Magnesium in PDB 6go5: Tdt Chimera (LOOP1 of Pol Mu) - Ternary Complex with 1-Nt Gapped Dna Substrate

All present enzymatic activity of Tdt Chimera (LOOP1 of Pol Mu) - Ternary Complex with 1-Nt Gapped Dna Substrate:
2.7.7.31; 2.7.7.7;

The structure of Tdt Chimera (LOOP1 of Pol Mu) - Ternary Complex with 1-Nt Gapped Dna Substrate, PDB code: 6go5 was solved by J.Loc'h, C.A.Gerodimos, S.Rosario, M.R.Lieber, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.86 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	234.180, 69.250, 59.690, 90.00, 95.20, 90.00
R / Rfree (%)	21.8 / 26.5

The structure of Tdt Chimera (LOOP1 of Pol Mu) - Ternary Complex with 1-Nt Gapped Dna Substrate also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Tdt Chimera (LOOP1 of Pol Mu) - Ternary Complex with 1-Nt Gapped Dna Substrate (pdb code 6go5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Tdt Chimera (LOOP1 of Pol Mu) - Ternary Complex with 1-Nt Gapped Dna Substrate, PDB code: 6go5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Tdt Chimera (LOOP1 of Pol Mu) - Ternary Complex with 1-Nt Gapped Dna Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tdt Chimera (LOOP1 of Pol Mu) - Ternary Complex with 1-Nt Gapped Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:52.8 occ:1.00 OD1 A:ASP343 2.0 48.4 1.0 O3G A:XC5603 2.1 72.4 1.0 OD2 A:ASP345 2.2 53.6 1.0 O2A A:XC5603 2.3 55.4 1.0 O3B A:XC5603 2.3 68.9 1.0 PG A:XC5603 2.7 73.6 1.0 O2G A:XC5603 3.1 75.5 1.0 CG A:ASP343 3.2 49.6 1.0 CG A:ASP345 3.3 47.5 1.0 PA A:XC5603 3.5 55.1 1.0 PB A:XC5603 3.6 60.6 1.0 C3A A:XC5603 3.6 57.6 1.0 O A:ASP343 3.8 58.1 1.0 OD1 A:ASP345 3.8 53.6 1.0 OD2 A:ASP343 3.8 46.2 1.0 C A:ASP343 4.0 57.6 1.0 O1G A:XC5603 4.0 70.0 1.0 O A:HOH701 4.1 43.8 1.0 N A:GLY333 4.2 48.2 1.0 ND1 A:HIS342 4.3 58.5 1.0 CB A:ASP343 4.3 54.2 1.0 O1B A:XC5603 4.3 58.9 1.0 N A:ASP343 4.3 56.6 1.0 CE1 A:HIS342 4.3 56.8 1.0 C5' A:XC5603 4.5 51.0 1.0 O5' A:XC5603 4.5 51.0 1.0 CA A:ASP343 4.5 54.4 1.0 CB A:ASP345 4.5 46.6 1.0 N A:VAL344 4.5 51.2 1.0 CA A:GLY332 4.5 44.3 1.0 N A:ASP345 4.5 48.1 1.0 O1A A:XC5603 4.6 52.9 1.0 O2B A:XC5603 4.6 64.3 1.0 CA A:VAL344 4.8 49.1 1.0 C A:VAL344 4.8 51.3 1.0 C A:GLY332 4.9 49.7 1.0

Magnesium binding site 2 out of 2 in the Tdt Chimera (LOOP1 of Pol Mu) - Ternary Complex with 1-Nt Gapped Dna Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tdt Chimera (LOOP1 of Pol Mu) - Ternary Complex with 1-Nt Gapped Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:51.1 occ:1.00 OD2 B:ASP345 1.9 59.8 1.0 O2A B:XC5603 2.1 52.5 1.0 O1B B:XC5603 2.1 60.6 1.0 OD1 B:ASP343 2.2 51.0 1.0 O B:HOH756 2.3 54.4 1.0 O3G B:XC5603 2.6 55.9 1.0 CG B:ASP345 3.0 54.6 1.0 PB B:XC5603 3.2 57.9 1.0 CG B:ASP343 3.3 49.5 1.0 PA B:XC5603 3.3 52.8 1.0 C3A B:XC5603 3.5 58.3 1.0 OD1 B:ASP345 3.5 53.9 1.0 PG B:XC5603 3.6 59.5 1.0 O3B B:XC5603 3.7 54.1 1.0 OD2 B:ASP343 3.8 50.3 1.0 O2G B:XC5603 3.9 63.6 1.0 C5' B:XC5603 4.0 50.1 1.0 N B:GLY333 4.0 48.0 1.0 O B:ASP343 4.1 57.6 1.0 O5' B:XC5603 4.1 52.8 1.0 O B:HOH702 4.1 58.7 1.0 CB B:ASP345 4.2 50.6 1.0 C B:ASP343 4.3 57.0 1.0 CA B:GLY332 4.4 48.1 1.0 O1A B:XC5603 4.5 51.0 1.0 N B:ASP345 4.5 50.8 1.0 ND1 B:HIS342 4.5 58.0 1.0 O2B B:XC5603 4.5 52.9 1.0 CE1 B:HIS342 4.5 56.0 1.0 CB B:ASP343 4.5 51.5 1.0 N B:ASP343 4.7 53.3 1.0 N B:VAL344 4.7 52.9 1.0 CA B:ASP343 4.8 52.0 1.0 C B:GLY332 4.8 51.8 1.0 CA B:GLY333 4.8 48.4 1.0 C B:VAL344 4.9 55.2 1.0 CA B:ASP345 5.0 49.6 1.0 O1G B:XC5603 5.0 57.7 1.0 CA B:VAL344 5.0 51.6 1.0

J.Loc'h, C.A.Gerodimos, S.Rosario, M.R.Lieber, M.Delarue. Tdt Chimera (LOOP1 of Pol Mu) - Ternary Complex with 1-Nt Gapped Dna Substrate To Be Published.