Magnesium in PDB 8vzk: Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Cfhhacs From Chloroflexi Bacterium in the Complex with Thdp and Adp

All present enzymatic activity of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Cfhhacs From Chloroflexi Bacterium in the Complex with Thdp and Adp:
4.1.1.8;

The structure of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Cfhhacs From Chloroflexi Bacterium in the Complex with Thdp and Adp, PDB code: 8vzk was solved by Y.Kim, P.Gade, A.Mayfield, 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)	48.23 / 2.65
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.327, 111.327, 193.164, 90, 90, 120
R / Rfree (%)	21.2 / 24.4

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

Magnesium binding site 1 out of 2 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Cfhhacs From Chloroflexi 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 Cfhhacs From Chloroflexi Bacterium in the Complex with Thdp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:70.5 occ:1.00 OD1 A:ASN475 1.9 73.2 1.0 O2A A:TPP601 2.0 66.0 1.0 OD1 A:ASP448 2.2 63.3 1.0 O1B A:TPP601 2.5 71.5 1.0 O A:GLY477 2.7 70.6 1.0 O2B A:TPP601 2.8 73.5 1.0 PB A:TPP601 2.9 67.0 1.0 CG A:ASN475 2.9 77.5 1.0 O3A A:TPP601 3.1 61.3 1.0 PA A:TPP601 3.1 65.6 1.0 ND2 A:ASN475 3.3 77.4 1.0 CG A:ASP448 3.3 64.3 1.0 O A:PHE473 3.7 68.2 1.0 C A:GLY477 3.7 70.5 1.0 N A:ASP448 3.8 63.9 1.0 OD2 A:ASP448 3.9 67.2 1.0 O7 A:TPP601 4.0 72.3 1.0 CB A:ASN475 4.2 69.2 1.0 N A:GLY477 4.2 76.6 1.0 N A:GLY449 4.2 64.7 1.0 N A:ASN475 4.3 63.2 1.0 O1A A:TPP601 4.3 62.8 1.0 CA A:GLY447 4.3 61.1 1.0 CA A:GLY477 4.4 72.1 1.0 O3B A:TPP601 4.4 69.6 1.0 N A:GLY479 4.5 71.3 1.0 C A:GLY447 4.5 62.8 1.0 CB A:ASP448 4.5 62.0 1.0 CA A:ASP448 4.6 65.9 1.0 CA A:ASN475 4.7 64.7 1.0 O A:GLY479 4.7 79.8 1.0 N A:ILE478 4.8 69.0 1.0 OH A:TYR374 4.9 77.9 1.0 N A:GLY476 4.9 66.5 1.0 C A:PHE473 4.9 64.4 1.0 C A:ASN475 4.9 67.4 1.0 C A:ASP448 4.9 63.3 1.0 OG1 A:THR398 4.9 65.0 1.0 C A:GLY479 5.0 78.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Cfhhacs From Chloroflexi 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 Cfhhacs From Chloroflexi Bacterium in the Complex with Thdp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:68.6 occ:1.00 O2A B:TPP601 2.0 70.5 1.0 OD1 B:ASN475 2.1 78.3 1.0 OD1 B:ASP448 2.3 65.8 1.0 O1B B:TPP601 2.3 78.5 1.0 CG B:ASN475 2.9 76.7 1.0 PB B:TPP601 3.0 76.3 1.0 O B:GLY477 3.1 71.5 1.0 PA B:TPP601 3.2 68.2 1.0 O2B B:TPP601 3.2 75.7 1.0 O3A B:TPP601 3.3 68.7 1.0 O B:PHE473 3.3 71.5 1.0 ND2 B:ASN475 3.4 82.3 1.0 CG B:ASP448 3.5 67.5 1.0 N B:ASP448 3.6 64.4 1.0 CA B:GLY447 4.1 62.7 1.0 CB B:ASN475 4.1 72.2 1.0 N B:ASN475 4.2 69.8 1.0 N B:GLY449 4.2 67.8 1.0 C B:GLY477 4.2 75.2 1.0 O7 B:TPP601 4.2 70.0 1.0 C B:GLY447 4.2 63.3 1.0 O1A B:TPP601 4.2 67.7 1.0 OD2 B:ASP448 4.3 68.7 1.0 CB B:ASP448 4.4 64.1 1.0 CA B:ASP448 4.4 65.8 1.0 O3B B:TPP601 4.5 73.7 1.0 C B:PHE473 4.6 64.0 1.0 OH B:TYR374 4.6 83.3 1.0 N B:GLY477 4.6 80.3 1.0 OG1 B:THR398 4.7 64.3 1.0 CA B:ASN475 4.7 73.4 1.0 N B:GLY479 4.7 75.8 1.0 C B:ASP448 4.8 66.0 1.0 CA B:GLY477 4.8 75.9 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