Magnesium in PDB 9do4: Structure of T4 Rna Ligase 1 Bound to Atp and Mg

All present enzymatic activity of Structure of T4 Rna Ligase 1 Bound to Atp and Mg:
6.5.1.3;

The structure of Structure of T4 Rna Ligase 1 Bound to Atp and Mg, PDB code: 9do4 was solved by G.M.Wimberly-Gard, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.83 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.197, 40.114, 107.032, 90, 116.37, 90
R / Rfree (%)	22.1 / 29.6

The binding sites of Magnesium atom in the Structure of T4 Rna Ligase 1 Bound to Atp and Mg (pdb code 9do4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of T4 Rna Ligase 1 Bound to Atp and Mg, PDB code: 9do4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of T4 Rna Ligase 1 Bound to Atp and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of T4 Rna Ligase 1 Bound to Atp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:59.7 occ:1.00 O B:HOH503 2.1 55.1 1.0 O B:HOH502 2.1 55.0 1.0 O B:HOH507 2.1 59.2 1.0 OD2 B:ASP272 2.1 63.5 1.0 OD1 B:ASP272 2.5 53.5 1.0 CG B:ASP272 2.7 53.6 1.0 O1B B:ATP403 2.9 71.4 1.0 O B:GLY269 3.1 70.5 1.0 O3G B:ATP403 3.3 65.5 1.0 CB B:ASP272 4.2 54.1 1.0 OD1 B:ASP273 4.2 50.6 1.0 PB B:ATP403 4.2 68.5 1.0 C B:GLY269 4.3 69.2 1.0 O1A B:ATP403 4.3 52.9 1.0 O3B B:ATP403 4.5 63.0 1.0 PG B:ATP403 4.6 69.9 1.0 CG B:ASP273 4.6 52.6 1.0 O3A B:ATP403 4.7 57.2 1.0 OD2 B:ASP273 4.7 47.5 1.0 CA B:ALA270 4.9 58.3 1.0

Magnesium binding site 2 out of 2 in the Structure of T4 Rna Ligase 1 Bound to Atp and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of T4 Rna Ligase 1 Bound to Atp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:43.9 occ:1.00 O B:HOH509 2.1 44.3 1.0 O B:HOH501 2.1 42.0 1.0 O B:HOH504 2.1 35.2 1.0 O B:HOH508 2.1 41.0 1.0 O B:HOH506 2.2 34.3 1.0 O2A B:ATP403 2.7 46.1 1.0 OE2 B:GLU159 3.9 37.9 1.0 NZ B:LYS99 4.1 42.8 1.0 OD1 B:ASP101 4.1 45.3 1.0 OE2 B:GLU227 4.1 38.9 1.0 O2B B:ATP403 4.1 65.6 1.0 OE1 B:GLU227 4.1 41.5 1.0 O B:GLY102 4.2 39.7 1.0 PA B:ATP403 4.2 54.0 1.0 O B:GLU100 4.4 42.2 1.0 O4' B:ATP403 4.5 42.7 1.0 C1' B:ATP403 4.5 36.6 1.0 N B:GLY102 4.6 43.3 1.0 C4' B:ATP403 4.6 43.1 1.0 CD B:GLU227 4.6 37.0 1.0 OH B:TYR246 4.7 52.0 1.0 O3A B:ATP403 4.8 57.2 1.0 CA B:ASP101 4.8 42.2 1.0 O B:HOH512 4.9 36.7 1.0 PB B:ATP403 4.9 68.5 1.0 CD B:GLU159 5.0 39.2 1.0

G.M.Wimberly-Gard, S.Shuman. Structure of T4 Rna Ligase 1 Bound to Atp and Mg To Be Published.