Structure-based sequence alignment of seven KH domains of high structural similarity to αCP1-KH3

Copyright information:Taken from "Structure and RNA binding of the third KH domain of poly(C)-binding protein 1"Nucleic Acids Research 2005;33(4):1213-1221.Published online 24 Feb 2005PMCID:PMC549569.© The Author 2005. Published by Oxford University Press. All rights reserved Each KH domain was structurally aligned using LSQMAN () against αCP1-KH3. Amino acid residues with α-carbon positions within 3.5 Å of a corresponding αCP1-KH3 residue are shown in black. Highlighted in purple are the amino acid residues that do not align well with residues of αCP1-KH3. Secondary structural elements, as defined in Lewis ., () are shown above the corresponding sequence in cartoon form. Parenthesized numbers represent the amino acid numbers at the start and finish of the superimposed core region for each structure, and indicate the extent of the structure used to calculate sequence identity with αCP1-KH3 (final column). The GXXG motif and the variable loop regions are blocked with grey. Amino acid residues reported to make contact with the oligonucleotide [in the cases of structures determined in complex with either RNA or ssDNA (–)] are highlighted in red, and the αCP1-KH3 predicted to make contact with oligonucleotide in the current study are highlighted in tan. NMR structures were structurally aligned on the basis of the first chain in the deposited PDB coordinate file and all were deemed to be representative of the set of structures.