We analyzed the coordination structure of G-quadruplexed DNA-heme complex which exhibits remarkably similar spectroscopic characters to hemoprotein such as myoglobin. We found that some exogenous ligands can be accommodated at the 6th coordination site of heme in the G-quadruplexed DNA-heme complex with a DNA base coordinated to the 5th site. The G-quadruplexed DNA-hemin complex is expected to play a role as a novel DNAzyme. These findings provide novel insights into molecular design for creating artificial heme enzymes using spontaneous assembly between G-quadruplexed DNA and heme.