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Each of the two homodimers shown here consists of five beta-strands, two relatively long alpha-helices, and several shorter alpha-or 310 helices.
For AaFd4, the overal beta-strand order from N to C terminus is 2-1-3-4-5 in which strands 3 and 5 are anti-parallel to the other three strands.
Chain A (109 residues) and chain B (110 residues) are nearly identical except for two regions. Both include a 5 stranded beta-sheet, 6 helices, 2 beat bulges, 2 beta hairpins, a beta alpha beta unit, and a psi-loop. One difference is the extended surface loop connecting beta-strand 1 to alpha-helix 1. The other difference is in residues 35 through 47. The secondary structure in this region is 310 helix for chain A and alpha-helix for chain B.
The interactions involving hydrogen bonds form the alpha-helices and hold the beta sheets next to each other. No disulfide bridges exist in AaFd4.
These interfacial residues are involved in dimer interactions.
The dimer interactions are mediated by 2-fold symmetric hydrogen bonds between the beta 2 strands. Also apolar contacts among sidechains of Phe3, His5, Phe7, Val49, Pro52, Gly54, Tyr68, Gly104, Lys105, and Pro106 mediate the dimer interactions.
Buried residues at the interface include 810 square angstroms of surface area per subunit.
Each of the two [2Fe-2S] clusters contains 2 iron atoms and 2 sulfide ions.
The clusters are located near the protein surface between two loop regions: (1)the loop between beta-strand 1 and alpha-helix 1 and (2)the loop between beta-strands 2 and 3.
The center-to-center destance between the two clusters is about 21 angstroms.
The cluster sulfide ions are possibly hydrogen bonded with average N-S bond distances of less than 3.8 angstroms. These hydrogen bonds could exist between the N(eta1) atom of Arg13 and S1, between the amide hydrogen atom of Cys22 and S1, and between S2 and the amide hydrogen atoms of Met56, Asn57, Ala58, and Cys59.
Four cysteine residues ligate the [2Fe-2S] clusters to the protein through sulfur atoms.
The four cysteine residues are located near the ends of two surface loops.
The sidechains of Cys9 and Cys22 coordinate Fe-1 of the cluster. The sidechains of Cys55 and Cys59 coordinate Fe-2 of the cluster. Fe-2 is more solvent accessible and more reducible.
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AaFd4 contains a relatively large number of proline residues with 11, and these residues are known to increase thermal stability because of cis-/trans-isomerization when located in strategic positions.