Analysis of cryoEM-resolved MAP and predicted Zn ²⁺ binding sites on microtubules. (A and B) 3D protein model of cryo-EM microtubule reconstructions (PDB ID: 6EVY), with 6 tubulin dimers shown across three protofilaments (red boxes from inset schematic). (A) Amino acids of α-tubulin (light gray) and β-tubulin (dark gray) are color-coded to represent which MAPs directly interact at that residue as calculated by the Protein-Ligand Interaction Profiler (PLIP) from cryo-EM reconstruction models for DCX (PDB ID: 6REV), tau (PDB ID: 6CVN), kinesin microtubule binding domain (“KinMTBD,” PDB ID: 3J8X), and dynein microtubule binding domain (“DynMTBD,” PDB ID: 6RZB). (B) Tubulin amino acids are color coded to represent predicted Zn²⁺-binding sites (red = high score, yellow = moderate score, light gray = low score) as calculated by the MIB Server (see Materials and methods) (Lin et al., 2016). Insets (i) in each black box show the amino acids on or near helix 12 of α-tubulin that interact directly with the color-coded MAPs (A) or that are predicted Zn²⁺ binding residues (B). (ii) Predicted Zn²⁺ binding site between H192, E420, and D424. Dotted lines represent 2–3 Å distances between the predicted Zn²⁺ binding residues and the Zn²⁺ ion (gray). (C and D) Zn²⁺-binding prediction scores of α-tubulin (C) and β-tubulin (D) amino acid residues within 5 Å of the residues that interact with the indicated MAPs. “X” indicates residues that directly interact with the specified MAP. Bolded residue names for amino acids that are shown in (Bii).