Magnesium in PDB 6p08: Ternary Structure of the E52D Mutant of Ant-4'' with Neomycin, Amp and Pyrophosphate

The structure of Ternary Structure of the E52D Mutant of Ant-4'' with Neomycin, Amp and Pyrophosphate, PDB code: 6p08 was solved by B.Selvaraj, M.J.Cuneo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.65 / 2.27
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.750, 99.300, 101.490, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.5

The binding sites of Magnesium atom in the Ternary Structure of the E52D Mutant of Ant-4'' with Neomycin, Amp and Pyrophosphate (pdb code 6p08). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Ternary Structure of the E52D Mutant of Ant-4'' with Neomycin, Amp and Pyrophosphate, PDB code: 6p08:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Ternary Structure of the E52D Mutant of Ant-4'' with Neomycin, Amp and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Structure of the E52D Mutant of Ant-4'' with Neomycin, Amp and Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:13.6 occ:1.00 O A:HOH901 1.8 42.4 1.0 OD2 A:ASP50 2.0 28.1 1.0 OE2 D:GLU145 2.2 29.5 1.0 O A:HOH913 2.3 40.7 1.0 O1P A:AMP306 2.5 21.7 1.0 O A:HOH911 2.5 26.3 1.0 OD1 A:ASP52 2.5 30.3 1.0 CG A:ASP50 2.8 26.9 1.0 OD1 A:ASP50 3.0 30.4 1.0 CD D:GLU145 3.1 39.2 1.0 O4 A:NMY301 3.2 27.3 1.0 CG A:ASP52 3.3 29.8 1.0 OD2 A:ASP52 3.4 31.5 1.0 P A:AMP306 3.4 27.8 1.0 OE1 D:GLU145 3.5 34.1 1.0 MG A:MG304 3.6 21.5 1.0 NZ A:LYS74 3.8 48.0 1.0 CB A:ASP50 4.2 26.7 1.0 O D:HOH908 4.3 32.9 1.0 CG D:GLU145 4.4 31.3 1.0 C4 A:NMY301 4.4 30.7 1.0 O3 A:NMY301 4.4 28.4 1.0 O2P A:AMP306 4.4 22.6 1.0 C3 A:NMY301 4.6 26.9 1.0 OE2 A:GLU76 4.6 26.2 1.0 O5' A:AMP306 4.7 22.5 1.0 CB A:ASP52 4.8 19.1 1.0 O A:ILE51 4.8 23.2 1.0 N6 A:NMY301 4.8 33.3 1.0 C5' A:AMP306 4.8 24.9 1.0

Magnesium binding site 2 out of 4 in the Ternary Structure of the E52D Mutant of Ant-4'' with Neomycin, Amp and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Structure of the E52D Mutant of Ant-4'' with Neomycin, Amp and Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:21.5 occ:1.00 OD1 A:ASP50 2.2 30.4 1.0 O31 A:PPV302 2.3 25.0 1.0 O1P A:AMP306 2.5 21.7 1.0 OD2 A:ASP52 2.6 31.5 1.0 O A:HOH927 2.9 26.6 1.0 O22 A:PPV302 3.1 35.3 1.0 O11 A:PPV302 3.2 31.9 1.0 P1 A:PPV302 3.3 30.7 1.0 CG A:ASP50 3.3 26.9 1.0 MG A:MG303 3.6 13.6 1.0 O D:HOH908 3.7 32.9 1.0 CG A:ASP52 3.8 29.8 1.0 OD2 A:ASP50 3.9 28.1 1.0 P A:AMP306 3.9 27.8 1.0 C5' A:AMP306 4.0 24.9 1.0 OPP A:PPV302 4.1 41.3 1.0 P2 A:PPV302 4.2 54.9 1.0 OD1 A:ASP52 4.2 30.3 1.0 O A:ASP50 4.2 23.7 1.0 O5' A:AMP306 4.3 22.5 1.0 O A:HOH901 4.3 42.4 1.0 N A:ASP50 4.3 20.8 1.0 OG A:SER39 4.4 27.7 1.0 OE2 D:GLU145 4.4 29.5 1.0 C A:ASP50 4.4 24.0 1.0 N A:SER39 4.5 21.5 1.0 O2P A:AMP306 4.5 22.6 1.0 O21 A:PPV302 4.5 30.2 1.0 CB A:ASP50 4.6 26.7 1.0 O A:HOH937 4.6 22.2 1.0 CA A:ASP50 4.6 24.1 1.0 O12 A:PPV302 4.8 45.3 1.0 CA A:GLY38 4.8 19.6 1.0 O4 A:NMY301 4.9 27.3 1.0 NZ D:LYS149 4.9 35.9 1.0

Magnesium binding site 3 out of 4 in the Ternary Structure of the E52D Mutant of Ant-4'' with Neomycin, Amp and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ternary Structure of the E52D Mutant of Ant-4'' with Neomycin, Amp and Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg308 b:8.5 occ:1.00 O D:HOH923 2.2 17.9 1.0 OD1 D:ASP52 2.2 20.8 1.0 OD2 D:ASP50 2.2 24.3 1.0 O1P A:AMP305 2.5 18.7 1.0 OE1 A:GLU145 2.5 25.1 1.0 O D:HOH914 2.7 24.2 1.0 O4 A:NMY307 2.8 24.2 1.0 CG D:ASP52 2.9 17.0 1.0 OD2 D:ASP52 3.0 26.1 1.0 CG D:ASP50 3.0 28.3 1.0 OD1 D:ASP50 3.1 23.3 1.0 P A:AMP305 3.3 21.0 1.0 CD A:GLU145 3.5 31.4 1.0 MG D:MG302 3.5 17.5 1.0 OE2 A:GLU145 3.9 29.2 1.0 O3 A:NMY307 4.0 22.1 1.0 C4 A:NMY307 4.0 18.3 1.0 O A:HOH959 4.1 35.9 1.0 C3 A:NMY307 4.2 21.1 1.0 CB D:ASP52 4.4 14.2 1.0 CB D:ASP50 4.4 27.1 1.0 O2P A:AMP305 4.4 15.0 1.0 O5' A:AMP305 4.5 23.0 1.0 OE2 D:GLU76 4.5 22.2 1.0 O D:HOH902 4.5 38.3 1.0 C5' A:AMP305 4.6 14.8 1.0 O D:ILE51 4.6 12.5 1.0 CG A:GLU145 4.7 32.8 1.0 O D:HOH901 4.7 26.5 1.0 C5 A:NMY307 4.8 20.0 1.0 N6 A:NMY307 4.8 25.6 1.0 CE D:LYS74 4.9 21.1 1.0

Magnesium binding site 4 out of 4 in the Ternary Structure of the E52D Mutant of Ant-4'' with Neomycin, Amp and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ternary Structure of the E52D Mutant of Ant-4'' with Neomycin, Amp and Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:17.5 occ:1.00 O D:HOH902 1.9 38.3 1.0 O D:HOH901 2.0 26.5 1.0 OD1 D:ASP50 2.2 23.3 1.0 O1P A:AMP305 2.3 18.7 1.0 O31 D:PPV301 2.5 24.0 1.0 OD2 D:ASP52 2.6 26.1 1.0 O D:HOH912 3.1 31.6 1.0 O11 D:PPV301 3.2 32.7 1.0 CG D:ASP50 3.3 28.3 1.0 P1 D:PPV301 3.4 26.1 1.0 O22 D:PPV301 3.4 30.1 1.0 MG A:MG308 3.5 8.5 1.0 O A:HOH959 3.5 35.9 1.0 P A:AMP305 3.7 21.0 1.0 CG D:ASP52 3.8 17.0 1.0 OD2 D:ASP50 3.8 24.3 1.0 C5' A:AMP305 4.0 14.8 1.0 O5' A:AMP305 4.1 23.0 1.0 OD1 D:ASP52 4.2 20.8 1.0 O D:ASP50 4.3 24.8 1.0 OPP D:PPV301 4.4 36.5 1.0 N D:ASP50 4.4 23.7 1.0 P2 D:PPV301 4.4 43.8 1.0 O2P A:AMP305 4.5 15.0 1.0 C D:ASP50 4.5 21.1 1.0 CB D:ASP50 4.6 27.1 1.0 OG D:SER39 4.6 26.4 1.0 O21 D:PPV301 4.6 29.7 1.0 O4 A:NMY307 4.7 24.2 1.0 OE1 A:GLU145 4.7 25.1 1.0 N D:SER39 4.7 24.4 1.0 NZ A:LYS149 4.7 35.1 1.0 CA D:ASP50 4.7 22.5 1.0 O D:HOH931 4.8 21.1 1.0 CA D:GLY38 4.9 18.3 1.0 O12 D:PPV301 4.9 38.0 1.0 CB D:ASP52 5.0 14.2 1.0

B.Selvaraj, M.J.Cuneo. Catch and Release: A Novel Variation of the Archetypal Nucleotidyl Transfer Reaction To Be Published.