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Co vs Mg

Download Co vs Mg

 

This algorithm is for the estimation of the possibility of Mg2+ cations replacement by Co2+ cations in 3D structures of proteins.

The algorithm works with PDB file containing results of X-Ray crystallographic analysis.

The algorithm works if comma is used as a decimal symbol by MS Excel.

 

Instructions

Open up PDB file by any text editor and copy all its lines that start from "ATOM" to the "Input" list.

Copy just those lines that describe amino acid residues from the same chain (for example, chain A).

Better delete lines that start from "ANISOU" from your input by the way of sorting.

Delete remaining lines of the previous file from the "Input" list.

Copy the lines with information on atoms of Mg2+ cations after the lines with information on atoms of proteins.

Lines with information on atoms of cations start from "HETATM".

Determine secondary structure of the protein with the help of DSSP program (https://www3.cmbi.umcn.nl/xssp/).

Copy the lines describing the chain of interest into the list "DSSP".

Delete remaining lines of the previous file from the "DSSP" list.

On the "Output" list one should type the number of a cation in a designated cell (for example, if there are 2 cations in a protein, first type "1" and see interactions the information on the first cation, then type "2" and see the information on the second cation).

Results

On the "Output" list one will see the table that shows: the number of a binding residue in PDB structure, the name of amino acid residue in three letter code, is it situated in β -5 0 specific motif or not (+/-), the element of secondary structure it is included in, the linear motif of secondary structure it is included in.

The algorithm considers that a given amino acid residue makes a contact with a cation in case if that cation is situated at the distance of less than 5 Angstrom from any atom of a given amino acid residue.

In a central cell of the "Output" list an information on the specificity of the inner sphere of a complex for Mg2+ and Co2+ cations appears, as well as an information on the suitability of the outer sphere of a complex for those cations.

 

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