Magnesium in PDB 5k3j: Crystals Structure of Acyl-Coa Oxidase-2 in Caenorhabditis Elegans Bound with Fad, Ascaroside-Coa, and Atp

The structure of Crystals Structure of Acyl-Coa Oxidase-2 in Caenorhabditis Elegans Bound with Fad, Ascaroside-Coa, and Atp, PDB code: 5k3j was solved by X.Zhang, K.Li, R.A.Jones, S.D.Bruner, R.A.Butcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.72 / 2.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.040, 85.571, 106.899, 90.00, 91.43, 90.00
R / Rfree (%)	21.3 / 24.5

The binding sites of Magnesium atom in the Crystals Structure of Acyl-Coa Oxidase-2 in Caenorhabditis Elegans Bound with Fad, Ascaroside-Coa, and Atp (pdb code 5k3j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystals Structure of Acyl-Coa Oxidase-2 in Caenorhabditis Elegans Bound with Fad, Ascaroside-Coa, and Atp, PDB code: 5k3j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystals Structure of Acyl-Coa Oxidase-2 in Caenorhabditis Elegans Bound with Fad, Ascaroside-Coa, and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystals Structure of Acyl-Coa Oxidase-2 in Caenorhabditis Elegans Bound with Fad, Ascaroside-Coa, and Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:44.2 occ:1.00 O2B A:ATP702 2.0 59.6 1.0 O2A A:ATP702 2.2 45.9 1.0 O2G A:ATP702 2.3 57.3 1.0 PB A:ATP702 3.4 62.0 1.0 PG A:ATP702 3.6 59.6 1.0 PA A:ATP702 3.6 50.6 1.0 OD1 B:ASP569 3.6 75.7 1.0 O3B A:ATP702 3.9 62.1 1.0 O3A A:ATP702 4.0 51.5 1.0 O3G A:ATP702 4.1 55.5 1.0 NH1 A:ARG525 4.3 46.4 1.0 C5' A:ATP702 4.4 44.7 1.0 O5' A:ATP702 4.4 52.0 1.0 CA B:ASP569 4.5 75.0 1.0 CG B:ASP569 4.6 78.8 1.0 O1B A:ATP702 4.6 53.0 1.0 O1A A:ATP702 4.8 43.7 1.0 CB B:ASP569 4.8 75.8 1.0 O1G A:ATP702 4.8 56.7 1.0 O B:LEU568 5.0 48.1 1.0

Magnesium binding site 2 out of 2 in the Crystals Structure of Acyl-Coa Oxidase-2 in Caenorhabditis Elegans Bound with Fad, Ascaroside-Coa, and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystals Structure of Acyl-Coa Oxidase-2 in Caenorhabditis Elegans Bound with Fad, Ascaroside-Coa, and Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:41.7 occ:1.00 O3B B:ATP703 2.1 68.4 1.0 O1A B:ATP703 2.3 66.6 1.0 O5' B:ATP703 2.7 66.0 1.0 O3G B:ATP703 2.8 67.2 1.0 PA B:ATP703 3.0 67.5 1.0 PG B:ATP703 3.1 67.8 1.0 PB B:ATP703 3.3 76.9 1.0 C8 B:ATP703 3.5 50.1 1.0 O3A B:ATP703 3.5 71.0 1.0 O2G B:ATP703 3.7 64.1 1.0 O1B B:ATP703 3.7 71.7 1.0 O4' B:ATP703 3.9 49.1 1.0 C5' B:ATP703 4.0 59.3 1.0 CZ B:ARG528 4.0 55.7 1.0 NH2 B:ARG528 4.1 54.9 1.0 NE B:ARG528 4.1 56.8 1.0 O1G B:ATP703 4.2 60.2 1.0 N7 B:ATP703 4.3 49.4 1.0 O2A B:ATP703 4.4 65.5 1.0 N9 B:ATP703 4.5 47.2 1.0 O2B B:ATP703 4.5 80.0 1.0 NH1 B:ARG528 4.6 54.8 1.0 O B:HOH808 4.6 40.0 1.0 C4' B:ATP703 4.6 52.9 1.0 C1' B:ATP703 4.8 48.5 1.0 CD B:ARG528 4.8 52.0 1.0

X.Zhang, K.Li, R.A.Jones, S.D.Bruner, R.A.Butcher. Structural Characterization of Acyl-Coa Oxidases Reveals A Direct Link Between Pheromone Biosynthesis and Metabolic State in Caenorhabditis Elegans. Proc.Natl.Acad.Sci.Usa V. 113 10055 2016.
ISSN: ESSN 1091-6490
PubMed: 27551084
DOI: 10.1073/PNAS.1608262113