Magnesium in PDB 2vjl: Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Formyl-Coa

All present enzymatic activity of Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Formyl-Coa:
2.8.3.16;

The structure of Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Formyl-Coa, PDB code: 2vjl was solved by C.L.Berthold, C.G.Toyota, N.G.J.Richards, Y.Lindqvist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.0
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	151.765, 151.765, 100.082, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.2

The structure of Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Formyl-Coa also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Formyl-Coa (pdb code 2vjl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Formyl-Coa, PDB code: 2vjl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Formyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Formyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4000 b:40.6 occ:1.00 OD2 A:ASP297 2.4 29.9 0.5 O A:HOH2245 2.4 47.5 1.0 O A:ASP294 2.6 25.2 1.0 O A:HOH2294 2.7 32.5 1.0 O A:HOH2244 3.3 53.3 1.0 CG A:ASP297 3.6 29.3 0.5 C A:ASP294 3.6 26.2 1.0 CA A:ASP294 4.2 26.5 1.0 CA A:ASP297 4.3 28.1 0.5 CA A:ASP297 4.3 28.2 0.5 OD2 A:ASP297 4.3 30.4 0.5 OD1 A:ASP297 4.4 31.3 0.5 N A:ASP297 4.4 28.0 1.0 CB A:ASP297 4.5 28.8 0.5 OH A:TYR343 4.5 24.4 1.0 CB A:ASP297 4.5 28.6 0.5 N A:MET295 4.7 26.2 1.0 CG A:ASP297 4.7 28.8 0.5 CB A:ASP294 4.7 28.1 1.0 O A:MET295 4.9 25.8 1.0 C A:MET295 5.0 25.7 1.0

Magnesium binding site 2 out of 2 in the Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Formyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Formyl-Coa Transferase with Aspartyl-Coa Thioester Intermediate Derived From Formyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4001 b:20.4 occ:1.00 O A:PHE245 2.6 25.8 1.0 O A:ILE248 2.7 21.8 1.0 O A:HOH2161 2.9 25.2 1.0 O A:HOH2168 3.0 41.9 1.0 O A:HOH2198 3.1 44.8 1.0 O A:GLY222 3.1 20.6 1.0 C A:PHE245 3.8 25.0 1.0 CA A:GLY222 3.8 21.5 1.0 C A:ILE248 3.8 21.8 1.0 C A:GLY222 3.8 20.5 1.0 CD1 A:LEU218 4.0 18.6 1.0 O A:HOH2067 4.0 44.2 1.0 N A:ILE248 4.2 25.5 1.0 O A:HOH2167 4.2 34.0 1.0 O A:ASP246 4.2 30.4 1.0 C A:ASP246 4.4 29.3 1.0 CA A:ILE248 4.5 23.6 1.0 CA A:PHE245 4.6 24.0 1.0 CB A:PHE245 4.7 22.6 1.0 N A:ASP246 4.7 27.8 1.0 N A:THR249 4.7 20.5 1.0 O A:LEU218 4.8 19.1 1.0 CA A:ASP246 4.8 28.9 1.0 CG A:LEU218 4.8 18.4 1.0 CA A:THR249 4.9 20.1 1.0 N A:ASN247 4.9 28.6 1.0 CG2 A:THR249 5.0 20.0 1.0

C.L.Berthold, C.G.Toyota, N.G.J.Richards, Y.Lindqvist. Reinvestigation of the Catalytic Mechanism of Formyl-Coa Transferase, A Class III Coa- Transferase. J.Biol.Chem. V. 283 6519 2008.
ISSN: ISSN 0021-9258
PubMed: 18162462
DOI: 10.1074/JBC.M709353200