Magnesium in PDB 8vzi: Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Cchacs From Conidiobolus Coronatus in the Complex with Thdp and Adp

The structure of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Cchacs From Conidiobolus Coronatus in the Complex with Thdp and Adp, PDB code: 8vzi was solved by Y.Kim, P.Gade, 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)	44.82 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.742, 179.286, 96.826, 90, 108.23, 90
R / Rfree (%)	15.6 / 19.6

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

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Cchacs From Conidiobolus Coronatus in the Complex with Thdp and Adp (pdb code 8vzi). 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 Cchacs From Conidiobolus Coronatus in the Complex with Thdp and Adp, PDB code: 8vzi:
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 Cchacs From Conidiobolus Coronatus 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 Cchacs From Conidiobolus Coronatus in the Complex with Thdp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg610 b:23.6 occ:1.00 O2A A:TPP601 2.0 19.6 1.0 OD1 A:ASN470 2.1 21.8 1.0 OD1 A:ASP443 2.1 23.5 1.0 O A:HOH740 2.2 18.4 1.0 O1B A:TPP601 2.2 20.8 1.0 O A:GLY472 2.2 19.9 1.0 CG A:ASN470 3.1 22.2 1.0 PA A:TPP601 3.2 19.6 1.0 PB A:TPP601 3.2 21.9 1.0 CG A:ASP443 3.3 21.7 1.0 O3A A:TPP601 3.3 18.3 1.0 C A:GLY472 3.4 24.4 1.0 ND2 A:ASN470 3.5 20.8 1.0 O7 A:TPP601 3.7 20.6 1.0 O2B A:TPP601 3.8 19.8 1.0 OD2 A:ASP443 3.8 24.3 1.0 N A:ASP443 4.0 19.2 1.0 N A:GLY472 4.1 21.0 1.0 N A:ASN470 4.1 24.9 1.0 N A:SER444 4.2 19.0 1.0 O A:ILE468 4.3 19.7 1.0 CA A:GLY472 4.3 20.7 1.0 CB A:ASN470 4.4 21.0 1.0 N A:TYR474 4.4 22.9 1.0 N A:ILE473 4.4 20.2 1.0 O1A A:TPP601 4.4 17.1 1.0 CB A:ASP443 4.5 21.0 1.0 O3B A:TPP601 4.5 22.0 1.0 CA A:ILE473 4.6 20.0 1.0 CA A:ASN470 4.7 22.4 1.0 CA A:ASP443 4.7 23.8 1.0 CA A:GLY442 4.8 19.1 1.0 C A:GLY442 4.8 19.1 1.0 C A:ASN470 4.8 25.6 1.0 CB A:SER444 4.8 21.6 1.0 N A:ASN471 4.9 20.8 1.0 C A:ILE473 5.0 23.2 1.0 C A:ASP443 5.0 20.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Cchacs From Conidiobolus Coronatus 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 Cchacs From Conidiobolus Coronatus in the Complex with Thdp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg609 b:19.0 occ:1.00 O2A B:TPP601 2.0 20.4 1.0 OD1 B:ASN470 2.0 22.1 1.0 OD1 B:ASP443 2.1 23.1 1.0 O B:GLY472 2.1 18.5 1.0 O1B B:TPP601 2.2 21.1 1.0 O B:HOH714 2.2 17.7 1.0 CG B:ASN470 3.0 22.0 1.0 PA B:TPP601 3.2 19.3 1.0 CG B:ASP443 3.2 21.7 1.0 PB B:TPP601 3.2 18.8 1.0 C B:GLY472 3.3 27.5 1.0 O3A B:TPP601 3.3 13.5 1.0 ND2 B:ASN470 3.4 21.4 1.0 OD2 B:ASP443 3.6 24.4 1.0 O7 B:TPP601 3.7 20.1 1.0 O2B B:TPP601 3.8 22.9 1.0 N B:GLY472 4.0 19.2 1.0 N B:ASP443 4.0 21.0 1.0 N B:ASN470 4.2 20.2 1.0 CA B:GLY472 4.2 20.6 1.0 N B:SER444 4.2 21.3 1.0 N B:ILE473 4.3 18.8 1.0 N B:TYR474 4.3 18.8 1.0 O B:ILE468 4.3 19.8 1.0 CB B:ASN470 4.3 19.9 1.0 CB B:ASP443 4.4 21.6 1.0 O1A B:TPP601 4.4 16.7 1.0 CA B:ILE473 4.5 22.2 1.0 O3B B:TPP601 4.5 17.1 1.0 CA B:ASP443 4.6 21.4 1.0 CA B:ASN470 4.6 25.7 1.0 CA B:GLY442 4.8 21.7 1.0 C B:ASN470 4.8 24.0 1.0 C B:GLY442 4.8 27.3 1.0 CB B:SER444 4.8 22.7 1.0 C B:ILE473 4.9 21.9 1.0 N B:ASN471 4.9 21.2 1.0 C B:ASP443 4.9 23.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Cchacs From Conidiobolus Coronatus 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 Cchacs From Conidiobolus Coronatus in the Complex with Thdp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg611 b:23.1 occ:1.00 O2A C:TPP601 2.0 19.1 1.0 OD1 C:ASN470 2.1 25.0 1.0 O C:GLY472 2.1 23.0 1.0 OD1 C:ASP443 2.2 25.5 1.0 O C:HOH765 2.2 18.2 1.0 O1B C:TPP601 2.2 24.2 1.0 CG C:ASN470 3.1 27.0 1.0 PB C:TPP601 3.2 21.3 1.0 PA C:TPP601 3.2 19.6 1.0 CG C:ASP443 3.2 22.9 1.0 O3A C:TPP601 3.3 17.0 1.0 C C:GLY472 3.3 26.5 1.0 ND2 C:ASN470 3.5 22.5 1.0 OD2 C:ASP443 3.7 23.0 1.0 O7 C:TPP601 3.7 22.6 1.0 O2B C:TPP601 3.8 23.4 1.0 N C:GLY472 4.0 26.8 1.0 N C:ASP443 4.0 21.9 1.0 N C:ASN470 4.2 24.2 1.0 CA C:GLY472 4.2 19.8 1.0 N C:TYR474 4.3 21.4 1.0 N C:SER444 4.3 22.2 1.0 N C:ILE473 4.3 22.1 1.0 O C:ILE468 4.3 24.9 1.0 CB C:ASN470 4.4 22.5 1.0 O1A C:TPP601 4.5 18.9 1.0 CB C:ASP443 4.5 22.4 1.0 CA C:ILE473 4.5 20.6 1.0 O3B C:TPP601 4.5 23.5 1.0 CA C:ASN470 4.6 26.6 1.0 CA C:ASP443 4.7 22.2 1.0 C C:ASN470 4.8 26.4 1.0 CA C:GLY442 4.8 21.4 1.0 C C:GLY442 4.8 23.8 1.0 C C:ILE473 4.8 20.4 1.0 CB C:SER444 4.9 22.7 1.0 N C:ASN471 4.9 21.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Cchacs From Conidiobolus Coronatus 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 Cchacs From Conidiobolus Coronatus in the Complex with Thdp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg607 b:21.4 occ:1.00 O2A D:TPP601 2.0 23.0 1.0 OD1 D:ASP443 2.0 24.1 1.0 O D:HOH804 2.2 21.1 1.0 OD1 D:ASN470 2.2 25.8 1.0 O1B D:TPP601 2.2 30.7 1.0 O D:GLY472 2.2 22.0 1.0 PA D:TPP601 3.1 22.4 1.0 CG D:ASN470 3.2 30.3 1.0 PB D:TPP601 3.2 25.0 1.0 CG D:ASP443 3.2 24.2 1.0 O3A D:TPP601 3.2 20.5 1.0 C D:GLY472 3.4 26.3 1.0 ND2 D:ASN470 3.6 24.1 1.0 O7 D:TPP601 3.7 25.4 1.0 OD2 D:ASP443 3.7 24.4 1.0 O2B D:TPP601 3.8 24.0 1.0 N D:ASP443 3.9 23.8 1.0 N D:GLY472 4.1 22.4 1.0 N D:SER444 4.2 23.5 1.0 N D:ASN470 4.3 23.8 1.0 O D:ILE468 4.3 28.8 1.0 CA D:GLY472 4.3 23.1 1.0 N D:TYR474 4.4 22.9 1.0 O1A D:TPP601 4.4 18.1 1.0 N D:ILE473 4.4 21.0 1.0 CB D:ASP443 4.4 24.3 1.0 O3B D:TPP601 4.5 21.3 1.0 CB D:ASN470 4.5 23.0 1.0 CA D:ILE473 4.6 20.9 1.0 CA D:ASP443 4.6 23.9 1.0 CA D:GLY442 4.7 26.8 1.0 C D:GLY442 4.7 27.8 1.0 CA D:ASN470 4.8 22.8 1.0 C D:ASN470 4.9 23.9 1.0 CB D:SER444 4.9 23.2 1.0 C D:ASP443 4.9 25.1 1.0 C D:ILE473 4.9 25.7 1.0 N D:ASN471 5.0 22.2 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