Sodium in PDB 8eql: Human Pu.1 Ets-Domain (165-270) Q226E Mutant Bound to D(Aataaccggaagtggg)

The structure of Human Pu.1 Ets-Domain (165-270) Q226E Mutant Bound to D(Aataaccggaagtggg), PDB code: 8eql 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)	24.11 / 1.52
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.033, 60.576, 44.605, 90, 116.71, 90
R / Rfree (%)	15.9 / 19.5

The binding sites of Sodium atom in the Human Pu.1 Ets-Domain (165-270) Q226E Mutant Bound to D(Aataaccggaagtggg) (pdb code 8eql). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Pu.1 Ets-Domain (165-270) Q226E Mutant Bound to D(Aataaccggaagtggg), PDB code: 8eql:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Pu.1 Ets-Domain (165-270) Q226E Mutant Bound to D(Aataaccggaagtggg)


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 (165-270) Q226E Mutant Bound to D(Aataaccggaagtggg) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:48.2 occ:1.00 O C:HOH252 2.4 49.5 1.0 OP2 C:DA5 2.4 32.7 1.0 H8 C:DA5 2.4 23.1 1.0 O F:HOH386 2.9 28.9 1.0 H2'' C:DA4 3.0 34.7 1.0 H2' C:DA5 3.1 25.1 1.0 O5' C:DA5 3.2 29.7 1.0 HE3 F:LYS206 3.3 22.3 1.0 C8 C:DA5 3.4 19.3 1.0 P C:DA5 3.4 34.6 1.0 H2' C:DA4 3.4 34.7 1.0 HZ1 F:LYS206 3.4 27.5 1.0 C2' C:DA4 3.6 28.9 1.0 HE2 F:LYS206 3.8 22.3 1.0 CE F:LYS206 3.9 18.6 1.0 C2' C:DA5 4.0 20.9 1.0 NZ F:LYS206 4.0 22.9 1.0 HD2 F:TYR225 4.1 18.6 1.0 H3' C:DA4 4.1 37.8 1.0 N7 C:DA5 4.2 20.8 1.0 C3' C:DA4 4.2 31.5 1.0 O3' C:DA4 4.3 28.5 1.0 N9 C:DA5 4.3 19.9 1.0 O C:HOH216 4.3 35.5 1.0 H3' C:DA5 4.4 27.2 1.0 HZ2 F:LYS206 4.4 27.5 1.0 C5' C:DA5 4.4 26.3 1.0 HD21 F:LEU248 4.5 26.4 1.0 C1' C:DA5 4.5 21.3 1.0 HE2 F:TYR225 4.5 17.7 1.0 O4' C:DA5 4.5 23.4 1.0 H2'' C:DA5 4.6 25.1 1.0 OP1 C:DA5 4.6 40.3 1.0 O F:HOH301 4.6 35.3 1.0 C3' C:DA5 4.7 22.7 1.0 H5 C:DC6 4.7 22.7 1.0 CD2 F:TYR225 4.7 15.5 1.0 HZ3 F:LYS206 4.7 27.5 1.0 O F:HOH305 4.8 29.9 1.0 C4' C:DA5 4.8 24.4 1.0 H5' C:DA5 4.9 31.6 1.0 C1' C:DA4 4.9 33.1 1.0 CE2 F:TYR225 5.0 14.7 1.0

Sodium binding site 2 out of 2 in the Human Pu.1 Ets-Domain (165-270) Q226E Mutant Bound to D(Aataaccggaagtggg)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Pu.1 Ets-Domain (165-270) Q226E Mutant Bound to D(Aataaccggaagtggg) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:59.9 occ:1.00 O5' D:DT32 2.5 55.5 1.0 HZ1 F:LYS247 2.6 56.2 1.0 O D:HOH235 3.0 38.8 1.0 NZ F:LYS247 3.5 46.8 0.6 O3' D:DA31 3.6 35.2 1.0 P D:DT32 3.7 40.6 1.0 HZ2 F:LYS247 3.7 56.2 1.0 H4' D:DA31 3.8 30.9 1.0 HZ3 F:LYS247 3.9 56.2 1.0 OP1 D:DT32 4.2 55.2 1.0 H1' D:DA31 4.3 31.0 1.0 HE3 F:LYS247 4.3 42.0 1.0 CE F:LYS247 4.4 35.0 0.0 HE2 F:LYS247 4.5 42.0 1.0 O C:HOH221 4.6 40.6 1.0 C4' D:DA31 4.6 25.8 1.0 C3' D:DA31 4.7 31.1 1.0 OP2 D:DT32 4.9 47.0 1.0 O4' D:DA31 5.0 32.6 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