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

Protein crystallography data

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

Other elements in 8cxl:

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

Magnesium Binding Sites:

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 8cxl

Go back to Magnesium Binding Sites List in 8cxl
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 8cxl

Go back to Magnesium Binding Sites List in 8cxl
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

Reference:

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
Page generated: Thu Oct 3 23:19:01 2024

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