Magnesium in PDB 8vzh: Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp

The structure of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp, PDB code: 8vzh was solved by Y.Kim, M.Maltseva, M.Endres, S.Lee, Y.Yoshikuni, R.Gonzalez, K.Michalska, A.Joachimiak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.39 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	120.591, 134.013, 173.399, 90, 90, 90
R / Rfree (%)	16 / 19.5

The structure of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Magnesium atom in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp (pdb code 8vzh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp, PDB code: 8vzh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg609 b:18.3 occ:1.00 OD1 A:ASN468 2.1 24.7 1.0 O3B A:TPP602 2.1 26.0 1.0 O2A A:TPP602 2.1 21.5 1.0 OD1 A:ASP441 2.2 24.1 1.0 O A:GLY470 2.2 24.3 1.0 O A:HOH744 2.2 22.0 1.0 CG A:ASN468 3.0 25.3 1.0 PB A:TPP602 3.2 23.1 1.0 PA A:TPP602 3.2 21.2 1.0 CG A:ASP441 3.3 25.3 1.0 O3A A:TPP602 3.4 22.9 1.0 ND2 A:ASN468 3.4 23.4 1.0 C A:GLY470 3.4 27.6 1.0 O7 A:TPP602 3.7 22.7 1.0 OD2 A:ASP441 3.8 23.6 1.0 O1B A:TPP602 3.8 26.8 1.0 N A:ASP441 4.0 20.5 1.0 N A:GLY472 4.0 28.6 1.0 N A:GLY470 4.1 26.2 1.0 N A:ASN468 4.2 22.4 1.0 N A:GLY473 4.3 27.8 1.0 CA A:GLY470 4.3 25.1 1.0 CB A:ASN468 4.4 23.2 1.0 N A:ILE471 4.4 27.0 1.0 N A:SER442 4.4 20.6 1.0 O A:ILE466 4.4 23.8 1.0 O2B A:TPP602 4.4 25.1 1.0 O1A A:TPP602 4.5 23.5 1.0 CB A:ASP441 4.5 21.5 1.0 CA A:ILE471 4.5 23.4 1.0 CA A:ASN468 4.6 24.4 1.0 C A:ILE471 4.7 29.0 1.0 CA A:ASP441 4.7 23.9 1.0 CA A:GLY440 4.8 22.6 1.0 C A:GLY440 4.8 23.2 1.0 CA A:GLY472 4.8 24.4 1.0 C A:ASN468 4.8 25.5 1.0 N A:ASN469 4.9 22.2 1.0 C A:GLY472 4.9 29.4 1.0 CA A:GLY473 5.0 28.0 1.0 CB A:SER442 5.0 21.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:17.2 occ:1.00 O2A B:TPP602 1.9 20.5 1.0 O3B B:TPP602 2.1 22.5 1.0 O B:GLY470 2.1 22.6 1.0 OD1 B:ASP441 2.2 19.1 1.0 OD1 B:ASN468 2.2 20.8 1.0 O B:HOH732 2.3 19.9 1.0 PA B:TPP602 3.1 18.8 1.0 CG B:ASN468 3.2 25.8 1.0 PB B:TPP602 3.2 23.9 1.0 CG B:ASP441 3.2 21.2 1.0 O3A B:TPP602 3.3 21.0 1.0 C B:GLY470 3.3 21.7 1.0 ND2 B:ASN468 3.5 21.4 1.0 O7 B:TPP602 3.6 19.1 1.0 OD2 B:ASP441 3.7 22.2 1.0 O1B B:TPP602 3.8 24.8 1.0 N B:GLY472 3.9 25.7 1.0 N B:ASP441 4.0 17.6 1.0 N B:GLY470 4.1 20.7 1.0 N B:SER442 4.3 18.2 1.0 N B:ASN468 4.3 19.8 1.0 CA B:GLY470 4.3 22.8 1.0 N B:ILE471 4.3 22.5 1.0 N B:GLY473 4.3 23.4 1.0 O1A B:TPP602 4.4 19.8 1.0 O2B B:TPP602 4.4 22.0 1.0 CA B:ILE471 4.4 21.6 1.0 CB B:ASP441 4.5 18.3 1.0 CB B:ASN468 4.5 20.5 1.0 O B:ILE466 4.5 22.8 1.0 C B:ILE471 4.6 27.6 1.0 CA B:ASP441 4.7 21.7 1.0 CA B:GLY472 4.7 28.1 1.0 C B:GLY440 4.8 20.8 1.0 CA B:ASN468 4.8 22.2 1.0 CA B:GLY440 4.8 19.2 1.0 CB B:SER442 4.8 21.0 1.0 C B:ASN468 4.9 24.2 1.0 C7 B:TPP602 5.0 22.1 1.0 C B:ASP441 5.0 19.9 1.0 C B:GLY472 5.0 27.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg607 b:26.0 occ:1.00 O2A C:TPP602 2.1 32.4 1.0 OD1 C:ASP441 2.1 33.9 1.0 O3B C:TPP602 2.1 33.7 1.0 O C:HOH713 2.2 34.4 1.0 O C:GLY470 2.2 32.8 1.0 OD1 C:ASN468 2.2 35.2 1.0 CG C:ASP441 3.1 33.8 1.0 CG C:ASN468 3.2 36.7 1.0 PA C:TPP602 3.2 31.9 1.0 PB C:TPP602 3.2 35.0 1.0 O3A C:TPP602 3.4 29.8 1.0 C C:GLY470 3.4 31.2 1.0 OD2 C:ASP441 3.5 37.2 1.0 ND2 C:ASN468 3.6 35.8 1.0 O7 C:TPP602 3.6 32.5 1.0 O1B C:TPP602 3.9 34.0 1.0 N C:GLY472 3.9 37.0 1.0 N C:ASP441 4.0 30.0 1.0 N C:GLY470 4.1 32.3 1.0 N C:GLY473 4.2 37.5 1.0 N C:ASN468 4.2 34.2 1.0 N C:SER442 4.3 27.9 1.0 N C:ILE471 4.3 32.9 1.0 CA C:GLY470 4.3 35.1 1.0 CB C:ASP441 4.4 30.5 1.0 CA C:ILE471 4.4 33.5 1.0 CB C:ASN468 4.5 36.0 1.0 O2B C:TPP602 4.5 29.0 1.0 O1A C:TPP602 4.5 28.6 1.0 C C:ILE471 4.6 35.0 1.0 CA C:GLY472 4.6 35.6 1.0 O C:ILE466 4.6 36.5 1.0 CA C:ASP441 4.7 33.7 1.0 CA C:ASN468 4.7 36.9 1.0 C C:ASN468 4.8 40.4 1.0 C C:GLY440 4.8 30.5 1.0 CA C:GLY440 4.8 28.4 1.0 C C:GLY472 4.8 40.5 1.0 CB C:SER442 4.9 32.6 1.0 N C:ASN469 4.9 35.3 1.0 C7 C:TPP602 5.0 35.6 1.0 CA C:GLY473 5.0 38.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg606 b:32.0 occ:1.00 O3B D:TPP602 2.0 35.5 1.0 OD1 D:ASP441 2.1 37.3 1.0 O2A D:TPP602 2.1 40.8 1.0 OD1 D:ASN468 2.1 39.0 1.0 O D:GLY470 2.2 40.4 1.0 O D:HOH714 2.2 37.2 1.0 CG D:ASN468 3.1 41.6 1.0 CG D:ASP441 3.2 41.7 1.0 PA D:TPP602 3.2 40.4 1.0 PB D:TPP602 3.2 40.4 1.0 O3A D:TPP602 3.3 37.1 1.0 C D:GLY470 3.4 38.2 1.0 ND2 D:ASN468 3.5 38.9 1.0 O7 D:TPP602 3.6 38.9 1.0 OD2 D:ASP441 3.7 43.3 1.0 N D:GLY472 3.8 44.0 1.0 O1B D:TPP602 4.0 41.1 1.0 N D:ASP441 4.0 35.2 1.0 N D:GLY470 4.1 38.9 1.0 N D:ASN468 4.3 42.0 1.0 N D:SER442 4.3 37.5 1.0 N D:ILE471 4.3 37.7 1.0 N D:GLY473 4.3 41.8 1.0 O2B D:TPP602 4.3 32.0 1.0 CA D:GLY470 4.3 41.9 1.0 CA D:ILE471 4.4 39.1 1.0 CB D:ASP441 4.4 36.1 1.0 O D:ILE466 4.5 38.7 1.0 CB D:ASN468 4.5 40.4 1.0 O1A D:TPP602 4.5 38.0 1.0 C D:ILE471 4.6 38.9 1.0 CA D:GLY472 4.6 40.2 1.0 CA D:ASP441 4.7 41.0 1.0 CA D:ASN468 4.7 41.5 1.0 C D:GLY440 4.8 37.0 1.0 CA D:GLY440 4.8 40.2 1.0 C D:ASN468 4.8 42.1 1.0 C D:GLY472 4.8 42.8 1.0 CB D:SER442 4.9 39.5 1.0 OH D:TYR367 5.0 41.5 1.0 C7 D:TPP602 5.0 34.9 1.0

Y.Kim, S.H.Lee, P.Gade, M.Nattermann, N.Maltseva, M.Endres, J.Chen, P.Wichmann, Y.Hu, D.G.Marchal, Y.Yoshikuni, T.J.Erb, R.Gonzalez, K.Michalska, A.Joachimiak. Revealing Reaction Intermediates in One-Carbon Elongation By Thiamine Diphosphate/Coa-Dependent Enzyme Family. Commun Chem V. 7 160 2024.
ISSN: ESSN 2399-3669
PubMed: 39034323
DOI: 10.1038/S42004-024-01242-Y