Magnesium in PDB 4od5: Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1

The structure of Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1, PDB code: 4od5 was solved by W.Li, W.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.73 / 3.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.104, 122.829, 423.416, 90.00, 90.00, 90.00
R / Rfree (%)	27.9 / 30.1

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1 (pdb code 4od5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1, PDB code: 4od5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:68.3 occ:1.00 OD1 A:ASP58 2.3 0.5 1.0 O1A A:GST301 2.4 0.7 1.0 CG A:ASP58 3.2 0.9 1.0 OD2 A:ASP58 3.4 0.5 1.0 PA A:GST301 3.5 1.0 1.0 O3A A:GST301 3.5 0.1 1.0 NZ A:LYS119 4.0 0.0 1.0 O A:HOH401 4.0 93.1 1.0 NH2 A:ARG67 4.1 99.9 1.0 OD2 A:ASP54 4.1 0.7 1.0 O2A A:GST301 4.2 0.2 1.0 CB A:ASP58 4.6 99.0 1.0 CD1 A:ILE57 4.6 87.7 1.0 CZ A:ARG67 4.7 0.6 1.0 O1B A:GST301 4.7 0.4 1.0 NH1 A:ARG63 4.7 0.3 1.0 CG A:ASP54 4.8 0.6 1.0 CG2 A:THR64 4.8 0.1 1.0 ND2 A:ASN61 4.8 0.6 1.0 OD2 A:ASP182 4.8 0.1 1.0 NH1 A:ARG67 4.9 0.3 1.0 OG1 A:THR64 4.9 93.5 1.0 MG A:MG304 5.0 0.5 1.0

Magnesium binding site 2 out of 12 in the Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:0.5 occ:1.00 O3A A:GST301 2.1 0.1 1.0 O A:HOH401 2.1 93.1 1.0 O3B A:GST301 3.0 0.8 1.0 PA A:GST301 3.5 1.0 1.0 O1B A:GST301 4.1 0.4 1.0 PB A:GST301 4.1 0.0 1.0 O2A A:GST301 4.2 0.2 1.0 OD2 A:ASP182 4.3 0.1 1.0 NH1 A:ARG63 4.3 0.3 1.0 O1A A:GST301 4.5 0.7 1.0 CD2 A:TYR178 4.5 0.7 1.0 CE2 A:TYR178 4.5 1.0 1.0 OD1 A:ASP175 4.6 69.4 1.0 NH2 A:ARG63 4.6 0.8 1.0 O2B A:GST301 4.8 0.5 1.0 OH A:TYR115 4.8 95.2 1.0 NZ A:LYS119 4.9 0.0 1.0 MG A:MG303 5.0 68.3 1.0 CZ A:ARG63 5.0 0.6 1.0

Magnesium binding site 3 out of 12 in the Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:68.3 occ:1.00 OD1 B:ASP58 2.2 0.7 1.0 O1A B:GST301 2.2 0.7 1.0 O3A B:GST301 3.2 0.1 1.0 CG B:ASP58 3.3 0.2 1.0 PA B:GST301 3.3 1.0 1.0 NZ B:LYS119 3.3 0.5 1.0 OD2 B:ASP54 3.4 92.5 1.0 OD2 B:ASP58 3.7 0.1 1.0 O B:HOH401 4.0 93.1 1.0 CG B:ASP54 4.0 0.9 1.0 CD1 B:ILE57 4.0 86.4 1.0 NH2 B:ARG67 4.1 99.4 1.0 O1B B:GST301 4.2 0.4 1.0 CB B:ASP54 4.2 90.2 1.0 O2A B:GST301 4.4 0.2 1.0 CB B:ASP58 4.5 0.8 1.0 MG B:MG304 4.7 0.5 1.0 CE B:LYS119 4.8 0.8 1.0 O B:ASP54 4.8 0.7 1.0 OD1 B:ASP54 4.9 0.5 1.0 CZ B:ARG67 4.9 0.4 1.0

Magnesium binding site 4 out of 12 in the Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:0.5 occ:1.00 O B:HOH401 2.1 93.1 1.0 O3A B:GST301 2.1 0.1 1.0 O3B B:GST301 2.6 0.8 1.0 PA B:GST301 3.5 1.0 1.0 PB B:GST301 3.8 0.0 1.0 O1B B:GST301 3.9 0.4 1.0 O2A B:GST301 4.2 0.2 1.0 OD2 B:ASP182 4.3 0.5 1.0 NZ B:LYS119 4.4 0.5 1.0 NH1 B:ARG63 4.4 0.8 1.0 O2B B:GST301 4.5 0.5 1.0 O1A B:GST301 4.5 0.7 1.0 OH B:TYR115 4.6 94.7 1.0 MG B:MG303 4.7 68.3 1.0 NH2 B:ARG63 4.7 0.0 1.0 CE B:LYS119 4.8 0.8 1.0 CE2 B:TYR178 4.9 99.3 1.0 OD1 B:ASP175 4.9 43.8 1.0 CD2 B:TYR178 5.0 94.2 1.0

Magnesium binding site 5 out of 12 in the Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:68.3 occ:1.00 O1A C:GST301 2.2 0.7 1.0 OD1 C:ASP58 2.2 0.1 1.0 CG C:ASP58 3.3 0.6 1.0 PA C:GST301 3.3 1.0 1.0 O3A C:GST301 3.4 0.1 1.0 NZ C:LYS119 3.6 0.8 1.0 OD2 C:ASP58 3.7 0.1 1.0 OD2 C:ASP54 3.9 0.6 1.0 CD1 C:ILE57 3.9 1.0 1.0 O2A C:GST301 4.2 0.2 1.0 O C:HOH401 4.3 93.1 1.0 NH2 C:ARG67 4.4 0.8 1.0 CG C:ASP54 4.5 0.2 1.0 O1B C:GST301 4.5 0.4 1.0 CB C:ASP58 4.5 0.5 1.0 CB C:ASP54 4.6 1.0 1.0 ND2 C:ASN61 4.9 0.9 1.0 CA C:ASP58 5.0 0.0 1.0 O C:ILE57 5.0 0.4 1.0 MG C:MG304 5.0 0.5 1.0 CE C:LYS119 5.0 0.7 1.0 OD2 C:ASP182 5.0 0.3 1.0

Magnesium binding site 6 out of 12 in the Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg304 b:0.5 occ:1.00 O C:HOH401 2.1 93.1 1.0 O3A C:GST301 2.1 0.1 1.0 O3B C:GST301 2.9 0.8 1.0 PA C:GST301 3.5 1.0 1.0 NZ C:LYS119 4.0 0.8 1.0 O1B C:GST301 4.0 0.4 1.0 PB C:GST301 4.0 0.0 1.0 CE C:LYS119 4.2 0.7 1.0 O2A C:GST301 4.2 0.2 1.0 OH C:TYR115 4.4 0.0 1.0 O1A C:GST301 4.5 0.7 1.0 OD2 C:ASP182 4.6 0.3 1.0 OD2 C:ASP186 4.7 0.2 1.0 O2B C:GST301 4.9 0.5 1.0 OG C:SER179 5.0 0.3 1.0 MG C:MG303 5.0 68.3 1.0 CD C:LYS119 5.0 83.8 1.0 OD1 C:ASP175 5.0 67.0 1.0

Magnesium binding site 7 out of 12 in the Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg303 b:68.3 occ:1.00 OD1 D:ASP58 2.2 0.2 1.0 O1A D:GST301 2.2 0.7 1.0 CG D:ASP58 3.3 0.2 1.0 PA D:GST301 3.4 1.0 1.0 O3A D:GST301 3.5 0.1 1.0 NZ D:LYS119 3.5 0.0 1.0 OD2 D:ASP58 3.7 0.7 1.0 CD1 D:ILE57 3.8 89.2 1.0 OD2 D:ASP54 3.9 0.8 1.0 O2A D:GST301 4.3 0.2 1.0 O D:HOH401 4.4 93.1 1.0 CG D:ASP54 4.4 0.6 1.0 NH2 D:ARG67 4.5 95.6 1.0 CB D:ASP54 4.5 91.4 1.0 CB D:ASP58 4.5 97.2 1.0 O1B D:GST301 4.6 0.4 1.0 O D:ILE57 4.9 0.9 1.0 CA D:ASP58 4.9 90.6 1.0 CE D:LYS119 4.9 0.2 1.0 ND2 D:ASN61 4.9 0.8 1.0 O D:ASP54 5.0 0.6 1.0

Magnesium binding site 8 out of 12 in the Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg304 b:0.5 occ:1.00 O D:HOH401 2.1 93.1 1.0 O3A D:GST301 2.1 0.1 1.0 O3B D:GST301 3.1 0.8 1.0 PA D:GST301 3.5 1.0 1.0 O1B D:GST301 4.1 0.4 1.0 OD2 D:ASP182 4.1 0.7 1.0 PB D:GST301 4.2 0.0 1.0 O2A D:GST301 4.2 0.2 1.0 O1A D:GST301 4.5 0.7 1.0 NH1 D:ARG63 4.6 0.1 1.0 NZ D:LYS119 4.6 0.0 1.0 OG D:SER179 4.8 0.5 1.0 OD2 D:ASP186 4.8 0.7 1.0 CB D:SER179 4.8 83.6 1.0 OH D:TYR115 4.9 93.4 1.0 CE D:LYS119 4.9 0.2 1.0 OD1 D:ASP175 4.9 68.2 1.0 O2B D:GST301 5.0 0.5 1.0 CG D:ASP182 5.0 0.3 1.0

Magnesium binding site 9 out of 12 in the Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg303 b:68.3 occ:1.00 OD1 E:ASP58 2.3 0.1 1.0 O1A E:GST301 2.3 0.7 1.0 NZ E:LYS119 3.1 0.7 1.0 CG E:ASP58 3.4 0.4 1.0 OD2 E:ASP54 3.4 0.6 1.0 PA E:GST301 3.5 1.0 1.0 O3A E:GST301 3.6 0.1 1.0 CD1 E:ILE57 3.9 0.1 1.0 OD2 E:ASP58 3.9 0.4 1.0 CG E:ASP54 4.0 0.4 1.0 O E:HOH401 4.0 93.1 1.0 CB E:ASP54 4.2 0.7 1.0 O2A E:GST301 4.2 0.2 1.0 NH2 E:ARG67 4.3 0.9 1.0 CE E:LYS119 4.6 0.6 1.0 CB E:ASP58 4.6 0.9 1.0 O1B E:GST301 4.7 0.4 1.0 OD1 E:ASP54 4.8 0.6 1.0 O E:ASP54 4.8 0.4 1.0 MG E:MG304 4.9 0.5 1.0

Magnesium binding site 10 out of 12 in the Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Substrate-Bound Structure of A Ubia Homolog From Aeropyrum Pernix K1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg304 b:0.5 occ:1.00 O3A E:GST301 2.1 0.1 1.0 O E:HOH401 2.1 93.1 1.0 PA E:GST301 3.2 1.0 1.0 O2A E:GST301 3.3 0.2 1.0 O3B E:GST301 3.4 0.8 1.0 OH E:TYR115 3.9 0.6 1.0 NZ E:LYS119 4.1 0.7 1.0 O1B E:GST301 4.2 0.4 1.0 O1A E:GST301 4.3 0.7 1.0 CE E:LYS119 4.4 0.6 1.0 PB E:GST301 4.4 0.0 1.0 OD1 E:ASP175 4.6 0.9 1.0 MG E:MG303 4.9 68.3 1.0

W.Cheng, W.Li. Structural Insights Into Ubiquinone Biosynthesis in Membranes. Science V. 343 878 2014.
ISSN: ISSN 0036-8075
PubMed: 24558159
DOI: 10.1126/SCIENCE.1246774