Magnesium in PDB 8x3y: Thdp-Dependent Hka Synthase

The structure of Thdp-Dependent Hka Synthase, PDB code: 8x3y 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)	44.19 / 2.15
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.383, 108.873, 110.757, 90, 90, 90
R / Rfree (%)	15.6 / 18.5

The binding sites of Magnesium atom in the Thdp-Dependent Hka Synthase (pdb code 8x3y). 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: 8x3y:
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:Mg603 b:26.3 occ:1.00 O1A A:TPP602 1.9 24.9 1.0 OD1 A:ASN475 2.1 29.3 1.0 O A:GLY477 2.1 24.6 1.0 O A:HOH735 2.1 23.5 1.0 O1B A:TPP602 2.1 30.8 1.0 OD1 A:ASP448 2.2 27.7 1.0 CG A:ASN475 3.0 33.4 1.0 PA A:TPP602 3.0 26.6 1.0 PB A:TPP602 3.1 28.4 1.0 O3A A:TPP602 3.2 27.5 1.0 C A:GLY477 3.3 28.6 1.0 ND2 A:ASN475 3.3 27.4 1.0 CG A:ASP448 3.3 34.7 1.0 O3B A:TPP602 3.8 30.2 1.0 O7 A:TPP602 3.8 23.5 1.0 N A:GLY479 3.8 29.3 1.0 N A:ASP448 3.9 27.7 1.0 OD2 A:ASP448 3.9 32.7 1.0 N A:HIS478 4.2 28.0 1.0 N A:GLY477 4.2 32.7 1.0 N A:ALA449 4.2 27.0 1.0 CA A:HIS478 4.2 26.5 1.0 O A:LEU473 4.3 30.7 1.0 CA A:GLY477 4.3 29.6 1.0 O2A A:TPP602 4.4 24.5 1.0 O2B A:TPP602 4.4 34.6 1.0 CB A:ASN475 4.4 24.8 1.0 N A:ASN475 4.5 31.4 1.0 CB A:ASP448 4.5 28.1 1.0 C A:HIS478 4.6 34.5 1.0 CA A:GLY447 4.7 27.5 1.0 CA A:ASP448 4.7 27.4 1.0 CA A:GLY479 4.7 32.2 1.0 C A:GLY447 4.7 31.1 1.0 CA A:ASN475 4.8 25.8 1.0 CB A:ALA449 4.8 20.7 1.0 C A:ASN475 4.9 32.0 1.0 C A:ASP448 5.0 31.9 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:Mg603 b:33.3 occ:1.00 O1A B:TPP602 2.0 30.2 1.0 O B:HOH733 2.0 26.1 1.0 O B:GLY477 2.1 28.2 1.0 OD1 B:ASN475 2.1 34.6 1.0 OD1 B:ASP448 2.1 31.5 1.0 O1B B:TPP602 2.2 30.0 1.0 CG B:ASN475 3.0 33.4 1.0 PA B:TPP602 3.1 28.9 1.0 PB B:TPP602 3.1 28.1 1.0 O3A B:TPP602 3.2 25.4 1.0 CG B:ASP448 3.2 31.1 1.0 C B:GLY477 3.3 28.2 1.0 ND2 B:ASN475 3.3 32.9 1.0 OD2 B:ASP448 3.7 32.1 1.0 O3B B:TPP602 3.8 32.7 1.0 O7 B:TPP602 3.9 25.8 1.0 N B:GLY479 3.9 32.4 1.0 N B:ASP448 4.0 25.2 1.0 N B:GLY477 4.0 28.1 1.0 N B:ALA449 4.2 28.0 1.0 O B:LEU473 4.2 32.0 1.0 N B:HIS478 4.2 29.3 1.0 CA B:GLY477 4.2 29.6 1.0 CA B:HIS478 4.3 27.5 1.0 CB B:ASN475 4.4 30.4 1.0 O2A B:TPP602 4.4 26.2 1.0 O2B B:TPP602 4.4 29.2 1.0 N B:ASN475 4.5 35.7 1.0 CB B:ASP448 4.5 27.2 1.0 C B:HIS478 4.6 31.9 1.0 CA B:ASP448 4.6 27.4 1.0 CA B:GLY447 4.7 27.2 1.0 CA B:ASN475 4.8 34.3 1.0 C B:GLY447 4.8 32.2 1.0 CB B:ALA449 4.8 25.8 1.0 CA B:GLY479 4.8 30.6 1.0 C B:ASN475 4.8 29.4 1.0 C B:ASP448 4.9 31.4 1.0 N B:GLY476 4.9 33.8 1.0

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