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

The structure of Human Pu.1 Ets-Domain (165-270) Bound to D(Aataaccggaagtggg), PDB code: 8eqk 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)	23.87 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.115, 60.64, 44.456, 90, 116.17, 90
R / Rfree (%)	15 / 17.9

The binding sites of Sodium atom in the Human Pu.1 Ets-Domain (165-270) Bound to D(Aataaccggaagtggg) (pdb code 8eqk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Human Pu.1 Ets-Domain (165-270) Bound to D(Aataaccggaagtggg), PDB code: 8eqk:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Human Pu.1 Ets-Domain (165-270) 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) Bound to D(Aataaccggaagtggg) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:53.0 occ:1.00 OP2 C:DA11 2.2 38.0 1.0 H8 C:DA11 2.6 26.5 1.0 H2'' C:DA10 2.9 43.0 1.0 P C:DA11 3.3 36.6 1.0 H2' C:DA11 3.4 28.9 1.0 O5' C:DA11 3.4 30.6 1.0 H2' C:DA10 3.4 43.0 1.0 C2' C:DA10 3.5 35.8 1.0 C8 C:DA11 3.5 22.1 1.0 H3' C:DA10 3.9 43.2 1.0 C3' C:DA10 4.0 36.0 1.0 O3' C:DA10 4.1 38.2 1.0 O C:HOH218 4.2 34.0 1.0 N7 C:DA11 4.2 20.4 1.0 C2' C:DA11 4.3 24.1 1.0 N9 C:DA11 4.5 20.7 1.0 OP1 C:DA11 4.6 41.7 1.0 C5' C:DA11 4.7 28.9 1.0 H3' C:DA11 4.8 29.5 1.0 C1' C:DA11 4.8 23.0 1.0 H2'' C:DA11 4.9 28.9 1.0 O4' C:DA11 4.9 24.1 1.0 C1' C:DA10 4.9 31.1 1.0

Sodium binding site 2 out of 3 in the Human Pu.1 Ets-Domain (165-270) 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) Bound to D(Aataaccggaagtggg) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:64.9 occ:1.00 OP2 D:DG27 2.3 45.0 1.0 O D:HOH257 2.4 50.1 1.0 H3' D:DC26 3.1 43.4 1.0 P D:DG27 3.6 43.7 1.0 C3' D:DC26 3.9 36.2 1.0 H2' D:DC26 4.2 41.5 1.0 O3' D:DC26 4.2 39.4 1.0 OP1 D:DG27 4.4 47.4 1.0 O5' D:DC26 4.4 39.2 1.0 C2' D:DC26 4.5 34.5 1.0 O D:HOH203 4.5 55.0 1.0 H2'' D:DC26 4.6 41.5 1.0 O5' D:DG27 4.8 47.0 1.0 OP2 D:DC26 4.8 42.6 1.0

Sodium binding site 3 out of 3 in the Human Pu.1 Ets-Domain (165-270) Bound to D(Aataaccggaagtggg)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Pu.1 Ets-Domain (165-270) Bound to D(Aataaccggaagtggg) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na102 b:62.2 occ:1.00 O5' D:DT32 2.4 39.5 1.0 HZ3 F:LYS247 2.4 45.7 1.0 O D:HOH228 3.0 35.1 1.0 NZ F:LYS247 3.2 38.1 0.4 HZ1 F:LYS247 3.3 45.7 1.0 O F:HOH379 3.4 63.0 1.0 HE3 F:LYS247 3.4 44.5 1.0 O3' D:DA31 3.4 34.4 1.0 P D:DT32 3.5 38.3 1.0 O F:HOH352 3.6 61.6 1.0 CE F:LYS247 3.8 37.1 0.6 HZ2 F:LYS247 3.9 45.7 1.0 HE2 F:LYS247 4.0 44.5 1.0 H4' D:DA31 4.0 37.0 1.0 OP1 D:DT32 4.1 39.5 1.0 H1' D:DA31 4.3 29.3 1.0 C3' D:DA31 4.6 31.2 1.0 O C:HOH228 4.7 40.0 1.0 OP2 D:DT32 4.7 41.6 1.0 C4' D:DA31 4.7 30.9 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