Sodium in PDB 6dx0: Hermes Transposase Deletion Dimer Complex with (A/T) Dna

The structure of Hermes Transposase Deletion Dimer Complex with (A/T) Dna, PDB code: 6dx0 was solved by F.Dyda, A.R.Voth, A.B.Hickman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.44 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	121.600, 135.500, 102.850, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 30.5

The binding sites of Sodium atom in the Hermes Transposase Deletion Dimer Complex with (A/T) Dna (pdb code 6dx0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Hermes Transposase Deletion Dimer Complex with (A/T) Dna, PDB code: 6dx0:

Sodium binding site 1 out of 1 in the Hermes Transposase Deletion Dimer Complex with (A/T) Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hermes Transposase Deletion Dimer Complex with (A/T) Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:71.3 occ:1.00 OD1 A:ASP180 2.2 93.6 1.0 OP2 C:DG18 2.3 0.4 1.0 O3' D:DA7 2.3 0.6 1.0 CG A:ASP180 3.0 99.1 1.0 OD2 A:ASP180 3.0 95.0 1.0 OD2 A:ASP248 3.3 64.6 1.0 C3' D:DA7 3.6 86.8 1.0 O A:LEU181 3.7 92.2 1.0 P C:DG18 3.7 0.7 1.0 N A:LEU181 3.9 84.4 1.0 C5' C:DG18 3.9 86.5 1.0 CG A:ASP248 4.1 84.5 1.0 OD1 A:ASP248 4.2 95.1 1.0 O5' C:DG18 4.3 95.0 1.0 CB A:ASP180 4.4 0.5 1.0 C A:LEU181 4.4 89.1 1.0 OP1 C:DG18 4.5 74.0 1.0 C2' D:DA7 4.5 82.0 1.0 CA A:LEU181 4.5 89.0 1.0 C4' D:DA7 4.6 62.6 1.0 CB A:LEU181 4.7 97.8 1.0 O3' C:DG17 4.8 0.9 1.0 CD1 A:LEU181 4.8 60.6 1.0 CA A:ASP180 4.9 89.8 1.0 C A:ASP180 4.9 93.0 1.0

A.B.Hickman, A.R.Voth, H.Ewis, X.Li, N.L.Craig, F.Dyda. Structural Insights Into the Mechanism of Double Strand Break Formation By Hermes, A Hat Family Eukaryotic Dna Transposase. Nucleic Acids Res. V. 46 10286 2018.
ISSN: ESSN 1362-4962
PubMed: 30239795
DOI: 10.1093/NAR/GKY838