Sodium 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:

Magnesium

(Mg)

2 atoms

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

Sodium 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 Sodium with other atoms in the Na 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:Na601 b:72.9 occ:1.00 O A:THR253 2.3 67.2 1.0 OP1 F:DT5 2.4 70.2 1.0 O A:VAL258 2.5 78.4 1.0 O A:VAL255 2.5 68.8 1.0 C A:THR253 3.3 71.2 1.0 C A:VAL258 3.5 79.3 1.0 C A:VAL255 3.5 69.8 1.0 P F:DT5 3.6 69.5 1.0 CA A:THR253 3.8 69.5 1.0 OP2 F:DT5 3.8 69.8 1.0 N A:VAL258 3.8 72.5 1.0 N A:GLY257 4.1 66.4 1.0 CA A:VAL258 4.1 74.3 1.0 CA A:PHE256 4.2 66.1 1.0 N A:PHE256 4.2 67.3 1.0 CB A:THR253 4.2 73.1 1.0 N A:VAL255 4.3 68.1 1.0 N A:SER254 4.4 69.9 1.0 CB A:VAL258 4.6 80.2 1.0 C A:SER254 4.6 72.7 1.0 CA A:VAL255 4.6 67.4 1.0 N A:GLY259 4.6 77.5 1.0 C A:PHE256 4.6 70.3 1.0 O3' F:DT4 4.6 69.6 1.0 O5' F:DT5 4.7 70.7 1.0 C A:GLY257 4.8 74.1 1.0 CA A:SER254 4.9 68.9 1.0 CA A:GLY259 4.9 76.4 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na602 b:55.7 occ:1.00 O B:THR253 2.3 63.3 1.0 O B:VAL258 2.4 54.7 1.0 O B:VAL255 2.5 61.5 1.0 O B:HOH782 2.5 63.2 1.0 O L:HOH102 2.5 56.2 1.0 OP1 L:DT5 2.5 68.5 1.0 C B:THR253 3.4 62.9 1.0 C B:VAL255 3.4 62.7 1.0 C B:VAL258 3.6 53.4 1.0 P L:DT5 3.7 66.2 1.0 OP2 L:DT5 3.9 65.2 1.0 N B:VAL258 3.9 49.9 1.0 CA B:THR253 3.9 59.0 1.0 CA B:PHE256 4.1 58.3 1.0 N B:PHE256 4.1 59.8 1.0 N B:GLY257 4.1 53.1 1.0 CA B:VAL258 4.2 48.1 1.0 N B:VAL255 4.2 60.3 1.0 CB B:THR253 4.4 57.8 1.0 C B:SER254 4.4 62.6 1.0 N B:SER254 4.5 60.0 1.0 CA B:VAL255 4.5 60.3 1.0 C B:PHE256 4.5 59.4 1.0 CB B:VAL258 4.6 51.6 1.0 N B:GLY259 4.7 50.0 1.0 O3' L:DT4 4.7 66.9 1.0 O5' L:DT5 4.8 66.3 1.0 CA B:SER254 4.8 59.1 1.0 O B:SER254 4.9 62.1 1.0 C B:GLY257 4.9 53.8 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.