Magnesium in PDB 8x3x: Thdp-Dependent Hka Synthase

The structure of Thdp-Dependent Hka Synthase, PDB code: 8x3x was solved by J.H.Yu, T.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.67 / 2.15
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.341, 110.365, 112.514, 90, 90, 90
R / Rfree (%)	15.5 / 19.6

The binding sites of Magnesium atom in the Thdp-Dependent Hka Synthase (pdb code 8x3x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Thdp-Dependent Hka Synthase, PDB code: 8x3x:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Thdp-Dependent Hka Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thdp-Dependent Hka Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:46.1 occ:1.00 OD1 A:ASP448 2.0 38.4 1.0 O2A A:TPP601 2.0 36.7 1.0 O A:GLY477 2.1 43.8 1.0 O2B A:TPP601 2.1 44.1 1.0 O A:HOH735 2.2 36.2 1.0 OD1 A:ASN475 2.2 44.4 1.0 CG A:ASN475 3.1 43.9 1.0 CG A:ASP448 3.2 42.4 1.0 PA A:TPP601 3.2 35.7 1.0 PB A:TPP601 3.2 40.3 1.0 O3A A:TPP601 3.3 39.1 1.0 C A:GLY477 3.3 47.1 1.0 ND2 A:ASN475 3.5 43.9 1.0 OD2 A:ASP448 3.7 44.5 1.0 N A:ASP448 3.9 39.5 1.0 O1B A:TPP601 3.9 43.3 1.0 N A:GLY479 3.9 54.4 1.0 O7 A:TPP601 3.9 39.6 1.0 N A:GLY477 4.1 41.1 1.0 N A:ALA449 4.2 32.6 1.0 N A:HIS478 4.2 48.2 1.0 O A:LEU473 4.3 37.4 1.0 CA A:GLY477 4.3 46.0 1.0 CA A:HIS478 4.3 40.8 1.0 CB A:ASP448 4.4 35.9 1.0 O1A A:TPP601 4.4 36.3 1.0 N A:ASN475 4.4 38.5 1.0 O3B A:TPP601 4.5 36.9 1.0 CB A:ASN475 4.5 42.0 1.0 CA A:ASP448 4.6 37.9 1.0 C A:HIS478 4.6 48.0 1.0 CA A:GLY447 4.7 35.7 1.0 C A:GLY447 4.7 36.3 1.0 CA A:GLY479 4.8 52.6 1.0 CA A:ASN475 4.8 43.2 1.0 CB A:ALA449 4.9 36.3 1.0 C A:ASN475 4.9 46.5 1.0 C A:ASP448 4.9 38.7 1.0 N A:GLY476 4.9 48.8 1.0

Magnesium binding site 2 out of 2 in the Thdp-Dependent Hka Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thdp-Dependent Hka Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:45.7 occ:1.00 O2A B:TPP601 1.8 42.4 1.0 O2B B:TPP601 2.1 42.5 1.0 O B:GLY477 2.1 39.4 1.0 OD1 B:ASN475 2.2 43.6 1.0 OD1 B:ASP448 2.2 40.1 1.0 O B:HOH741 2.3 38.9 1.0 PA B:TPP601 3.0 42.3 1.0 CG B:ASN475 3.1 46.2 1.0 PB B:TPP601 3.1 39.9 1.0 O3A B:TPP601 3.2 40.8 1.0 CG B:ASP448 3.3 45.1 1.0 C B:GLY477 3.3 43.7 1.0 ND2 B:ASN475 3.4 37.1 1.0 O1B B:TPP601 3.8 50.5 1.0 O7 B:TPP601 3.8 43.4 1.0 OD2 B:ASP448 3.9 44.6 1.0 N B:GLY479 3.9 40.5 1.0 N B:ASP448 3.9 35.4 1.0 N B:ALA449 4.2 36.6 1.0 N B:GLY477 4.2 43.9 1.0 N B:HIS478 4.2 38.3 1.0 CA B:HIS478 4.2 40.8 1.0 O1A B:TPP601 4.3 41.2 1.0 O B:LEU473 4.3 51.6 1.0 CA B:GLY477 4.3 46.1 1.0 O3B B:TPP601 4.4 42.2 1.0 CB B:ASN475 4.5 44.9 1.0 CB B:ASP448 4.5 40.7 1.0 N B:ASN475 4.5 42.8 1.0 C B:HIS478 4.6 42.4 1.0 CA B:ASP448 4.6 32.7 1.0 CA B:GLY447 4.7 38.2 1.0 C B:GLY447 4.7 37.4 1.0 CB B:ALA449 4.8 33.1 1.0 CA B:GLY479 4.8 43.6 1.0 CA B:ASN475 4.8 44.6 1.0 C B:ASN475 4.9 46.2 1.0 C B:ASP448 4.9 36.3 1.0 N B:GLY476 5.0 46.1 1.0

J.H.Yu, T.Liu. Thdp-Dependent Hka Synthase To Be Published.