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Magnesium in PDB 7pcn: Burg (Holo) in Complex with Gonyenediol (14), Trigonic Acid (6) and Dms: Biosynthesis of Cyclopropanol Rings in Bacterial Toxins

Enzymatic activity of Burg (Holo) in Complex with Gonyenediol (14), Trigonic Acid (6) and Dms: Biosynthesis of Cyclopropanol Rings in Bacterial Toxins

All present enzymatic activity of Burg (Holo) in Complex with Gonyenediol (14), Trigonic Acid (6) and Dms: Biosynthesis of Cyclopropanol Rings in Bacterial Toxins:
1.1.1.86;

Protein crystallography data

The structure of Burg (Holo) in Complex with Gonyenediol (14), Trigonic Acid (6) and Dms: Biosynthesis of Cyclopropanol Rings in Bacterial Toxins, PDB code: 7pcn 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 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.88, 76.13, 79.11, 90, 105.14, 90
R / Rfree (%) 13.4 / 15.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Burg (Holo) in Complex with Gonyenediol (14), Trigonic Acid (6) and Dms: Biosynthesis of Cyclopropanol Rings in Bacterial Toxins (pdb code 7pcn). 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 Gonyenediol (14), Trigonic Acid (6) and Dms: Biosynthesis of Cyclopropanol Rings in Bacterial Toxins, PDB code: 7pcn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7pcn

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Magnesium binding site 1 out of 4 in the Burg (Holo) in Complex with Gonyenediol (14), Trigonic Acid (6) and Dms: 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 Gonyenediol (14), Trigonic Acid (6) and Dms: Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:14.9
occ:1.00
 O5 B:7BI901 2.0 9.3 0.5
OD1 A:ASP191 2.1 13.1 1.0
O5 B:78I902 2.1 21.4 0.5
O B:HOH1061 2.1 13.3 1.0
O B:HOH1081 2.1 12.0 1.0
O A:HOH948 2.1 12.3 1.0
O7 B:7BI901 2.2 8.9 0.5
O7 B:78I902 2.3 21.8 0.5
C4 B:7BI901 2.8 11.0 0.5
C6 B:7BI901 2.9 11.2 0.5
C4 B:78I902 3.1 23.2 0.5
CG A:ASP191 3.1 12.5 1.0
C6 B:78I902 3.1 23.8 0.5
OD2 A:ASP191 3.4 12.9 1.0
MG A:MG803 3.6 13.8 1.0
OE2 A:GLU195 3.8 12.9 1.0
NH2 A:ARG131 3.9 12.9 1.0
OE1 B:GLU232 4.1 14.3 1.0
O A:HOH936 4.2 13.7 1.0
C2 B:7BI901 4.3 10.2 0.5
OE2 B:GLU232 4.3 15.2 1.0
C2 B:78I902 4.3 22.7 0.5
CB A:ASP191 4.4 13.2 1.0
C8 B:7BI901 4.4 12.7 0.5
C8 B:78I902 4.4 24.5 0.5
OE1 A:GLN194 4.5 15.1 1.0
CZ A:ARG131 4.5 12.3 1.0
C4N A:NAI801 4.5 14.9 1.0
C9 B:78I902 4.5 24.7 0.5
O A:PRO130 4.5 13.6 1.0
OE1 B:GLU226 4.5 16.5 1.0
O A:HOH1002 4.6 13.0 1.0
C5N A:NAI801 4.6 13.7 1.0
CD B:GLU232 4.7 14.6 1.0
O1 B:78I902 4.7 21.1 0.5
C12 B:7BI901 4.7 20.6 0.5
O1 B:7BI901 4.7 9.4 0.5
CD A:GLU195 4.9 12.2 1.0
CD1 A:MSM804 4.9 25.7 0.5
CA A:ASP191 4.9 12.8 1.0
NH1 A:ARG131 4.9 11.9 1.0

Magnesium binding site 2 out of 4 in 7pcn

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Magnesium binding site 2 out of 4 in the Burg (Holo) in Complex with Gonyenediol (14), Trigonic Acid (6) and Dms: 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 Gonyenediol (14), Trigonic Acid (6) and Dms: Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:13.8
occ:1.00
 O5 B:7BI901 2.0 9.3 0.5
OD2 A:ASP191 2.0 12.9 1.0
O5 B:78I902 2.0 21.4 0.5
OE2 A:GLU195 2.1 12.9 1.0
O A:HOH988 2.1 13.4 1.0
O1 B:78I902 2.1 21.1 0.5
O A:HOH1002 2.1 13.0 1.0
O1 B:7BI901 2.2 9.4 0.5
C4 B:7BI901 2.7 11.0 0.5
C2 B:7BI901 2.8 10.2 0.5
C2 B:78I902 2.9 22.7 0.5
C4 B:78I902 2.9 23.2 0.5
CD A:GLU195 3.1 12.2 1.0
CG A:ASP191 3.1 12.5 1.0
OE1 A:GLU195 3.5 14.1 1.0
OD1 A:ASP191 3.6 13.1 1.0
MG A:MG802 3.6 14.9 1.0
O B:HOH1081 3.7 12.0 1.0
O3 B:7BI901 4.0 10.2 0.5
O3 B:78I902 4.1 21.5 0.5
O A:HOH936 4.1 13.7 1.0
C6 B:7BI901 4.2 11.2 0.5
C6 B:78I902 4.2 23.8 0.5
OG B:SER254 4.3 13.6 1.0
NE2 A:HIS108 4.3 14.2 1.0
CE1 A:HIS108 4.4 14.4 1.0
CG A:GLU195 4.4 12.3 1.0
CB A:ASP191 4.4 13.2 1.0
O2D A:NAI801 4.5 12.1 1.0
O A:HOH948 4.5 12.3 1.0
CD2 A:HIS108 4.5 14.1 1.0
ND1 A:HIS108 4.6 13.4 1.0
CB B:CYS257 4.7 12.2 1.0
O7 B:78I902 4.7 21.8 0.5
O7 B:7BI901 4.7 8.9 0.5
C6N A:NAI801 4.7 14.6 1.0
CG A:HIS108 4.7 13.5 1.0
N1N A:NAI801 5.0 12.9 1.0

Magnesium binding site 3 out of 4 in 7pcn

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Magnesium binding site 3 out of 4 in the Burg (Holo) in Complex with Gonyenediol (14), Trigonic Acid (6) and Dms: 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 Gonyenediol (14), Trigonic Acid (6) and Dms: Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg904

b:13.2
occ:1.00
 O5 A:7BI805 2.0 8.1 0.5
OD1 B:ASP191 2.0 11.1 1.0
O5 A:78I806 2.0 18.3 0.5
O B:HOH1074 2.1 12.9 1.0
O A:HOH921 2.2 12.8 1.0
O A:HOH964 2.2 11.9 1.0
O7 A:7BI805 2.3 8.1 0.5
O7 A:78I806 2.3 19.4 0.5
C4 A:7BI805 2.8 8.8 0.5
C6 A:7BI805 2.9 9.3 0.5
C4 A:78I806 3.0 20.2 0.5
CG B:ASP191 3.0 12.0 1.0
C6 A:78I806 3.1 20.4 0.5
OD2 B:ASP191 3.4 13.3 1.0
MG B:MG905 3.6 14.2 1.0
OE2 B:GLU195 3.9 13.8 1.0
NH2 B:ARG131 3.9 13.2 1.0
OE1 A:GLU232 4.1 14.1 1.0
O B:HOH1008 4.2 14.0 1.0
C2 A:7BI805 4.2 8.9 0.5
C2 A:78I806 4.3 20.0 0.5
OE2 A:GLU232 4.3 14.7 1.0
CB B:ASP191 4.3 12.9 1.0
C8 A:78I806 4.4 22.0 0.5
C8 A:7BI805 4.4 11.3 0.5
CZ B:ARG131 4.5 13.0 1.0
O B:HOH1112 4.5 11.8 1.0
O B:PRO130 4.5 14.3 1.0
OE1 B:GLN194 4.5 14.6 1.0
C4N B:NAI903 4.5 14.5 1.0
C9 A:78I806 4.5 22.2 0.5
C5N B:NAI903 4.5 14.9 1.0
OE1 A:GLU226 4.6 17.1 1.0
O3 A:78I806 4.6 19.4 0.5
CD A:GLU232 4.7 12.2 1.0
O3 A:7BI805 4.7 8.8 0.5
C12 A:7BI805 4.7 16.9 0.5
NH1 B:ARG131 4.9 13.4 1.0
CA B:ASP191 4.9 13.2 1.0
CD B:GLU195 4.9 12.5 1.0
CD1 B:MSM906 4.9 21.2 0.5

Magnesium binding site 4 out of 4 in 7pcn

Go back to Magnesium Binding Sites List in 7pcn
Magnesium binding site 4 out of 4 in the Burg (Holo) in Complex with Gonyenediol (14), Trigonic Acid (6) and Dms: 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 Gonyenediol (14), Trigonic Acid (6) and Dms: Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg905

b:14.2
occ:1.00
 O5 A:7BI805 2.0 8.1 0.5
OD2 B:ASP191 2.0 13.3 1.0
O5 A:78I806 2.0 18.3 0.5
OE2 B:GLU195 2.1 13.8 1.0
O B:HOH1112 2.1 11.8 1.0
O3 A:78I806 2.1 19.4 0.5
O3 A:7BI805 2.2 8.8 0.5
O B:HOH1125 2.2 12.8 1.0
C4 A:7BI805 2.7 8.8 0.5
C2 A:7BI805 2.8 8.9 0.5
C2 A:78I806 2.9 20.0 0.5
C4 A:78I806 2.9 20.2 0.5
CG B:ASP191 3.1 12.0 1.0
CD B:GLU195 3.1 12.5 1.0
OE1 B:GLU195 3.5 13.9 1.0
OD1 B:ASP191 3.5 11.1 1.0
MG B:MG904 3.6 13.2 1.0
O A:HOH964 3.7 11.9 1.0
O1 A:7BI805 4.0 9.5 0.5
O1 A:78I806 4.1 20.1 0.5
O B:HOH1008 4.1 14.0 1.0
C6 A:7BI805 4.2 9.3 0.5
C6 A:78I806 4.2 20.4 0.5
OG A:SER254 4.3 12.5 1.0
CB B:ASP191 4.3 12.9 1.0
CG B:GLU195 4.4 12.7 1.0
O2D B:NAI903 4.4 12.9 1.0
NE2 B:HIS108 4.4 14.9 1.0
O B:HOH1074 4.4 12.9 1.0
CE1 B:HIS108 4.5 14.6 1.0
CB A:CYS257 4.6 13.7 1.0
ND1 B:HIS108 4.6 14.0 1.0
CD2 B:HIS108 4.6 15.1 1.0
O7 A:78I806 4.6 19.4 0.5
C6N B:NAI903 4.7 15.2 1.0
O7 A:7BI805 4.7 8.1 0.5
CG B:HIS108 4.8 14.2 1.0
N1N B:NAI903 5.0 13.4 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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