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

The structure of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp, Formyl-Coa and Adp, PDB code: 8vzd 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)	37.38 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	100.173, 182.511, 123.92, 90, 90, 90
R / Rfree (%)	19.8 / 23.4

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

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp, Formyl-Coa and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:18.5 occ:1.00 OD1 A:ASP441 2.1 19.7 1.0 OD1 A:ASN468 2.1 19.9 1.0 O2B A:TPP601 2.2 19.1 1.0 O A:GLY470 2.2 20.3 1.0 O1A A:TPP601 2.3 20.9 1.0 O A:HOH727 2.3 19.9 1.0 CG A:ASN468 3.1 20.6 1.0 CG A:ASP441 3.1 19.7 1.0 PA A:TPP601 3.2 20.0 1.0 PB A:TPP601 3.3 20.1 1.0 O3A A:TPP601 3.4 19.7 1.0 C A:GLY470 3.4 20.6 1.0 ND2 A:ASN468 3.4 21.0 1.0 OD2 A:ASP441 3.5 19.4 1.0 O7 A:TPP601 3.6 20.7 1.0 O1B A:TPP601 4.0 19.9 1.0 N A:GLY472 4.0 22.4 1.0 N A:ASP441 4.0 20.2 1.0 N A:GLY470 4.1 21.2 1.0 N A:ASN468 4.2 20.1 1.0 CA A:GLY470 4.3 20.4 1.0 N A:SER442 4.3 19.9 1.0 N A:ILE471 4.3 21.1 1.0 N A:GLY473 4.4 20.6 1.0 CB A:ASN468 4.4 21.0 1.0 CB A:ASP441 4.4 19.8 1.0 CA A:ILE471 4.5 20.0 1.0 O3B A:TPP601 4.5 21.2 1.0 O A:ILE466 4.5 19.2 1.0 O2A A:TPP601 4.6 19.6 1.0 CA A:ASP441 4.7 20.3 1.0 CA A:ASN468 4.7 20.5 1.0 C A:ILE471 4.7 20.6 1.0 CA A:GLY472 4.8 21.6 1.0 C A:GLY440 4.8 19.8 1.0 CA A:GLY440 4.8 19.8 1.0 C A:ASN468 4.8 20.6 1.0 CB A:SER442 4.8 20.5 1.0 N A:ASN469 4.9 20.7 1.0 C A:ASP441 5.0 20.6 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp, Formyl-Coa and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:18.0 occ:1.00 OD1 B:ASP441 2.2 19.6 1.0 OD1 B:ASN468 2.2 19.4 1.0 O2B B:TPP601 2.2 19.1 1.0 O1A B:TPP601 2.2 19.3 1.0 O B:GLY470 2.3 18.6 1.0 O B:HOH750 2.3 18.2 1.0 CG B:ASN468 3.1 19.8 1.0 PA B:TPP601 3.1 17.6 1.0 PB B:TPP601 3.2 19.5 1.0 CG B:ASP441 3.2 19.0 1.0 O3A B:TPP601 3.3 18.6 1.0 ND2 B:ASN468 3.5 19.1 1.0 C B:GLY470 3.5 20.3 1.0 O7 B:TPP601 3.6 20.0 1.0 OD2 B:ASP441 3.7 19.1 1.0 O1B B:TPP601 3.7 20.9 1.0 N B:GLY472 3.9 20.6 1.0 N B:ASP441 4.1 18.9 1.0 N B:ASN468 4.1 19.3 1.0 N B:GLY470 4.2 20.6 1.0 N B:GLY473 4.3 19.6 1.0 N B:SER442 4.4 18.2 1.0 CB B:ASN468 4.4 20.0 1.0 N B:ILE471 4.4 20.2 1.0 O B:ILE466 4.5 17.8 1.0 CA B:GLY470 4.5 20.8 1.0 CB B:ASP441 4.5 18.4 1.0 O3B B:TPP601 4.5 19.0 1.0 CA B:ILE471 4.5 20.1 1.0 O2A B:TPP601 4.5 19.6 1.0 CA B:GLY472 4.6 18.7 1.0 C B:ILE471 4.6 19.8 1.0 CA B:ASN468 4.7 19.8 1.0 CA B:ASP441 4.8 18.4 1.0 C B:ASN468 4.8 20.9 1.0 C B:GLY472 4.9 19.6 1.0 C B:GLY440 4.9 18.5 1.0 CA B:GLY440 4.9 18.5 1.0 C7 B:TPP601 4.9 19.1 1.0 CB B:SER442 4.9 19.4 1.0 N B:ASN469 5.0 20.3 1.0 OH B:TYR367 5.0 20.3 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