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Sodium 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:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was 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:

Sodium binding site 1 out of 1 in 7pcm

Go back to Sodium Binding Sites List in 7pcm
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na805

b:40.4
occ:1.00
 OE1 A:GLU247 2.3 35.3 1.0
O B:HOH512 2.9 24.4 1.0
CD A:GLU247 3.5 37.0 1.0
CB A:ALA250 3.6 26.0 1.0
CD2 B:LEU312 3.7 42.6 1.0
CG B:ARG308 3.8 32.1 1.0
CG B:LEU312 3.9 41.7 1.0
CA A:GLU247 4.0 28.6 1.0
CD1 B:LEU312 4.1 41.7 1.0
CD B:ARG308 4.1 32.7 1.0
CB A:GLU247 4.2 30.6 1.0
CG A:GLU247 4.4 34.1 1.0
OE2 A:GLU247 4.4 43.1 1.0
O B:ARG308 4.5 28.4 1.0
N A:GLU247 4.6 28.2 1.0
O A:HOH929 4.7 22.7 1.0
O A:ASP246 4.7 26.7 1.0
NE B:ARG308 4.9 33.5 1.0
C A:ASP246 4.9 27.1 1.0
O A:GLU247 5.0 25.2 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: Mon Aug 18 11:21:19 2025

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