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Magnesium in PDB 7pcg: Burg (Holo) in Complex with Cyclopropane-1,1-Dicarboxylate (7): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins

Enzymatic activity of Burg (Holo) in Complex with Cyclopropane-1,1-Dicarboxylate (7): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins

All present enzymatic activity of Burg (Holo) in Complex with Cyclopropane-1,1-Dicarboxylate (7): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins:
1.1.1.86;

Protein crystallography data

The structure of Burg (Holo) in Complex with Cyclopropane-1,1-Dicarboxylate (7): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins, PDB code: 7pcg 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 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.63, 83.26, 101.21, 90, 90, 90
R / Rfree (%) 19.5 / 22.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Burg (Holo) in Complex with Cyclopropane-1,1-Dicarboxylate (7): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins (pdb code 7pcg). 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 Cyclopropane-1,1-Dicarboxylate (7): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins, PDB code: 7pcg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7pcg

Go back to Magnesium Binding Sites List in 7pcg
Magnesium binding site 1 out of 4 in the Burg (Holo) in Complex with Cyclopropane-1,1-Dicarboxylate (7): 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 Cyclopropane-1,1-Dicarboxylate (7): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:27.6
occ:1.00
 OD1 A:ASP191 2.0 22.2 1.0
O B:HOH525 2.0 24.2 1.0
O A:HOH502 2.1 26.2 1.0
O A:HOH523 2.1 22.1 1.0
O05 B:9TY401 2.4 27.6 1.0
O06 B:9TY401 2.4 26.7 1.0
C04 B:9TY401 2.7 28.5 1.0
CG A:ASP191 3.1 22.8 1.0
NH2 A:ARG131 3.5 25.4 1.0
OD2 A:ASP191 3.6 24.0 1.0
OE1 B:GLU232 3.7 25.4 1.0
OE1 B:GLU226 3.9 25.6 1.0
MG A:MG403 3.9 24.4 1.0
OE2 A:GLU195 4.0 23.0 1.0
OE1 A:GLN194 4.1 22.7 1.0
C03 B:9TY401 4.1 29.5 1.0
CZ A:ARG131 4.1 24.9 1.0
OE2 B:GLU232 4.2 24.9 1.0
CB A:ASP191 4.3 22.9 1.0
CD B:GLU232 4.4 24.6 1.0
O A:HOH534 4.4 23.0 1.0
O A:PRO130 4.5 23.0 1.0
C08 B:9TY401 4.6 30.3 1.0
CA A:ASP191 4.6 22.2 1.0
NE A:ARG131 4.6 24.6 1.0
NH1 A:ARG131 4.7 25.4 1.0
O A:HOH543 4.8 25.0 1.0
CD A:GLN194 4.8 21.9 1.0
C5N A:NAD401 4.8 29.9 1.0
O A:ASP191 4.9 21.0 1.0
NE2 A:GLN194 4.9 22.5 1.0
O B:HOH547 5.0 25.8 1.0
O01 B:9TY401 5.0 26.1 1.0
CA A:ARG131 5.0 22.1 1.0
C4N A:NAD401 5.0 30.3 1.0
C07 B:9TY401 5.0 30.2 1.0

Magnesium binding site 2 out of 4 in 7pcg

Go back to Magnesium Binding Sites List in 7pcg
Magnesium binding site 2 out of 4 in the Burg (Holo) in Complex with Cyclopropane-1,1-Dicarboxylate (7): 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 Cyclopropane-1,1-Dicarboxylate (7): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:24.4
occ:1.00
 OD2 A:ASP191 2.0 24.0 1.0
OE2 A:GLU195 2.0 23.0 1.0
O06 B:9TY401 2.1 26.7 1.0
O01 B:9TY401 2.2 26.1 1.0
O A:HOH543 2.2 25.0 1.0
O A:HOH557 2.2 24.5 1.0
CG A:ASP191 3.0 22.8 1.0
CD A:GLU195 3.1 22.5 1.0
C04 B:9TY401 3.2 28.5 1.0
C02 B:9TY401 3.2 28.4 1.0
OE1 A:GLU195 3.4 21.9 1.0
OD1 A:ASP191 3.5 22.2 1.0
C03 B:9TY401 3.6 29.5 1.0
O A:HOH502 3.8 26.2 1.0
MG A:MG402 3.9 27.6 1.0
O A:HOH534 4.2 23.0 1.0
O05 B:9TY401 4.3 27.6 1.0
CB A:ASP191 4.3 22.9 1.0
O09 B:9TY401 4.3 28.5 1.0
OG B:SER254 4.3 23.6 1.0
CG A:GLU195 4.4 22.3 1.0
O2D A:NAD401 4.4 27.6 1.0
O A:HOH523 4.5 22.1 1.0
CE1 A:HIS108 4.6 25.8 1.0
C08 B:9TY401 4.6 30.3 1.0
ND1 A:HIS108 4.6 24.9 1.0
CB B:CYS257 4.7 26.1 1.0
C6N A:NAD401 4.7 30.1 1.0
NE2 A:HIS108 4.8 26.0 1.0
CG A:HIS108 4.9 24.9 1.0
C5N A:NAD401 4.9 29.9 1.0
O A:ASP191 4.9 21.0 1.0
N1N A:NAD401 4.9 29.4 1.0
CD2 A:HIS108 4.9 25.9 1.0

Magnesium binding site 3 out of 4 in 7pcg

Go back to Magnesium Binding Sites List in 7pcg
Magnesium binding site 3 out of 4 in the Burg (Holo) in Complex with Cyclopropane-1,1-Dicarboxylate (7): 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 Cyclopropane-1,1-Dicarboxylate (7): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:26.5
occ:1.00
 OD1 B:ASP191 1.9 26.1 1.0
O A:HOH529 2.0 21.3 1.0
O B:HOH533 2.1 22.8 1.0
O05 A:9TY404 2.3 32.2 1.0
O B:HOH521 2.3 30.5 1.0
O06 A:9TY404 2.5 32.2 1.0
C04 A:9TY404 2.6 32.6 1.0
CG B:ASP191 3.0 26.1 1.0
NH2 B:ARG131 3.5 22.7 1.0
OD2 B:ASP191 3.5 27.0 1.0
OE1 A:GLU232 3.9 25.7 1.0
MG B:MG404 4.0 25.4 1.0
OE1 A:GLU226 4.0 27.2 1.0
CZ B:ARG131 4.1 21.0 1.0
C03 A:9TY404 4.1 33.5 1.0
OE2 B:GLU195 4.1 27.4 1.0
CB B:ASP191 4.2 25.9 1.0
O B:HOH516 4.2 23.8 1.0
OE1 B:GLN194 4.3 26.3 1.0
OE2 A:GLU232 4.3 25.1 1.0
O B:PRO130 4.4 22.4 1.0
CD A:GLU232 4.5 24.7 1.0
NH1 B:ARG131 4.5 20.8 1.0
C08 A:9TY404 4.5 34.1 1.0
CA B:ASP191 4.6 25.2 1.0
NE B:ARG131 4.7 20.5 1.0
O B:HOH580 4.7 26.6 1.0
C5N B:NAD402 4.8 31.8 1.0
CD B:GLN194 4.9 24.5 1.0
CA B:ARG131 4.9 21.0 1.0
C07 A:9TY404 4.9 33.4 1.0
C4N B:NAD402 4.9 32.0 1.0
O01 A:9TY404 4.9 30.6 1.0
O B:ASP191 5.0 25.4 1.0

Magnesium binding site 4 out of 4 in 7pcg

Go back to Magnesium Binding Sites List in 7pcg
Magnesium binding site 4 out of 4 in the Burg (Holo) in Complex with Cyclopropane-1,1-Dicarboxylate (7): 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 Cyclopropane-1,1-Dicarboxylate (7): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:25.4
occ:1.00
 O B:HOH580 2.0 26.6 1.0
O B:HOH579 2.0 25.1 1.0
OD2 B:ASP191 2.1 27.0 1.0
O01 A:9TY404 2.2 30.6 1.0
O06 A:9TY404 2.2 32.2 1.0
OE2 B:GLU195 2.2 27.4 1.0
CG B:ASP191 3.1 26.1 1.0
C02 A:9TY404 3.2 31.8 1.0
CD B:GLU195 3.2 27.8 1.0
C04 A:9TY404 3.2 32.6 1.0
OE1 B:GLU195 3.5 28.7 1.0
OD1 B:ASP191 3.6 26.1 1.0
C03 A:9TY404 3.6 33.5 1.0
O B:HOH521 3.9 30.5 1.0
MG B:MG403 4.0 26.5 1.0
OG A:SER254 4.2 24.1 1.0
O B:HOH516 4.2 23.8 1.0
O09 A:9TY404 4.2 31.4 1.0
O2D B:NAD402 4.3 29.9 1.0
O05 A:9TY404 4.3 32.2 1.0
CB B:ASP191 4.4 25.9 1.0
CG B:GLU195 4.5 27.3 1.0
NE2 B:HIS108 4.6 29.1 1.0
C6N B:NAD402 4.6 31.5 1.0
CE1 B:HIS108 4.6 28.6 1.0
O B:HOH533 4.6 22.8 1.0
C08 A:9TY404 4.6 34.1 1.0
CD2 B:HIS108 4.6 28.5 1.0
ND1 B:HIS108 4.6 28.2 1.0
CG B:HIS108 4.7 27.6 1.0
CB A:CYS257 4.8 27.9 1.0
N1N B:NAD402 4.8 30.8 1.0
C5N B:NAD402 4.8 31.8 1.0
C4N B:NAD402 4.9 32.0 1.0
C2N B:NAD402 5.0 31.2 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 Apr 6 18:33:27 2023

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