Potassium in PDB 4cn5: Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element

The structure of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element, PDB code: 4cn5 was solved by A.G.Mcewen, P.Poussin-Courmontagne, J.Osz, N.Rochel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.093 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.286, 44.327, 63.915, 90.00, 98.95, 90.00
R / Rfree (%)	16.73 / 22.7

The structure of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Zinc	(Zn)	4 atoms

The binding sites of Potassium atom in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element (pdb code 4cn5). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element, PDB code: 4cn5:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ C:K1018 b:29.8 occ:1.00 O C:HOH2046 2.8 33.3 1.0 O2 C:DT13 2.8 20.2 1.0 O C:HOH2048 2.8 36.6 1.0 O4' C:DC14 2.8 25.6 1.0 O2 C:DC14 3.0 25.7 1.0 C4' C:DC14 3.5 28.7 1.0 C1' C:DC14 3.7 23.8 1.0 O D:HOH2017 3.7 24.8 1.0 C2 C:DC14 3.8 17.9 1.0 C2 C:DT13 3.8 18.5 1.0 O D:HOH2014 4.1 35.1 1.0 N1 C:DC14 4.1 18.9 1.0 C5' C:DC14 4.1 30.7 1.0 C2 D:DA5 4.2 15.4 1.0 N2 D:DG4 4.3 20.9 1.0 O D:HOH2010 4.3 34.0 1.0 C1' C:DT13 4.4 22.7 1.0 N1 C:DT13 4.5 18.0 1.0 O C:HOH2044 4.5 42.6 1.0 N3 C:DT13 4.8 19.2 1.0 N3 C:DC14 4.8 18.3 1.0 N3 D:DA5 4.8 22.7 1.0 C3' C:DC14 4.8 26.8 1.0 C2' C:DT13 5.0 21.0 1.0 N1 D:DA5 5.0 14.9 1.0

Potassium binding site 2 out of 4 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ C:K1019 b:32.1 occ:1.00 O2 C:DT6 2.7 32.8 1.0 O C:HOH2064 2.7 37.6 1.0 O C:HOH2018 2.8 31.6 1.0 O2 C:DC7 2.9 27.6 1.0 O4' C:DC7 3.0 27.7 1.0 O C:HOH2016 3.1 44.0 1.0 O C:HOH2065 3.3 53.9 1.0 C2 C:DC7 3.7 30.3 1.0 C2 C:DT6 3.8 30.6 1.0 C4' C:DC7 3.8 32.1 1.0 C1' C:DC7 3.8 26.4 1.0 N1 C:DC7 4.1 28.8 1.0 O C:HOH2013 4.2 51.7 1.0 C1' C:DT6 4.3 33.9 1.0 N2 D:DG11 4.3 25.2 1.0 C2 D:DA12 4.5 23.8 1.0 N1 C:DT6 4.5 31.1 1.0 O D:HOH2028 4.5 31.4 1.0 C5' C:DC7 4.5 31.0 1.0 O C:HOH2067 4.6 42.0 1.0 N3 C:DC7 4.6 27.8 1.0 N3 C:DT6 4.7 26.5 1.0 C2' C:DT6 4.8 31.6 1.0 O D:HOH2030 4.9 24.0 1.0 C3' C:DC7 5.0 32.1 1.0

Potassium binding site 3 out of 4 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ C:K1020 b:48.8 occ:1.00 O6 C:DG9 2.8 22.3 1.0 O C:HOH2033 2.9 42.1 1.0 N7 C:DA8 3.0 21.9 1.0 O C:HOH2025 3.0 25.4 1.0 O C:HOH2034 3.1 36.9 1.0 O C:HOH2023 3.2 44.2 1.0 C6 C:DG9 3.7 25.4 1.0 C8 C:DA8 3.8 24.9 1.0 N7 C:DG9 3.9 20.2 1.0 O C:HOH2072 3.9 52.7 1.0 C5 C:DA8 4.0 26.6 1.0 C5 C:DG9 4.1 25.7 1.0 O C:HOH2066 4.1 44.5 1.0 O C:HOH2022 4.1 43.0 1.0 N6 C:DA8 4.1 24.4 1.0 N4 D:DC9 4.5 20.9 1.0 C6 C:DA8 4.5 20.4 1.0 O D:HOH2025 4.8 31.2 1.0 O4 D:DT8 4.8 23.8 1.0 C2' C:DC7 4.8 28.4 1.0 O C:HOH2075 4.8 53.5 1.0 N1 C:DG9 4.9 17.5 1.0 N9 C:DA8 5.0 23.6 1.0

Potassium binding site 4 out of 4 in the Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of the Human Retinoid X Receptor Dna- Binding Domain Bound to the Human NR1D1 Response Element within 5.0Å range: probe atom residue distance (Å) B Occ D:K1018 b:19.2 occ:1.00 O B:HOH2064 2.6 44.5 1.0 O2 D:DT10 2.7 20.9 1.0 O D:HOH2027 2.8 28.1 1.0 O1 D:NO31019 2.9 26.1 1.0 O C:HOH2027 2.9 16.0 1.0 O4' D:DG11 2.9 18.3 1.0 O3 D:NO31019 3.0 34.9 1.0 N D:NO31019 3.3 18.3 1.0 C4' D:DG11 3.7 14.5 1.0 N3 D:DG11 3.8 18.2 1.0 C2 D:DT10 3.9 18.0 1.0 C1' D:DG11 4.0 21.2 1.0 C4 D:DG11 4.2 19.5 1.0 C5' D:DG11 4.2 12.2 1.0 O C:HOH2031 4.3 17.2 1.0 O B:HOH2078 4.3 35.8 1.0 N9 D:DG11 4.3 18.3 1.0 N2 C:DG9 4.4 16.4 1.0 C2 C:DA8 4.4 19.8 1.0 C1' D:DT10 4.4 19.2 1.0 O D:HOH2037 4.5 35.3 1.0 O C:HOH2026 4.5 24.9 1.0 C2 D:DG11 4.5 23.3 1.0 O2 D:NO31019 4.6 29.1 1.0 N1 D:DT10 4.7 17.1 1.0 N2 D:DG11 4.8 25.2 1.0 N3 D:DT10 4.8 21.1 1.0 C3' D:DG11 5.0 15.3 1.0

J.Osz, A.G.Mcewen, P.Poussin-Courmontagne, E.Moutier, C.Birck, I.Davidson, D.Moras, N.Rochel. Structural Basis of Natural Promoter Recognition By the Retinoid X Nuclear Receptor. Sci.Rep. V. 5 8216 2015.
ISSN: ISSN 2045-2322
PubMed: 25645674
DOI: 10.1038/SREP08216