Manganese in PDB 7rue: Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone

All present enzymatic activity of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone:
2.5.1.54;

The structure of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone, PDB code: 7rue was solved by M.Heimhalt, P.Mukherjee, R.Grainger, R.Szabla, C.Brown, R.Turner, M.S.Junop, P.J.Berti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.21 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	210.281, 53.2, 150.79, 90, 116.01, 90
R / Rfree (%)	20.1 / 26.3

The structure of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Manganese atom in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone (pdb code 7rue). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone, PDB code: 7rue:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:53.5 occ:1.00 OD2 A:ASP326 2.0 46.9 1.0 OE1 A:GLU302 2.0 50.4 1.0 NE2 A:HIS268 2.8 49.4 1.0 O03 A:7QH401 2.8 46.0 0.9 SG A:CYS61 2.8 44.0 1.0 CD A:GLU302 3.0 53.4 1.0 CG A:ASP326 3.1 52.4 1.0 OE2 A:GLU302 3.3 50.1 1.0 CD2 A:HIS268 3.3 53.2 1.0 CB A:CYS61 3.6 49.3 1.0 CB A:ASP326 3.7 51.1 1.0 C04 A:7QH401 3.8 48.9 0.9 NZ A:LYS97 3.9 45.4 1.0 CE1 A:HIS268 3.9 52.4 1.0 NH2 A:ARG92 4.0 44.6 1.0 OD1 A:ASP326 4.1 51.4 1.0 N01 A:7QH401 4.1 55.4 0.9 N02 A:7QH401 4.2 58.3 0.9 CG A:GLU302 4.4 44.3 1.0 CA A:CYS61 4.4 49.8 1.0 CG A:HIS268 4.6 56.0 1.0 O A:CYS61 4.8 48.8 1.0 CE A:LYS97 4.8 50.7 1.0 ND1 A:HIS268 4.8 54.5 1.0 N03 A:7QH401 4.9 44.3 0.9 C A:CYS61 4.9 46.6 1.0 CZ A:ARG92 5.0 49.5 1.0

Manganese binding site 2 out of 4 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:26.7 occ:1.00 OD2 B:ASP326 2.1 32.1 1.0 OE1 B:GLU302 2.1 32.7 1.0 O03 B:7QH401 2.3 29.5 0.8 NE2 B:HIS268 2.5 25.2 1.0 SG B:CYS61 2.5 28.1 1.0 CG B:ASP326 3.0 27.8 1.0 CD B:GLU302 3.1 30.1 1.0 CD2 B:HIS268 3.3 25.7 1.0 OE2 B:GLU302 3.3 25.5 1.0 C04 B:7QH401 3.3 28.4 0.8 CE1 B:HIS268 3.5 27.6 1.0 CB B:ASP326 3.6 27.5 1.0 CB B:CYS61 3.8 29.0 1.0 OD1 B:ASP326 4.0 35.3 1.0 NZ B:LYS97 4.0 24.3 1.0 NH1 B:ARG92 4.1 26.2 1.0 N01 B:7QH401 4.2 34.9 0.8 N03 B:7QH401 4.2 23.3 0.8 N02 B:7QH401 4.2 31.5 0.8 CA B:CYS61 4.4 23.7 1.0 CG B:GLU302 4.5 24.0 1.0 O B:HOH520 4.5 25.4 1.0 CG B:HIS268 4.5 24.5 1.0 ND1 B:HIS268 4.6 28.2 1.0 CA B:ASP326 4.9 23.3 1.0 CZ B:ARG92 4.9 24.9 1.0 O B:CYS61 4.9 24.1 1.0 N B:ASP326 4.9 24.0 1.0

Manganese binding site 3 out of 4 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn402 b:48.9 occ:1.00 OD2 C:ASP326 1.9 42.4 1.0 OE2 C:GLU302 2.2 48.8 1.0 NE2 C:HIS268 2.7 57.8 1.0 O03 C:7QH401 2.9 51.5 0.8 CG C:ASP326 2.9 46.8 1.0 SG C:CYS61 2.9 50.6 1.0 CD C:GLU302 3.0 51.1 1.0 OE1 C:GLU302 3.0 51.2 1.0 CB C:ASP326 3.3 51.0 1.0 CD2 C:HIS268 3.3 52.3 1.0 CB C:CYS61 3.4 47.3 1.0 C04 C:7QH401 3.6 54.3 0.8 N02 C:7QH401 3.6 54.0 0.8 CE1 C:HIS268 3.9 56.7 1.0 N01 C:7QH401 3.9 58.3 0.8 OD1 C:ASP326 4.0 46.2 1.0 NH2 C:ARG92 4.1 50.0 1.0 CA C:CYS61 4.2 48.4 1.0 NZ C:LYS97 4.4 50.1 1.0 CG C:GLU302 4.4 49.6 1.0 CG C:HIS268 4.6 56.8 1.0 CA C:ASP326 4.7 55.4 1.0 O C:CYS61 4.8 55.1 1.0 NZ C:LYS273 4.8 55.0 1.0 C C:CYS61 4.8 51.9 1.0 ND1 C:HIS268 4.8 57.7 1.0 N03 C:7QH401 4.8 55.1 0.8 N C:ASP326 4.8 53.2 1.0

Manganese binding site 4 out of 4 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn402 b:40.8 occ:1.00 OD2 D:ASP326 2.1 33.9 1.0 OE2 D:GLU302 2.2 37.0 1.0 O D:HOH518 2.4 35.1 1.0 NE2 D:HIS268 2.6 43.0 1.0 SG D:CYS61 2.7 29.4 1.0 CD D:GLU302 3.0 30.7 1.0 OE1 D:GLU302 3.1 32.2 1.0 CG D:ASP326 3.2 31.4 1.0 O03 D:7QH401 3.3 38.0 0.7 CD2 D:HIS268 3.3 41.5 1.0 CB D:ASP326 3.6 27.5 1.0 CB D:CYS61 3.6 29.3 1.0 CE1 D:HIS268 3.7 42.3 1.0 NZ D:LYS97 4.0 28.0 1.0 C04 D:7QH401 4.2 40.1 0.7 CA D:CYS61 4.3 30.1 1.0 OD1 D:ASP326 4.3 25.0 1.0 NH2 D:ARG92 4.3 32.3 1.0 CG D:GLU302 4.4 30.7 1.0 N02 D:7QH401 4.5 42.3 0.7 CG D:HIS268 4.6 41.0 1.0 ND1 D:HIS268 4.7 38.1 1.0 O D:CYS61 4.7 32.5 1.0 O02 D:7QH401 4.8 52.9 0.7 CE D:LYS97 4.8 39.8 1.0 CA D:ASP326 4.9 24.9 1.0 C D:CYS61 4.9 31.7 1.0

M.Heimhalt, P.Mukherjee, R.A.Grainger, R.Szabla, C.Brown, R.Turner, M.S.Junop, P.J.Berti. An Inhibitor-in-Pieces Approach to Dahp Synthase Inhibition: Potent Enzyme and Bacterial Growth Inhibition Acs Infect Dis. 2021.
ISSN: ESSN 2373-8227
DOI: 10.1021/ACSINFECDIS.1C00462