Magnesium in PDB 8cxl: Structure of NAPH3, A Vanadium-Dependent Haloperoxidase Homolog Catalyzing the Stereospecific Alpha-Hydroxyketone Rearrangement Reaction in Napyradiomycin Biosynthesis

The structure of Structure of NAPH3, A Vanadium-Dependent Haloperoxidase Homolog Catalyzing the Stereospecific Alpha-Hydroxyketone Rearrangement Reaction in Napyradiomycin Biosynthesis, PDB code: 8cxl was solved by P.Y.-T.Chen, J.R.Chekan, B.S.Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.64 / 1.98
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	155.447, 96.095, 72.28, 90, 90, 90
R / Rfree (%)	18.3 / 20.1

The structure of Structure of NAPH3, A Vanadium-Dependent Haloperoxidase Homolog Catalyzing the Stereospecific Alpha-Hydroxyketone Rearrangement Reaction in Napyradiomycin Biosynthesis also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Structure of NAPH3, A Vanadium-Dependent Haloperoxidase Homolog Catalyzing the Stereospecific Alpha-Hydroxyketone Rearrangement Reaction in Napyradiomycin Biosynthesis (pdb code 8cxl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of NAPH3, A Vanadium-Dependent Haloperoxidase Homolog Catalyzing the Stereospecific Alpha-Hydroxyketone Rearrangement Reaction in Napyradiomycin Biosynthesis, PDB code: 8cxl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of NAPH3, A Vanadium-Dependent Haloperoxidase Homolog Catalyzing the Stereospecific Alpha-Hydroxyketone Rearrangement Reaction in Napyradiomycin Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of NAPH3, A Vanadium-Dependent Haloperoxidase Homolog Catalyzing the Stereospecific Alpha-Hydroxyketone Rearrangement Reaction in Napyradiomycin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:32.2 occ:1.00 ND2 A:ASN86 3.2 28.4 1.0 N A:LEU297 3.2 25.6 1.0 O A:HOH755 3.3 30.5 1.0 O A:HOH632 3.3 33.6 1.0 CA A:ASP296 3.7 26.9 1.0 CB A:ASP296 3.8 27.9 1.0 C A:ASP296 3.9 26.4 1.0 CB A:LEU297 4.0 24.1 1.0 CA A:LEU297 4.1 25.6 1.0 CG A:ASN86 4.2 27.9 1.0 OD1 A:ASN86 4.4 27.0 1.0 O A:ASN16 4.7 28.4 1.0 O A:GLY17 4.9 27.7 1.0 ND2 A:ASN18 4.9 25.5 1.0 CB A:ASN18 5.0 26.5 1.0 O A:ASP296 5.0 24.6 1.0

Magnesium binding site 2 out of 2 in the Structure of NAPH3, A Vanadium-Dependent Haloperoxidase Homolog Catalyzing the Stereospecific Alpha-Hydroxyketone Rearrangement Reaction in Napyradiomycin Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of NAPH3, A Vanadium-Dependent Haloperoxidase Homolog Catalyzing the Stereospecific Alpha-Hydroxyketone Rearrangement Reaction in Napyradiomycin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:35.3 occ:1.00 O B:HOH684 3.2 31.5 1.0 ND2 B:ASN86 3.2 32.9 1.0 N B:LEU297 3.3 29.0 1.0 CA B:ASP296 3.6 32.8 1.0 CB B:ASP296 3.7 35.6 1.0 C B:ASP296 3.9 32.6 1.0 CB B:LEU297 4.2 31.4 1.0 CA B:LEU297 4.2 31.8 1.0 CG B:ASN86 4.3 32.2 1.0 O B:ASN16 4.4 39.5 1.0 OD1 B:ASN86 4.5 32.5 1.0 O B:GLY17 4.8 35.5 1.0 NH1 B:ARG21 4.8 39.8 1.0 N B:ASP296 5.0 32.5 1.0 O B:LEU295 5.0 31.7 1.0

P.Y.Chen, S.Adak, J.R.Chekan, D.K.Liscombe, A.Miyanaga, P.Bernhardt, S.Diethelm, E.N.Fielding, J.H.George, Z.D.Miles, L.A.M.Murray, T.S.Steele, J.M.Winter, J.P.Noel, B.S.Moore. Structural Basis of Stereospecific Vanadium-Dependent Haloperoxidase Family Enzymes in Napyradiomycin Biosynthesis. Biochemistry V. 61 1844 2022.
ISSN: ISSN 0006-2960
PubMed: 35985031
DOI: 10.1021/ACS.BIOCHEM.2C00338