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

The structure of Human Pu.1 Ets-Domain (165-270) Q226E Mutant Bound to D(Aataagcggaagtggg), PDB code: 8emd 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)	33.26 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.009, 60.549, 44.566, 90, 116.72, 90
R / Rfree (%)	16.2 / 20.2

The binding sites of Sodium atom in the Human Pu.1 Ets-Domain (165-270) Q226E Mutant Bound to D(Aataagcggaagtggg) (pdb code 8emd). 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(Aataagcggaagtggg), PDB code: 8emd:
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(Aataagcggaagtggg)


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(Aataagcggaagtggg) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:49.8 occ:1.00 OP2 C:DA5 2.0 40.0 1.0 H2'' C:DA4 2.7 50.4 1.0 H8 C:DA5 2.7 32.6 1.0 O C:HOH263 2.8 39.2 1.0 O5' C:DA5 2.9 38.7 1.0 P C:DA5 2.9 43.1 1.0 HZ1 F:LYS206 3.3 33.9 1.0 C2' C:DA4 3.4 42.0 1.0 HE3 F:LYS206 3.4 27.8 1.0 H2' C:DA4 3.4 50.4 1.0 H2' C:DA5 3.5 32.6 1.0 C8 C:DA5 3.7 27.2 1.0 H3' C:DA4 3.7 46.5 1.0 O3' C:DA4 3.7 51.8 1.0 C3' C:DA4 3.8 38.8 1.0 HE2 F:LYS206 3.8 27.8 1.0 CE F:LYS206 3.9 23.1 1.0 NZ F:LYS206 4.0 28.2 1.0 HD2 F:TYR225 4.2 25.9 1.0 C5' C:DA5 4.2 32.5 1.0 OP1 C:DA5 4.2 43.9 1.0 C2' C:DA5 4.3 27.2 1.0 HZ3 F:LYS206 4.4 33.9 1.0 H3' C:DA5 4.4 38.0 1.0 O F:HOH402 4.5 42.6 1.0 N7 C:DA5 4.5 27.4 1.0 O4' C:DA5 4.5 32.3 1.0 H5' C:DA5 4.6 38.9 1.0 N9 C:DA5 4.6 25.6 1.0 HZ2 F:LYS206 4.6 33.9 1.0 HD21 F:LEU248 4.7 29.7 1.0 C4' C:DA5 4.7 32.3 1.0 C1' C:DA5 4.7 29.3 1.0 C3' C:DA5 4.8 31.7 1.0 C1' C:DA4 4.8 40.4 1.0 HE2 F:TYR225 4.8 30.1 1.0 H5'' C:DA5 4.8 38.9 1.0 CD2 F:TYR225 4.8 21.6 1.0 O F:HOH406 4.9 40.6 1.0 H1' C:DA4 4.9 48.5 1.0

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


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(Aataagcggaagtggg) within 5.0Å range: probe atom residue distance (Å) B Occ F:Na301 b:48.6 occ:1.00 HH F:TYR250 2.1 29.1 1.0 OH F:TYR225 2.2 29.6 1.0 OP2 C:DG6 2.2 35.0 1.0 HE2 F:TYR225 2.5 30.1 1.0 O C:HOH257 2.6 36.3 1.0 OH F:TYR250 2.8 24.3 1.0 CZ F:TYR225 3.0 22.7 1.0 CE2 F:TYR225 3.1 25.1 1.0 HD23 F:LEU248 3.1 29.7 1.0 HE1 F:TYR250 3.3 24.7 1.0 HE2 F:LYS243 3.4 28.7 1.0 P C:DG6 3.5 30.5 1.0 HA F:LEU248 3.6 26.7 1.0 HB1 F:ALA229 3.7 24.7 1.0 HB2 F:ALA229 3.7 24.7 1.0 CZ F:TYR250 3.7 21.9 1.0 O5' C:DG6 3.8 28.4 1.0 CE1 F:TYR250 3.8 20.6 1.0 O C:HOH222 4.0 24.3 1.0 CD2 F:LEU248 4.0 24.8 1.0 H3' C:DA5 4.0 38.0 1.0 CB F:ALA229 4.1 20.6 1.0 H2'' C:DA5 4.2 32.6 1.0 HD22 F:LEU248 4.2 29.7 1.0 CE F:LYS243 4.3 23.9 1.0 HD21 F:LEU248 4.3 29.7 1.0 CE1 F:TYR225 4.3 27.1 1.0 HE3 F:LYS243 4.4 28.7 1.0 O F:HOH483 4.4 35.2 1.0 CD2 F:TYR225 4.4 21.6 1.0 H2' C:DA5 4.5 32.6 1.0 HB3 F:ALA229 4.5 24.7 1.0 O3' C:DA5 4.5 33.4 1.0 C3' C:DA5 4.5 31.7 1.0 OP1 C:DG6 4.6 31.6 1.0 H3' C:DG6 4.6 28.7 1.0 C2' C:DA5 4.6 27.2 1.0 CA F:LEU248 4.6 22.3 1.0 HD3 F:LYS243 4.7 28.1 1.0 HE1 F:TYR225 4.7 32.5 1.0 H F:LEU248 4.8 25.4 1.0 HD2 F:TYR225 4.8 25.9 1.0 H2' C:DG6 4.9 29.2 1.0 CE2 F:TYR250 5.0 20.5 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