Magnesium in PDB 5k3i: Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp

The structure of Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp, PDB code: 5k3i 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)	38.74 / 2.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	152.339, 141.501, 154.968, 90.00, 116.76, 90.00
R / Rfree (%)	21.7 / 23.2

The binding sites of Magnesium atom in the Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp (pdb code 5k3i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp, PDB code: 5k3i:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp


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 Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:18.6 occ:1.00 O1A B:ATP703 2.2 19.2 1.0 O3G B:ATP703 2.4 17.9 1.0 O1B B:ATP703 2.4 19.2 1.0 OD1 A:ASP577 3.5 22.2 1.0 PA B:ATP703 3.6 19.7 1.0 PB B:ATP703 3.7 18.6 1.0 PG B:ATP703 3.7 17.1 1.0 NH2 B:ARG533 3.9 24.2 1.0 O A:HOH818 4.0 33.2 1.0 O3A B:ATP703 4.1 19.1 1.0 O3B B:ATP703 4.1 18.0 1.0 O2G B:ATP703 4.2 17.2 1.0 C5' B:ATP703 4.3 18.5 1.0 O5' B:ATP703 4.4 19.3 1.0 CG A:ASP577 4.4 21.8 1.0 CA A:ASP577 4.5 20.8 1.0 O A:HOH858 4.6 33.2 1.0 CB A:ASP577 4.7 21.2 1.0 O A:HOH809 4.7 33.2 1.0 O2A B:ATP703 4.8 19.7 1.0 O B:HOH851 4.8 33.2 1.0 O1G B:ATP703 4.9 16.9 1.0 O2B B:ATP703 5.0 18.2 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp


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 Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:14.8 occ:1.00 O3G A:ATP702 2.4 16.6 1.0 O1B A:ATP702 2.5 16.9 1.0 O1A A:ATP702 2.5 16.8 1.0 O A:HOH839 2.7 33.2 1.0 OD1 B:ASP577 3.2 22.6 1.0 PB A:ATP702 3.8 16.7 1.0 PG A:ATP702 3.8 16.6 1.0 PA A:ATP702 3.9 16.9 1.0 CG B:ASP577 4.1 22.6 1.0 O B:HOH814 4.2 33.2 1.0 NH2 A:ARG533 4.3 23.2 1.0 C5' A:ATP702 4.3 16.6 1.0 O3A A:ATP702 4.3 16.8 1.0 O3B A:ATP702 4.3 16.6 1.0 CA B:ASP577 4.3 22.6 1.0 CB B:ASP577 4.4 22.7 1.0 O2G A:ATP702 4.5 16.6 1.0 O5' A:ATP702 4.6 16.7 1.0 O B:HOH812 4.8 33.2 1.0 O1G A:ATP702 4.9 16.5 1.0 N B:ASP577 4.9 22.1 1.0 OH B:TYR573 5.0 20.4 1.0 O2A A:ATP702 5.0 16.9 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp


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 Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:20.6 occ:1.00 O1A D:ATP801 2.3 22.1 1.0 O1B D:ATP801 2.3 22.3 1.0 O3G D:ATP801 2.5 23.6 1.0 O D:HOH935 3.0 33.2 1.0 OD1 C:ASP577 3.5 29.4 1.0 PB D:ATP801 3.6 21.9 1.0 PA D:ATP801 3.6 22.0 1.0 PG D:ATP801 3.8 23.9 1.0 O3A D:ATP801 4.0 22.0 1.0 NH2 D:ARG533 4.0 23.1 1.0 O3B D:ATP801 4.2 22.9 1.0 C5' D:ATP801 4.3 21.8 1.0 CG C:ASP577 4.4 27.4 1.0 CA C:ASP577 4.5 27.6 1.0 O5' D:ATP801 4.5 22.0 1.0 O2G D:ATP801 4.6 23.2 1.0 CB C:ASP577 4.7 27.7 1.0 O2A D:ATP801 4.7 21.7 1.0 O2B D:ATP801 4.9 21.8 1.0 O1G D:ATP801 4.9 22.7 1.0 N C:ASP577 5.0 27.4 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp


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 Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg802 b:23.4 occ:1.00 O3G C:ATP703 2.3 21.4 1.0 O1A C:ATP703 2.3 22.1 1.0 O1B C:ATP703 2.4 20.8 1.0 O D:HOH972 3.5 33.2 1.0 NH2 C:ARG533 3.6 26.7 1.0 PG C:ATP703 3.7 21.1 1.0 PB C:ATP703 3.7 20.8 1.0 PA C:ATP703 3.7 22.5 1.0 OD1 D:ASP577 3.8 26.1 1.0 O3B C:ATP703 4.2 21.2 1.0 O2G C:ATP703 4.2 21.5 1.0 O3A C:ATP703 4.2 21.6 1.0 CA D:ASP577 4.5 26.8 1.0 C5' C:ATP703 4.5 22.1 1.0 O5' C:ATP703 4.6 22.7 1.0 CG D:ASP577 4.7 24.7 1.0 CZ C:ARG533 4.8 25.8 1.0 CB D:ASP577 4.8 26.0 1.0 O1G C:ATP703 4.8 20.9 1.0 O2A C:ATP703 4.8 22.7 1.0 N D:ASP577 4.9 26.3 1.0 O2B C:ATP703 5.0 21.2 1.0 CG D:LEU576 5.0 24.3 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg702 b:22.4 occ:1.00 O3G F:ATP702 2.1 22.2 1.0 O1B F:ATP702 2.1 22.2 1.0 O1A F:ATP702 2.3 23.2 1.0 O E:HOH839 2.3 33.2 1.0 O E:HOH876 3.4 33.2 1.0 PB F:ATP702 3.4 22.4 1.0 PG F:ATP702 3.5 21.6 1.0 OD1 E:ASP577 3.6 25.9 1.0 PA F:ATP702 3.7 23.1 1.0 O3B F:ATP702 3.8 21.9 1.0 O3A F:ATP702 4.0 23.0 1.0 NH2 F:ARG533 4.0 26.2 1.0 O2G F:ATP702 4.2 22.0 1.0 C5' F:ATP702 4.3 23.0 1.0 O5' F:ATP702 4.4 23.4 1.0 O1G F:ATP702 4.6 21.2 1.0 O2B F:ATP702 4.7 21.9 1.0 CG E:ASP577 4.7 24.7 1.0 CA E:ASP577 4.7 24.9 1.0 O2A F:ATP702 4.8 23.5 1.0 O E:HOH862 4.9 33.2 1.0 CB E:ASP577 5.0 24.7 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg703 b:23.9 occ:1.00 O3G E:ATP703 2.2 19.9 1.0 O1B E:ATP703 2.2 20.6 1.0 O1A E:ATP703 2.6 20.7 1.0 OD1 F:ASP577 3.4 27.0 1.0 PG E:ATP703 3.6 19.9 1.0 PB E:ATP703 3.6 21.5 1.0 PA E:ATP703 3.9 21.9 1.0 O2G E:ATP703 4.1 19.3 1.0 O3B E:ATP703 4.2 20.5 1.0 O3A E:ATP703 4.2 21.4 1.0 C5' E:ATP703 4.3 21.9 1.0 NH2 E:ARG533 4.4 30.6 1.0 CG F:ASP577 4.4 26.7 1.0 O F:HOH810 4.6 33.2 1.0 CA F:ASP577 4.6 27.5 1.0 O5' E:ATP703 4.6 21.8 1.0 O F:HOH815 4.7 33.2 1.0 CB F:ASP577 4.7 27.3 1.0 O1G E:ATP703 4.8 19.6 1.0 O2B E:ATP703 4.8 21.1 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg702 b:22.7 occ:1.00 O1B H:ATP702 2.4 23.8 1.0 O3G H:ATP702 2.4 23.8 1.0 O1A H:ATP702 2.5 25.5 1.0 OD1 G:ASP577 3.2 23.5 1.0 PB H:ATP702 3.7 23.6 1.0 PG H:ATP702 3.9 24.6 1.0 PA H:ATP702 3.9 24.5 1.0 NH2 H:ARG533 4.1 22.7 1.0 CG G:ASP577 4.2 24.2 1.0 O3B H:ATP702 4.3 23.5 1.0 C5' H:ATP702 4.3 23.6 1.0 O3A H:ATP702 4.3 24.2 1.0 CA G:ASP577 4.3 24.6 1.0 CB G:ASP577 4.5 24.6 1.0 O2G H:ATP702 4.5 23.6 1.0 O5' H:ATP702 4.6 24.4 1.0 O1G H:ATP702 4.9 23.3 1.0 N G:ASP577 5.0 24.6 1.0 O2A H:ATP702 5.0 26.1 1.0 O2B H:ATP702 5.0 23.3 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Acyl-Coa Oxidase-1 in Caenorhabditis Elegans Complexed with Fad and Atp within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg703 b:14.2 occ:1.00 O1B G:ATP703 2.3 19.0 1.0 O3G G:ATP703 2.3 19.1 1.0 O1A G:ATP703 2.5 18.9 1.0 OD1 H:ASP577 3.3 27.8 1.0 PB G:ATP703 3.7 18.9 1.0 PG G:ATP703 3.8 19.1 1.0 PA G:ATP703 3.9 19.0 1.0 NH2 G:ARG533 4.1 23.1 1.0 O3B G:ATP703 4.2 19.0 1.0 CG H:ASP577 4.3 27.4 1.0 CA H:ASP577 4.3 25.6 1.0 O3A G:ATP703 4.3 19.0 1.0 O2G G:ATP703 4.5 19.3 1.0 C5' G:ATP703 4.5 19.0 1.0 CB H:ASP577 4.5 26.4 1.0 O5' G:ATP703 4.7 19.0 1.0 O1G G:ATP703 4.8 19.2 1.0 O H:HOH809 4.8 33.2 1.0 O H:HOH848 4.9 33.2 1.0 O2B G:ATP703 4.9 18.9 1.0 N H:ASP577 4.9 25.1 1.0 O2A G:ATP703 5.0 18.9 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