Sodium in PDB 6m5b: X-Ray Crystal Structure of Cyclic-Pip and Dna Complex in A Reverse Binding Orientation

The structure of X-Ray Crystal Structure of Cyclic-Pip and Dna Complex in A Reverse Binding Orientation, PDB code: 6m5b was solved by K.Abe, Y.Hirose, H.Eki, K.Takeda, T.Bando, M.Endo, H.Sugiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.07 / 1.50
Space group	I 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	82.235, 82.235, 82.235, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 18.9

The structure of X-Ray Crystal Structure of Cyclic-Pip and Dna Complex in A Reverse Binding Orientation also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Magnesium	(Mg)	1 atom

The binding sites of Sodium atom in the X-Ray Crystal Structure of Cyclic-Pip and Dna Complex in A Reverse Binding Orientation (pdb code 6m5b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Crystal Structure of Cyclic-Pip and Dna Complex in A Reverse Binding Orientation, PDB code: 6m5b:

Sodium binding site 1 out of 1 in the X-Ray Crystal Structure of Cyclic-Pip and Dna Complex in A Reverse Binding Orientation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of Cyclic-Pip and Dna Complex in A Reverse Binding Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:29.8 occ:1.00 O A:HOH241 2.4 38.6 1.0 O4 A:S7E101 2.4 19.6 1.0 O A:HOH242 2.5 30.1 1.0 O5 A:S7E101 2.8 26.4 1.0 O A:HOH233 3.4 32.7 1.0 C22 A:S7E101 3.6 19.6 1.0 C26 A:S7E101 3.6 23.0 1.0 C30 A:S7E101 3.8 20.1 1.0 N23 A:S7E101 4.2 21.1 1.0 C31 A:S7E101 4.3 18.3 1.0 N13 A:S7E101 4.3 20.0 1.0 C49 A:S7E101 4.5 20.8 1.0 N12 A:S7E101 4.5 20.1 1.0 C51 A:S7E101 4.6 21.7 1.0

K.Abe, Y.Hirose, H.Eki, K.Takeda, T.Bando, M.Endo, H.Sugiyama. X-Ray Crystal Structure of A Cyclic-Pip-Dna Complex in the Reverse-Binding Orientation. J.Am.Chem.Soc. V. 142 10544 2020.
ISSN: ESSN 1520-5126
PubMed: 32401492
DOI: 10.1021/JACS.0C03972