Sodium in PDB 8e5y: Human Pu.1 Ets-Domain Bound to D(Aataagcggaagtggg) Acetate Free at pH 5.4

The structure of Human Pu.1 Ets-Domain Bound to D(Aataagcggaagtggg) Acetate Free at pH 5.4, PDB code: 8e5y was solved by J.R.Terrell, G.M.K.Poon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.60 / 1.32
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.059, 60.807, 44.437, 90, 116.24, 90
R / Rfree (%)	14.9 / 16.2

The binding sites of Sodium atom in the Human Pu.1 Ets-Domain Bound to D(Aataagcggaagtggg) Acetate Free at pH 5.4 (pdb code 8e5y). 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 Human Pu.1 Ets-Domain Bound to D(Aataagcggaagtggg) Acetate Free at pH 5.4, PDB code: 8e5y:

Sodium binding site 1 out of 1 in the Human Pu.1 Ets-Domain Bound to D(Aataagcggaagtggg) Acetate Free at pH 5.4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Pu.1 Ets-Domain Bound to D(Aataagcggaagtggg) Acetate Free at pH 5.4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:55.4 occ:1.00 OP2 C:DA5 2.1 38.0 1.0 H8 C:DA5 2.5 32.6 1.0 O C:HOH222 2.6 44.7 1.0 O5' C:DA5 2.7 33.9 1.0 O F:HOH381 2.7 46.4 1.0 H2'' C:DA4 2.8 39.1 1.0 P C:DA5 2.9 36.1 1.0 H2' C:DA5 3.1 35.3 1.0 HE3 F:LYS206 3.3 24.8 1.0 O F:HOH406 3.3 41.0 1.0 HZ1 F:LYS206 3.4 27.0 1.0 C8 C:DA5 3.4 27.2 1.0 C2' C:DA4 3.5 32.6 1.0 H2' C:DA4 3.6 39.1 1.0 HE2 F:LYS206 3.7 24.8 1.0 O3' C:DA4 3.8 34.2 1.0 CE F:LYS206 3.9 20.7 1.0 H3' C:DA4 3.9 39.0 1.0 C3' C:DA4 3.9 32.5 1.0 C2' C:DA5 4.0 29.4 1.0 NZ F:LYS206 4.0 22.5 1.0 C5' C:DA5 4.1 30.8 1.0 OP1 C:DA5 4.1 38.2 1.0 H3' C:DA5 4.2 35.7 1.0 HD21 F:LEU248 4.2 26.0 1.0 HD2 F:TYR225 4.2 22.7 1.0 N7 C:DA5 4.3 26.0 1.0 N9 C:DA5 4.3 26.5 1.0 O4' C:DA5 4.4 28.8 1.0 HE21 F:GLN226 4.4 31.8 0.5 O C:HOH242 4.4 56.0 1.0 HZ2 F:LYS206 4.5 27.0 1.0 C1' C:DA5 4.5 28.5 1.0 C3' C:DA5 4.5 29.7 1.0 H5' C:DA5 4.5 36.9 1.0 C4' C:DA5 4.5 29.5 1.0 HE2 F:TYR225 4.6 23.9 1.0 H5'' C:DA5 4.6 36.9 1.0 HZ3 F:LYS206 4.7 27.0 1.0 H2'' C:DA5 4.7 35.3 1.0 O C:HOH267 4.8 70.5 1.0 O F:HOH316 4.8 36.8 1.0 CD2 F:TYR225 4.8 18.9 1.0 C1' C:DA4 4.9 31.5 1.0 HG2 F:GLN226 4.9 27.6 0.5 H1' C:DA4 5.0 37.8 1.0

J.R.Terrell, S.J.Taylor, A.L.Schneider, Y.Lu, T.N.Vernon, S.Xhani, R.H.Gumpper, M.Luo, W.D.Wilson, U.Steidl, G.M.K.Poon. Dna Selection By the Master Transcription Factor Pu.1. Cell Rep V. 42 12671 2023.
ISSN: ESSN 2211-1247
PubMed: 37352101
DOI: 10.1016/J.CELREP.2023.112671