Magnesium in PDB 6nmn: Ternary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin and Atp (No Pyrophosphate)

The structure of Ternary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin and Atp (No Pyrophosphate), PDB code: 6nmn 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)	57.32 / 1.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.050, 58.050, 363.450, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21.8

The binding sites of Magnesium atom in the Ternary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin and Atp (No Pyrophosphate) (pdb code 6nmn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Ternary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin and Atp (No Pyrophosphate), PDB code: 6nmn:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Ternary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin and Atp (No Pyrophosphate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin and Atp (No Pyrophosphate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:30.1 occ:1.00 OD2 B:ASP50 2.0 30.5 1.0 OP1 B:A901 2.3 47.7 0.6 O B:HOH1016 2.3 38.9 1.0 OE1 A:GLU145 2.6 50.4 1.0 CG B:ASP50 2.8 28.5 1.0 OD1 B:ASP50 2.9 38.5 1.0 CD A:GLU145 2.9 35.6 1.0 O B:HOH1003 3.1 32.4 1.0 MG A:MG305 3.3 21.8 1.0 OE2 A:GLU145 3.3 49.5 1.0 P B:A901 3.5 57.0 0.6 O4 B:NMY900 3.5 40.2 0.9 CD B:GLU52 3.8 40.3 1.0 CG A:GLU145 3.8 27.6 1.0 C5' B:A901 3.9 42.5 0.6 O B:HOH1036 4.0 21.8 1.0 OE1 B:GLU52 4.0 39.2 1.0 CG B:GLU52 4.0 22.0 1.0 O5' B:A901 4.0 41.8 0.6 OE2 B:GLU52 4.0 43.2 1.0 CB B:ASP50 4.2 22.5 1.0 NZ B:LYS74 4.2 26.4 1.0 O3 B:NMY900 4.6 45.0 0.9 OP2 B:A901 4.7 51.4 0.6 C4 B:NMY900 4.8 39.2 0.9 C3 B:NMY900 4.9 42.0 0.9 O A:HOH495 4.9 18.7 1.0 O B:HOH1005 4.9 30.9 1.0 CB A:GLU145 5.0 18.6 1.0

Magnesium binding site 2 out of 3 in the Ternary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin and Atp (No Pyrophosphate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin and Atp (No Pyrophosphate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:18.6 occ:1.00 OD2 A:ASP50 2.2 23.6 1.0 OE2 A:GLU52 2.2 16.6 0.5 OE2 B:GLU145 2.3 32.4 1.0 OP2 A:A302 2.3 30.6 0.8 O A:HOH451 2.6 27.9 1.0 O A:HOH445 2.6 25.5 1.0 OE1 B:GLU145 2.6 30.1 1.0 CD B:GLU145 2.7 35.5 1.0 CG A:ASP50 3.0 27.9 1.0 OD1 A:ASP50 3.2 31.5 1.0 CD A:GLU52 3.2 23.4 0.5 O A:HOH418 3.4 29.8 1.0 P A:A302 3.5 32.0 0.8 O4 A:NMY301 3.7 37.7 1.0 CG A:GLU52 3.8 21.2 0.5 O A:HOH421 3.8 21.6 1.0 C5' A:A302 4.0 26.5 0.8 OE1 A:GLU52 4.1 24.9 0.5 CG B:GLU145 4.1 21.4 1.0 O5' A:A302 4.2 26.2 0.8 NZ A:LYS74 4.2 24.1 1.0 OE1 A:GLU52 4.3 17.9 0.6 NZ B:LYS149 4.4 34.8 1.0 CB A:ASP50 4.4 23.5 1.0 O B:HOH1031 4.6 31.2 1.0 O3 A:NMY301 4.7 28.7 1.0 OP1 A:A302 4.7 34.5 0.8 O B:HOH1126 4.9 25.1 1.0 O A:HOH612 4.9 35.6 1.0 C4 A:NMY301 4.9 36.1 1.0 C3 A:NMY301 5.0 27.0 1.0

Magnesium binding site 3 out of 3 in the Ternary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin and Atp (No Pyrophosphate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ternary Complex Structure of the T130K Mutant of Ant-4'' with Neomycin and Atp (No Pyrophosphate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:21.8 occ:1.00 O4 B:NMY900 2.1 40.2 0.9 O B:HOH1005 2.3 30.9 1.0 O B:HOH1003 2.3 32.4 1.0 OE2 A:GLU145 2.3 49.5 1.0 C4 B:NMY900 2.7 39.2 0.9 OE1 A:GLU145 2.8 50.4 1.0 C5 B:NMY900 2.8 42.0 0.9 CD A:GLU145 2.9 35.6 1.0 C3 B:NMY900 2.9 42.0 0.9 N9 B:NMY900 3.2 31.1 0.9 MG A:MG303 3.3 30.1 1.0 P B:A901 3.4 57.0 0.6 OE1 B:GLU76 3.4 27.2 1.0 N6 B:NMY900 3.5 46.8 0.9 OP1 B:A901 3.6 47.7 0.6 C6 B:NMY900 3.6 41.6 0.9 O3 B:NMY900 3.8 45.0 0.9 NZ B:LYS74 4.0 26.4 1.0 O5 B:NMY900 4.0 35.7 0.9 C2 B:NMY900 4.1 36.7 0.9 O1 B:NMY900 4.1 37.6 0.9 C1 B:NMY900 4.3 40.1 0.9 O A:HOH427 4.3 36.5 1.0 O5' B:A901 4.3 41.8 0.6 OE1 B:GLU67 4.3 20.0 1.0 CG A:GLU145 4.4 27.6 1.0 OE1 B:GLU52 4.4 39.2 1.0 C9 B:NMY900 4.5 29.4 0.9 OP2 B:A901 4.5 51.4 0.6 CD B:GLU76 4.6 24.8 1.0 C10 B:NMY900 4.6 38.0 0.9 O A:GLU141 4.7 18.6 1.0 OD2 B:ASP50 4.7 30.5 1.0 N2 B:NMY900 4.8 34.2 0.9

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