Sodium in PDB 8eng: Human Pu.1 Ets-Domain (165-270) Bound to D(Aataagcggaagtggg) with Hemi-Methylated Cpg (Forward Strand)

The structure of Human Pu.1 Ets-Domain (165-270) Bound to D(Aataagcggaagtggg) with Hemi-Methylated Cpg (Forward Strand), PDB code: 8eng 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)	33.35 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.908, 60.829, 44.631, 90, 116.71, 90
R / Rfree (%)	13.5 / 15.8

The binding sites of Sodium atom in the Human Pu.1 Ets-Domain (165-270) Bound to D(Aataagcggaagtggg) with Hemi-Methylated Cpg (Forward Strand) (pdb code 8eng). 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) Bound to D(Aataagcggaagtggg) with Hemi-Methylated Cpg (Forward Strand), PDB code: 8eng:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Pu.1 Ets-Domain (165-270) Bound to D(Aataagcggaagtggg) with Hemi-Methylated Cpg (Forward Strand)


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) Bound to D(Aataagcggaagtggg) with Hemi-Methylated Cpg (Forward Strand) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:30.2 occ:1.00 OP2 C:DA11 2.1 35.4 1.0 H8 C:DA11 2.5 21.6 1.0 H2'' C:DA10 2.7 37.9 1.0 H2' C:DA11 3.2 24.5 1.0 O5' C:DA11 3.2 26.1 1.0 P C:DA11 3.2 32.8 1.0 H2' C:DA10 3.2 37.9 1.0 C2' C:DA10 3.3 31.6 1.0 C8 C:DA11 3.4 18.0 1.0 H3' C:DA10 3.8 37.0 1.0 C3' C:DA10 3.9 30.8 1.0 O3' C:DA10 4.0 33.3 1.0 C2' C:DA11 4.1 20.4 1.0 N7 C:DA11 4.2 17.0 1.0 N9 C:DA11 4.4 17.5 1.0 OP1 C:DA11 4.5 37.6 1.0 O C:HOH211 4.5 32.5 1.0 C5' C:DA11 4.5 23.7 1.0 C1' C:DA11 4.6 19.2 1.0 H3' C:DA11 4.6 24.9 1.0 O4' C:DA11 4.7 19.9 1.0 H2'' C:DA11 4.7 24.5 1.0 C1' C:DA10 4.7 28.8 1.0 H5' C:DA11 4.8 28.4 1.0 C3' C:DA11 4.9 20.8 1.0 H1' C:DA10 4.9 34.5 1.0 C4' C:DA11 4.9 21.9 1.0 O C:HOH260 5.0 58.1 1.0

Sodium binding site 2 out of 2 in the Human Pu.1 Ets-Domain (165-270) Bound to D(Aataagcggaagtggg) with Hemi-Methylated Cpg (Forward Strand)


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) Bound to D(Aataagcggaagtggg) with Hemi-Methylated Cpg (Forward Strand) within 5.0Å range: probe atom residue distance (Å) B Occ F:Na301 b:65.3 occ:1.00 HZ1 F:LYS247 2.0 39.8 1.0 HZ3 F:LYS247 2.0 39.8 1.0 NZ F:LYS247 2.4 33.2 0.3 O D:HOH148 2.5 49.8 1.0 O5' D:DT32 2.7 40.0 1.0 HZ2 F:LYS247 3.0 39.8 1.0 HE3 F:LYS247 3.3 39.6 1.0 CE F:LYS247 3.5 33.0 0.6 O3' D:DA31 3.5 33.0 1.0 P D:DT32 3.8 39.1 1.0 HE2 F:LYS247 4.1 39.6 1.0 O C:HOH272 4.1 58.3 1.0 O C:HOH225 4.1 39.6 1.0 H1' D:DA31 4.2 25.7 1.0 H4' D:DA31 4.3 30.9 1.0 HD2 F:LYS247 4.4 37.3 1.0 CD F:LYS247 4.5 31.1 0.2 OP1 D:DT32 4.5 38.6 1.0 HD3 F:LYS247 4.7 37.3 1.0 C3' D:DA31 4.8 26.1 1.0 O C:HOH271 4.8 33.9 1.0 OP2 D:DT32 4.9 41.4 1.0 C4' D:DA31 4.9 25.7 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