 1.9 33.2 1.0
OD2 B:ASP191 2.1 27.0 1.0
OE2 B:GLU195 2.1 26.3 1.0
O B:HOH542 2.1 19.9 1.0
O B:HOH534 2.1 22.0 1.0
O1 A:7I3804 2.2 29.9 1.0
C4 A:7I3804 2.7 32.4 1.0
C2 A:7I3804 2.7 30.1 1.0
CG B:ASP191 3.1 25.5 1.0
CD B:GLU195 3.1 26.2 1.0
OD1 B:ASP191 3.5 23.3 1.0
OE1 B:GLU195 3.6 27.5 1.0
MG B:MG403 3.7 27.6 1.0
O B:HOH521 3.8 26.4 1.0
O3 A:7I3804 3.8 27.9 1.0
O B:HOH532 4.0 26.6 1.0
C6 A:7I3804 4.1 34.3 1.0
O2D B:NAI402 4.3 24.5 1.0
OG A:SER254 4.3 24.5 1.0
CB B:ASP191 4.4 24.1 1.0
CG B:GLU195 4.4 25.6 1.0
NE2 B:HIS108 4.5 26.4 1.0
CE1 B:HIS108 4.5 27.4 1.0
CD2 B:HIS108 4.6 26.5 1.0
O B:HOH509 4.6 21.3 1.0
C6N B:NAI402 4.6 28.7 1.0
CB A:CYS257 4.6 28.0 1.0
ND1 B:HIS108 4.6 26.6 1.0
CG B:HIS108 4.7 26.2 1.0
O7 A:7I3804 4.8 35.7 1.0
N1N B:NAI402 4.9 27.1 1.0
O B:ASP191 4.9 23.2 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 04:07:57 2024

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