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Magnesium in PDB 7pcc: Burg in Complex with MG2+ and Nad+ (Holo): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins

Enzymatic activity of Burg in Complex with MG2+ and Nad+ (Holo): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins

All present enzymatic activity of Burg in Complex with MG2+ and Nad+ (Holo): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins:
1.1.1.86;

Protein crystallography data

The structure of Burg in Complex with MG2+ and Nad+ (Holo): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins, PDB code: 7pcc 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 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.49, 82.74, 100.87, 90, 90, 90
R / Rfree (%) 18.5 / 21.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Burg in Complex with MG2+ and Nad+ (Holo): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins (pdb code 7pcc). 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 in Complex with MG2+ and Nad+ (Holo): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins, PDB code: 7pcc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7pcc

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Magnesium binding site 1 out of 4 in the Burg in Complex with MG2+ and Nad+ (Holo): 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 in Complex with MG2+ and Nad+ (Holo): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:29.0
occ:1.00
 O B:HOH901 2.0 25.1 1.0
O A:HOH928 2.1 24.0 1.0
O B:HOH916 2.1 23.5 1.0
OD1 A:ASP191 2.1 22.6 1.0
O A:HOH985 2.2 28.6 1.0
O A:HOH955 2.3 23.4 1.0
CG A:ASP191 3.2 23.7 1.0
MG A:MG803 3.7 20.9 1.0
OD2 A:ASP191 3.7 26.4 1.0
OE1 B:GLU232 3.9 29.3 1.0
OE2 A:GLU195 3.9 19.1 1.0
OE1 A:GLN194 4.0 19.9 1.0
OE2 B:GLU232 4.1 32.0 1.0
NH2 A:ARG131 4.1 21.6 1.0
C4N A:NAD801 4.2 25.2 1.0
CD B:GLU232 4.4 29.0 1.0
O A:HOH954 4.4 24.1 1.0
O A:HOH958 4.5 24.6 1.0
CB A:ASP191 4.5 22.3 1.0
C5N A:NAD801 4.5 24.0 1.0
O A:PRO130 4.5 18.2 1.0
OE1 B:GLU226 4.6 22.1 1.0
CZ A:ARG131 4.6 21.2 1.0
O B:HOH930 4.8 24.4 1.0
O1 B:GOL804 4.8 46.4 1.0
O B:HOH993 4.9 38.2 1.0
CA A:ASP191 4.9 20.4 1.0
CD A:GLN194 4.9 19.4 1.0
CD A:GLU195 5.0 18.7 1.0
NH1 A:ARG131 5.0 21.6 1.0

Magnesium binding site 2 out of 4 in 7pcc

Go back to Magnesium Binding Sites List in 7pcc
Magnesium binding site 2 out of 4 in the Burg in Complex with MG2+ and Nad+ (Holo): 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 in Complex with MG2+ and Nad+ (Holo): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:20.9
occ:1.00
 O A:HOH985 1.9 28.6 1.0
OD2 A:ASP191 2.0 26.4 1.0
O B:HOH930 2.1 24.4 1.0
O A:HOH958 2.1 24.6 1.0
OE2 A:GLU195 2.1 19.1 1.0
O A:HOH968 2.2 20.0 1.0
CG A:ASP191 3.0 23.7 1.0
CD A:GLU195 3.2 18.7 1.0
OD1 A:ASP191 3.4 22.6 1.0
OE1 A:GLU195 3.7 19.0 1.0
MG A:MG802 3.7 29.0 1.0
O A:HOH928 3.8 24.0 1.0
O B:HOH993 4.1 38.2 1.0
O A:HOH954 4.1 24.1 1.0
O2D A:NAD801 4.2 19.3 1.0
OG B:SER254 4.3 21.9 1.0
CB A:ASP191 4.4 22.3 1.0
NE2 A:HIS108 4.4 21.1 1.0
O A:HOH955 4.4 23.4 1.0
CD2 A:HIS108 4.5 21.0 1.0
CG A:GLU195 4.5 17.9 1.0
CE1 A:HIS108 4.5 21.0 1.0
CG A:HIS108 4.6 20.6 1.0
ND1 A:HIS108 4.6 20.4 1.0
CB B:CYS257 4.7 23.0 1.0
C4N A:NAD801 4.8 25.2 1.0
C3N A:NAD801 4.8 25.0 1.0
C2N A:NAD801 4.8 23.2 1.0
O B:HOH901 4.8 25.1 1.0
N1N A:NAD801 4.9 22.9 1.0
O A:ASP191 5.0 17.7 1.0
C6N A:NAD801 5.0 24.1 1.0

Magnesium binding site 3 out of 4 in 7pcc

Go back to Magnesium Binding Sites List in 7pcc
Magnesium binding site 3 out of 4 in the Burg in Complex with MG2+ and Nad+ (Holo): 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 in Complex with MG2+ and Nad+ (Holo): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:28.4
occ:1.00
 O A:HOH913 1.9 28.0 1.0
OD1 B:ASP191 2.1 23.8 1.0
O B:HOH928 2.1 31.8 1.0
O B:HOH948 2.1 20.5 1.0
O A:HOH934 2.2 26.4 1.0
O B:HOH994 2.3 29.9 1.0
CG B:ASP191 3.1 24.3 1.0
OD2 B:ASP191 3.6 27.4 1.0
MG B:MG803 3.8 28.3 1.0
OE1 A:GLU232 3.8 28.4 1.0
NH2 B:ARG131 3.9 21.6 1.0
OE2 B:GLU195 4.0 20.2 1.0
OE1 B:GLN194 4.0 21.6 1.0
OE2 A:GLU232 4.2 30.4 1.0
C4N B:NAD801 4.2 26.7 1.0
O B:HOH964 4.3 22.6 1.0
CZ B:ARG131 4.4 20.7 1.0
CB B:ASP191 4.4 22.9 1.0
CD A:GLU232 4.4 26.1 1.0
OE1 A:GLU226 4.5 23.6 1.0
O B:PRO130 4.5 18.1 1.0
C5N B:NAD801 4.6 25.6 1.0
O B:HOH963 4.7 24.5 1.0
NH1 B:ARG131 4.8 21.2 1.0
CA B:ASP191 4.8 21.7 1.0
CD B:GLN194 4.8 20.2 1.0
O A:HOH921 4.9 26.5 1.0

Magnesium binding site 4 out of 4 in 7pcc

Go back to Magnesium Binding Sites List in 7pcc
Magnesium binding site 4 out of 4 in the Burg in Complex with MG2+ and Nad+ (Holo): 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 in Complex with MG2+ and Nad+ (Holo): Biosynthesis of Cyclopropanol Rings in Bacterial Toxins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:28.3
occ:1.00
 O B:HOH963 2.0 24.5 1.0
OD2 B:ASP191 2.0 27.4 1.0
O B:HOH994 2.0 29.9 1.0
OE2 B:GLU195 2.2 20.2 1.0
O A:HOH921 2.2 26.5 1.0
O B:HOH965 2.2 21.5 1.0
CG B:ASP191 3.1 24.3 1.0
CD B:GLU195 3.2 20.4 1.0
OD1 B:ASP191 3.5 23.8 1.0
OE1 B:GLU195 3.6 20.2 1.0
MG B:MG802 3.8 28.4 1.0
O B:HOH928 3.9 31.8 1.0
O B:HOH964 4.0 22.6 1.0
O2D B:NAD801 4.2 18.8 1.0
O A:HOH1014 4.2 35.6 1.0
OG A:SER254 4.3 24.7 1.0
NE2 B:HIS108 4.3 25.2 1.0
CB B:ASP191 4.4 22.9 1.0
CD2 B:HIS108 4.4 24.9 1.0
CE1 B:HIS108 4.4 24.6 1.0
ND1 B:HIS108 4.5 24.7 1.0
O B:HOH948 4.5 20.5 1.0
CG B:GLU195 4.5 19.5 1.0
CG B:HIS108 4.5 24.2 1.0
O A:HOH913 4.7 28.0 1.0
C2N B:NAD801 4.7 25.1 1.0
C3N B:NAD801 4.7 26.3 1.0
CB A:CYS257 4.8 25.5 1.0
C4N B:NAD801 4.8 26.7 1.0
N1N B:NAD801 4.8 22.8 1.0
C6N B:NAD801 4.9 24.0 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 04:06:28 2024

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