Recently, I became aware of the metallo-base pairs, such as T-Hg-T (PDB id: 4l24) and C-Ag-C (5ay2) from the work of Kondo et al (Pubmed: 24478025 and 26448329). As of v1.4.3-2015oct23, DSSR can detect such metallo-bps automatically, as shown below:
# x3dna-dssr -i=4l24.pdb -o=4l24.out
List of 12 base pairs
nt1 nt2 bp name Saenger LW DSSR
1 A.DC1 B.DG24 C-G WC 19-XIX cWW cW-W
2 A.DG2 B.DC23 G-C WC 19-XIX cWW cW-W
3 A.DC3 B.DG22 C-G WC 19-XIX cWW cW-W
4 A.DG4 B.DC21 G-C WC 19-XIX cWW cW-W
5 A.DA5 B.DT20 A-T WC 20-XX cWW cW-W
6 A.DT6 B.DT19 T-T Metal n/a cWW cW-W
7 A.DT7 B.DT18 T-T Metal n/a cWW cW-W
8 A.DT8 B.DA17 T-A WC 20-XX cWW cW-W
9 A.DC9 B.DG16 C-G WC 19-XIX cWW cW-W
10 A.DG10 B.DC15 G-C WC 19-XIX cWW cW-W
11 A.DC11 B.DG14 C-G WC 19-XIX cWW cW-W
12 A.DG12 B.DC13 G-C WC 19-XIX cWW cW-W
and
# x3dna-dssr -i=5ay2.pdb -o=5ay2.out
List of 24 base pairs
nt1 nt2 bp name Saenger LW DSSR
1 A.G1 B.C12 G-C WC 19-XIX cWW cW-W
2 A.G2 B.C11 G-C WC 19-XIX cWW cW-W
3 A.A3 B.U10 A-U WC 20-XX cWW cW-W
4 A.C4 B.C9 C-C Metal n/a cWW cW-W
5 A.U5 B.A8 U-A WC 20-XX cWW cW-W
6 A.CBR6 B.G7 c-G WC 19-XIX cWW cW-W
7 A.G7 B.CBR6 G-c WC 19-XIX cWW cW-W
8 A.A8 B.U5 A-U WC 20-XX cWW cW-W
9 A.C9 B.C4 C-C Metal n/a cWW cW-W
10 A.U10 B.A3 U-A WC 20-XX cWW cW-W
11 A.C11 B.G2 C-G WC 19-XIX cWW cW-W
12 A.C12 B.G1 C-G WC 19-XIX cWW cW-W
13 C.G1 D.C12 G-C WC 19-XIX cWW cW-W
14 C.G2 D.C11 G-C WC 19-XIX cWW cW-W
15 C.A3 D.U10 A-U WC 20-XX cWW cW-W
16 C.C4 D.C9 C-C Metal n/a cWW cW-W
17 C.U5 D.A8 U-A WC 20-XX cWW cW-W
18 C.CBR6 D.G7 c-G WC 19-XIX cWW cW-W
19 C.G7 D.CBR6 G-c WC 19-XIX cWW cW-W
20 C.A8 D.U5 A-U WC 20-XX cWW cW-W
21 C.C9 D.C4 C-C Metal n/a cWW cW-W
22 C.U10 D.A3 U-A WC 20-XX cWW cW-W
23 C.C11 D.G2 C-G WC 19-XIX cWW cW-W
24 C.C12 D.G1 C-G WC 19-XIX cWW cW-W
Note the name “Metal” for the metallo-bps. Moreover, the corresponding entries in the ‘dssr-pairs.pdb’ file also include the metal ions, as shown below:
It is worth noting that in a metallo-bp, the metal ion lies approximately in the bp plane. Moreover, it is in the middle of the two bases, which would otherwise not form a pair in the conventional sense.
