Potassium in PDB 3ut9: Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L)

The structure of Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L), PDB code: 3ut9 was solved by E.Y.D.Chua, D.Vasudevan, G.E.Davey, B.Wu, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.55 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.494, 109.533, 174.822, 90.00, 90.00, 90.00
R / Rfree (%)	25.7 / 28.9

The structure of Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) also contains other interesting chemical elements:

Manganese	(Mn)	29 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Potassium atom in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) (pdb code 3ut9). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L), PDB code: 3ut9:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L)


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 Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) within 5.0Å range: probe atom residue distance (Å) B Occ I:K1052 b:0.4 occ:1.00 O2 I:DT-26 3.0 0.1 1.0 O4' I:DA-25 3.5 0.3 1.0 C4' I:DA-25 3.9 0.2 1.0 O4' J:DA28 4.0 0.5 1.0 C2 I:DT-26 4.1 0.2 1.0 N2 J:DG27 4.3 0.8 1.0 C1' I:DA-25 4.3 0.5 1.0 N3 I:DA-25 4.4 0.8 1.0 C4' J:DA28 4.4 0.8 1.0 C2 J:DA26 4.5 0.5 1.0 C1' I:DT-26 4.6 0.9 1.0 C5' I:DA-25 4.7 0.6 1.0 C1' J:DA28 4.8 0.0 1.0 N1 I:DT-26 4.8 0.5 1.0 N3 J:DG27 4.8 0.8 1.0 N9 I:DA-25 4.9 0.0 1.0 C4 I:DA-25 4.9 0.1 1.0 N1 J:DA26 5.0 0.5 1.0 O3' I:DA-25 5.0 0.3 1.0 N3 I:DT-26 5.0 0.1 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L)


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 Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) within 5.0Å range: probe atom residue distance (Å) B Occ J:K1051 b:83.1 occ:1.00 O2 J:DT-26 3.0 83.8 1.0 O4' J:DA-25 3.3 74.6 1.0 C4' J:DA-25 3.6 74.5 1.0 C5' J:DA-25 4.1 75.7 1.0 C2 J:DT-26 4.2 84.4 1.0 O4' I:DA28 4.2 74.7 1.0 C2 I:DA26 4.3 85.1 1.0 C1' J:DA-25 4.4 74.3 1.0 N3 J:DA-25 4.4 74.9 1.0 N2 I:DG27 4.6 78.8 1.0 C4' I:DA28 4.6 74.2 1.0 C1' J:DT-26 4.7 83.6 1.0 N1 I:DA26 4.9 85.0 1.0 O4' J:DG-24 4.9 75.0 1.0 N1 J:DT-26 4.9 83.9 1.0 C3' J:DA-25 4.9 73.8 1.0 N9 J:DA-25 5.0 74.4 1.0 C4 J:DA-25 5.0 75.1 1.0 C5' J:DG-24 5.0 74.9 1.0

E.Y.D.Chua, D.Vasudevan, G.E.Davey, B.Wu, C.A.Davey. The Mechanics Behind Dna Sequence-Dependent Properties of the Nucleosome Nucleic Acids Res. V. 40 6338 2012.
ISSN: ISSN 0305-1048
PubMed: 22453276
DOI: 10.1093/NAR/GKS261