## 2 Materials and Methods  
### Data  
We selected two ferredoxin structures (FdI and FdII) from the Protein Data Bank (PDB) [20; 21]. Biological assemblies of these proteins are homodimeric (as assigned by their authors) with cyclic complex symmetry. Both molecules belong to the same CATH homologous superfamily 3.30.70.20 [22; 23], the alpha-beta plaits. We also accessed two other PDB structures for comparative analysis in Section 3.8: a globular, monomeric type III antifreeze protein and a symmetric, homodimeric complex of Rad50 domains from Me11--helix hairpins involved in chromosomal maintenance. Basic information of all four molecules summarized in Table 1 while their 3D presentation is available in Figure 1.  
The structure of Ferredoxin I (FdI, PDB code: 1 FXR [24], Figure 1a) is a homodimer with 64 amino acids and one [4F4S] cluster in each chain. These ligands are located in pockets located at opposite sides of the symmetric complex. Each ligand interacts with 11 residues from the chain, detected in accordance with PDBsum atom distance criterion for non-bonded contacts [28; 29] (two residues are assumed to be in contact if there is at least one pair of non-hydrogen atoms--one from each residue--with Euclidean distance not greater than 3.9 A). Among these residues are four cysteines (C11, C14, C17 and C54), experimentally determined to coordinate the iron-sulfur cluster. \begin{table}
\begin{tabular}{c c c c c c c} \hline \hline
**Protein** & **PDB Code** & **Organism** & **Quaternary** & **Chain** & **Ligand** & **CATH** & **Ref.** \\ \hline Ferredoxin I (FdI) & 1 FXR & _Desulfovibrio grieans_ & homodimer, & 64 aa & [4F4S] & 3.30.70.20 & [24] \\ Ferredoxin II (FdII) & 1 FXD & _Desulfovibrio grieans_ & symmetric & 58 aa & [3F4S] & 3.30.70.20 & [25] \\ Antifreeze type III (AFP) & 9 MSI & _Maczoances americanus_ & monomer & 66 aa & none & 3.90.1210.10 & [26] \\ Rad50 domain & 118D & _Pyrocccus furiosus_ & homodimer, & 103 aa & Hg\({}^{2*}\) & 1.10.287.510 & [27] \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Protein structures under consideration. Figure 1: 3D presentation of structures under consideration: FdI (1 FXR) **(a)**, FdII (1 FXD) **(b)**, type III AFP (9 MSI) (c) and Rad50 domain (1L8D) (d). Green segments on (**a,b**) denote residues engaged in non-bonded interaction with the ligand (atomic distance within 3.9 Å), with its coordinating cysteines shown in lighter color (lime). Purple segments and lines on (**a,b,d**) mark the location of protein–protein interface (also within 3.9 Å distance). The single disulfide bond in FdII (C18-C42) is shown on (**b**) as brown sticks. Violet/blue segments on (**d**) correspond to Pfam coiled-coil zn region in Rad50 (residues 423–474). The structure of Ferredoxin II (FdII, PDB code: 1 FXD [25], Figure 1b) is a 58 amino acid monomer, although it is isolated as a tetramer (according to [PERSON] et al., \"there are four molecules in the unit cell, but it is apparent from an examination of the crystal packing interactions that their arrangement is unlikely to be relevant to tetramer formation\" [25]). PDB file data of 1 FXD provides symmetry operators in REMARK 350, application of which results in a perfectly symmetric homodimeric complex. A single [3F4S] cluster is present in each chain, involved in non-bonded contacts with 10 residues. Ligand coordination is handled by C8, C14 and C50. The fact that FdI is bound to the cluster by four cysteines, and FdII by three, has already been described [9]. The structure of type III antifreeze protein (PDB code: 9 MSI [26], Figure 1c) is a 66 amino acid monomer with no partner molecules present along its structure. The structure of Rad50 domain (PDB code: 1L8D [27], Figure 1d) is a component of the Mre11-Rad50-Nbs1 complex, which plays role in several DNA-related processes. Unlike the other three proteins presented here, it assumes the form of a long coiled coil, limited in the PDB file to the neighborhood of a hook-shaped region in the middle of its sequence.