Magnesium in PDB 6nml: Ternary Structure of the T130K Mutant of Ant-4'' with Neomycin and Ampcpp

The structure of Ternary Structure of the T130K Mutant of Ant-4'' with Neomycin and Ampcpp, PDB code: 6nml was solved by M.J.Cuneo, B.Selvaraj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.42 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.210, 98.030, 102.380, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 22.9

The binding sites of Magnesium atom in the Ternary Structure of the T130K Mutant of Ant-4'' with Neomycin and Ampcpp (pdb code 6nml). 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 T130K Mutant of Ant-4'' with Neomycin and Ampcpp, PDB code: 6nml:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Ternary Structure of the T130K Mutant of Ant-4'' with Neomycin and Ampcpp


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 T130K Mutant of Ant-4'' with Neomycin and Ampcpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:42.8 occ:1.00 OD2 A:ASP50 2.1 29.1 0.7 O4 A:NMY800 2.2 44.7 1.0 O2A A:APC801 2.2 38.5 0.7 O A:HOH936 2.5 43.2 1.0 OE1 A:GLU52 2.8 39.9 0.5 OE2 B:GLU145 3.0 51.8 1.0 CG A:ASP50 3.0 31.8 0.7 OE2 A:GLU52 3.0 41.2 0.5 CD A:GLU52 3.0 37.7 0.5 CD B:GLU145 3.1 51.9 1.0 OD1 A:ASP50 3.2 28.4 0.7 OE1 A:GLU52 3.3 39.4 0.5 OE1 B:GLU145 3.4 44.7 1.0 PA A:APC801 3.4 35.3 0.7 O1A A:APC801 3.5 36.2 0.7 CD A:GLU52 3.5 36.7 0.5 MG A:MG803 3.5 40.9 1.0 C4 A:NMY800 3.6 46.7 1.0 OE2 A:GLU52 3.6 38.7 0.5 O A:HOH945 3.7 36.5 1.0 CG A:GLU52 3.7 30.8 0.5 OD2 A:ASP50 3.9 32.9 0.3 CG B:GLU145 3.9 29.9 1.0 O A:HOH944 4.0 28.8 1.0 O3 A:NMY800 4.0 48.4 1.0 C3 A:NMY800 4.0 41.7 1.0 O5' A:APC801 4.2 41.9 0.7 CB A:ASP50 4.2 32.4 0.3 CB A:ASP50 4.4 32.4 0.7 C5 A:NMY800 4.4 46.3 1.0 CG A:ASP50 4.5 30.6 0.3 C5' A:APC801 4.6 37.6 0.7 C6 A:NMY800 4.8 43.5 1.0 O1G A:APC801 4.9 36.7 0.7 OE2 A:GLU76 4.9 36.3 1.0 CG A:GLU52 4.9 30.5 0.5 C3A A:APC801 4.9 41.9 0.7 O1B A:APC801 5.0 36.0 0.7

Magnesium binding site 2 out of 4 in the Ternary Structure of the T130K Mutant of Ant-4'' with Neomycin and Ampcpp


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 T130K Mutant of Ant-4'' with Neomycin and Ampcpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:40.9 occ:1.00 OD1 A:ASP50 2.0 28.4 0.7 OE2 A:GLU52 2.0 38.7 0.5 O1B A:APC801 2.1 36.0 0.7 OE1 A:GLU52 2.2 39.4 0.5 O2A A:APC801 2.3 38.5 0.7 O1G A:APC801 2.4 36.7 0.7 O A:HOH939 2.6 42.8 1.0 CG A:ASP50 3.1 31.8 0.7 CD A:GLU52 3.1 36.7 0.5 PB A:APC801 3.3 43.4 0.7 CD A:GLU52 3.3 37.7 0.5 PA A:APC801 3.4 35.3 0.7 MG A:MG802 3.5 42.8 1.0 OD2 A:ASP50 3.6 29.1 0.7 O A:HOH945 3.6 36.5 1.0 PG A:APC801 3.6 39.7 0.7 OE1 A:GLU52 3.6 39.9 0.5 C3A A:APC801 3.7 41.9 0.7 O3B A:APC801 3.8 47.5 0.7 O A:ASP50 3.9 31.3 0.7 OE2 A:GLU52 3.9 41.2 0.5 C5' A:APC801 4.0 37.6 0.7 O A:ASP50 4.1 31.4 0.3 N A:ASP50 4.1 30.5 0.3 N A:ASP50 4.1 30.4 0.7 CB A:ASP50 4.1 32.4 0.3 OG A:SER39 4.2 43.5 1.0 C A:ASP50 4.2 30.4 0.7 O3G A:APC801 4.3 35.6 0.7 O5' A:APC801 4.3 41.9 0.7 C A:ASP50 4.3 30.4 0.3 CB A:ASP50 4.3 32.4 0.7 CG A:GLU52 4.4 30.5 0.5 CG A:GLU52 4.4 30.8 0.5 N A:SER39 4.4 30.3 1.0 CA A:ASP50 4.4 30.6 0.3 CA A:ASP50 4.5 30.6 0.7 O2B A:APC801 4.5 40.0 0.7 O1A A:APC801 4.6 36.2 0.7 OD2 A:ASP50 4.7 32.9 0.3 O A:HOH919 4.7 26.2 1.0 O2G A:APC801 4.8 35.8 0.7 CB A:SER39 4.8 37.2 1.0 CA A:GLY38 4.9 30.7 1.0 CG A:ASP50 4.9 30.6 0.3 N A:ILE51 5.0 24.8 1.0

Magnesium binding site 3 out of 4 in the Ternary Structure of the T130K Mutant of Ant-4'' with Neomycin and Ampcpp


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 T130K Mutant of Ant-4'' with Neomycin and Ampcpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:24.6 occ:1.00 O2A B:APC801 2.1 25.1 0.8 OD2 B:ASP50 2.1 24.4 1.0 O4 B:NMY800 2.2 26.1 1.0 OE1 B:GLU52 2.2 28.3 1.0 OE1 A:GLU145 2.3 38.6 1.0 O B:HOH955 2.3 27.2 1.0 CD A:GLU145 3.1 36.2 1.0 CG B:ASP50 3.1 24.8 1.0 CD B:GLU52 3.2 28.9 1.0 PA B:APC801 3.3 30.4 0.8 OD1 B:ASP50 3.3 28.4 1.0 OE2 A:GLU145 3.4 31.8 1.0 O1A B:APC801 3.4 29.8 0.8 C4 B:NMY800 3.5 32.7 1.0 OE2 B:GLU52 3.5 27.9 1.0 O3 B:NMY800 3.7 25.0 1.0 MG B:MG803 3.8 37.3 1.0 C3 B:NMY800 3.9 30.9 1.0 O5' B:APC801 4.0 30.0 0.8 O A:HOH958 4.0 30.6 1.0 O B:HOH948 4.1 22.0 1.0 CG A:GLU145 4.2 28.7 1.0 C5' B:APC801 4.3 28.8 0.8 C5 B:NMY800 4.4 32.4 1.0 CB B:ASP50 4.5 23.6 1.0 CG B:GLU52 4.5 24.4 1.0 C6 B:NMY800 4.8 38.5 1.0 OE1 B:GLU76 4.8 26.0 1.0 O1B B:APC801 4.8 22.7 0.8 NZ A:LYS149 4.8 28.7 1.0 C3A B:APC801 4.8 29.3 0.8 CB B:GLU52 4.8 18.5 1.0 O3G B:APC801 4.9 29.1 0.8

Magnesium binding site 4 out of 4 in the Ternary Structure of the T130K Mutant of Ant-4'' with Neomycin and Ampcpp


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 T130K Mutant of Ant-4'' with Neomycin and Ampcpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg803 b:37.3 occ:1.00 OE2 B:GLU52 2.0 27.9 1.0 O1B B:APC801 2.1 22.7 0.8 O3G B:APC801 2.1 29.1 0.8 OD1 B:ASP50 2.1 28.4 1.0 O B:HOH937 2.1 28.8 1.0 O2A B:APC801 2.6 25.1 0.8 CD B:GLU52 3.1 28.9 1.0 PB B:APC801 3.2 27.7 0.8 CG B:ASP50 3.3 24.8 1.0 PG B:APC801 3.4 37.2 0.8 O3B B:APC801 3.6 36.7 0.8 OE1 B:GLU52 3.7 28.3 1.0 PA B:APC801 3.7 30.4 0.8 OD2 B:ASP50 3.8 24.4 1.0 O A:HOH958 3.8 30.6 1.0 O B:ASP50 3.8 20.3 1.0 MG B:MG802 3.8 24.6 1.0 C3A B:APC801 3.8 29.3 0.8 OG B:SER39 3.9 33.0 1.0 O2G B:APC801 4.1 29.5 0.8 N B:SER39 4.1 23.3 1.0 O B:HOH934 4.1 19.6 1.0 N B:ASP50 4.1 19.3 1.0 C B:ASP50 4.2 19.7 1.0 C5' B:APC801 4.3 28.8 0.8 CG B:GLU52 4.4 24.4 1.0 CB B:ASP50 4.5 23.6 1.0 CA B:ASP50 4.5 21.2 1.0 O1G B:APC801 4.5 29.5 0.8 O2B B:APC801 4.5 29.5 0.8 CB B:SER39 4.5 26.8 1.0 O5' B:APC801 4.6 30.0 0.8 CA B:GLY38 4.7 21.6 1.0 CB B:SER49 4.9 23.6 1.0 O1A B:APC801 4.9 29.8 0.8 CA B:SER39 5.0 29.3 1.0 N B:ILE51 5.0 17.7 1.0 C B:GLY38 5.0 24.5 1.0

P.Kumar, E.H.Serpersu, M.J.Cuneo. Catch and Release: A Novel Variation of the Archetypal Nucleotidyl Transfer Reaction To Be Published.