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The structural motif discovery method presented herein is general and can be …


Biology Articles » Biochemistry » Protein Biochemistry » Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites » Figures

Figures
- Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites

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Figure 1. Zn-binding site structural motifs derived from the structural alphabet representation of 3 Zn-finger proteins. For each protein, the PDB entry and chain is given, followed below by its amino acid sequence (in capital letters), aligned with the corresponding structural alphabet representation (lower-case letters); 'Z', means a letter cannot be assigned to this residue (see Methods). Zn2+-binding residues are underlined and in bold. Only the first 30 amino acid residues are shown. The Cα root-mean-square deviation RMSD of 1LAT and 2NLL from 1HCQ are 1.73 and 1.33 Å, respectively, whereas that of 1LAT from 2NLL is 1.25 Å.

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Figure 2. The percentage letter frequency distributions of first-shell amino acid residues (gray), second-shell amino acid residues (white), and all amino acid residues (black) in the Mg2+-proteins. There is a total of 25,406 amino acid residues in the Mg2+-proteins, of which 250 are in the first shell, while 898 are in the second shell

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Figure 3. The percentage secondary structure frequency distributions of first-shell amino acid residues (gray), second-shell amino acid residues (white), and all amino acid residues (black) in the Mg2+-proteins. The amino acid residues found in α-helices, β-strands, or loops are according to the secondary structure information in the PDB files.

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Figure 4. The conserved local structures of the 4 Mg2+-structural motifs. (a) e(24–47)h(24)k, (b) f(1)h(109–349)b, (c) f(2)h(126–158)m, and (d) k(26–29)h(1)a.

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Figure 5. The conserved binding site of 2 nonhomologous Mg2+-proteins. (a) Cartoon diagram of the metal-binding domain in N-acylamino acid racemase (1SJC). (b) Cartoon diagram of the metal-binding domain in gamma enolase (2AKZ). (c) Superposition of the first-shell structural letters of 1SJC (blue) and 2AKZ (yellow).

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Figure 6. Conversion of the 3D protein backbone into a 1D structural alphabet representation. The first 2 and the last 2 residues are assigned 'Z', meaning a letter cannot be assigned at these residues. The first valid assignment is 'd', at Val 3 and spanning residues 1 to 5. The next is assigned to Asp 4 and spans residues 2 to 6.

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