Square Antiprismatic Chelation Is a Key Determinant for Potassium Ion Selectivity

DESCRIPTION

The datasets and tables below correspond to the article  "Square Antiprismatic Chelation Is a Key Determinant for Potassium Ion Selectivity" (https://doi.org/10.1016/j.ijbiomac.2025.140690). See the "Methods" section in the original paper for details.

DATASETS

Files presented here are archives KDB.tar.gz, MEMB_DB.tar.gz and PDB70.tar.gz. 

Archives KDB.tar.gz, MEMB_DB.tar.gz and PDB70.tar.gz contain the results of K+-binding sites scanning in datasets 1–3, respectively. Each subfolder, named according to the PDB ID, contains the following files:

.pdb — the original pdb file, which in many cases was modified by reconstruction of the molecular ensemble and removal of heteroatoms;

.ref — a subset of the structure file (in pdb format) with atoms extracted for scanning (basically, all oxygen and side chain nitrogen atoms of lysines (Nζ) and histidines (Nδ and Nε) according to the algorithm plot presented in Fig. 1);

_COMBS.txt — combinations of atoms (octets) that were used for superposition with the solvated K+ template and RMSD calculation;

_alignment_X.pdb — the solvated K+ template, aligned to the matching protein atoms. X is the serial number of the alignment. Alignment is performed only if RMSD ⩽ 1.25 Å;

_site_X.pdb — corresponding protein atoms with original numbering and chain/residue hierarchy;

_RES.txt — parameters of all the alignments found: octets of atoms and corresponding RMSD value;

_RMSD.log — RMSD values for the corresponding site number.

SUPPLEMENTARY TABLES S1-S5

Tables S1–S5 come from the original paper. Tables S1, S3, and S4 describe K+-binding sites in K+-channels (dataset 1), other K+-transport proteins and Na+/K+-ATPases, respectively. Tables S2 and S5 describe the identified K+-binding sites in other MPs (dataset 2) and a representative set (10% of the PDB70 database) of non-MPs (dataset 3), respectively.