Zr3Cu4Si6 crystallizes in the monoclinic C2/m space group. There are two inequivalent Zr sites. In the first Zr site, Zr(1) is bonded in a 16-coordinate geometry to eight equivalent Cu(1) and eight equivalent Si(2) atoms. In the second Zr site, Zr(2) is bonded to four equivalent Cu(1), four equivalent Si(1), and four equivalent Si(3) atoms to form distorted ZrCu4Si8 cuboctahedra that share corners with four equivalent Zr(2)Cu4Si8 cuboctahedra, edges with four equivalent Zr(2)Cu4Si8 cuboctahedra, edges with eight equivalent Cu(1)Zr4Cu4Si4 cuboctahedra, faces with four equivalent Zr(2)Cu4Si8 cuboctahedra, and faces with four equivalent Cu(1)Zr4Cu4Si4 cuboctahedra. Cu(1) is bonded to two equivalent Zr(1), two equivalent Zr(2), four equivalent Cu(1), two equivalent Si(2), and two equivalent Si(3) atoms to form CuZr4Cu4Si4 cuboctahedra that share corners with ten equivalent Cu(1)Zr4Cu4Si4 cuboctahedra,  an edgeedge with one Cu(1)Zr4Cu4Si4 cuboctahedra, edges with four equivalent Zr(2)Cu4Si8 cuboctahedra, faces with two equivalent Zr(2)Cu4Si8 cuboctahedra, and faces with eight equivalent Cu(1)Zr4Cu4Si4 cuboctahedra. There are three inequivalent Si sites. In the first Si site, Si(1) is bonded in a 8-coordinate geometry to four equivalent Zr(2) and four equivalent Si(1) atoms. In the second Si site, Si(2) is bonded in a 9-coordinate geometry to four equivalent Zr(1), four equivalent Cu(1), and one Si(2) atom. In the third Si site, Si(3) is bonded in a 8-coordinate geometry to four equivalent Zr(2) and four equivalent Cu(1) atoms.
Zr3Cu4Si6 crystallizes in the monoclinic C2/m space group. There are two inequivalent Zr sites. In the first Zr site, Zr(1) is bonded in a 16-coordinate geometry to eight equivalent Cu(1) and eight equivalent Si(2) atoms. There are four shorter (3.14 Å) and four longer (3.15 Å) Zr(1)-Cu(1) bond lengths. There are two shorter (2.86 Å) and six longer (2.87 Å) Zr(1)-Si(2) bond lengths. In the second Zr site, Zr(2) is bonded to four equivalent Cu(1), four equivalent Si(1), and four equivalent Si(3) atoms to form distorted ZrCu4Si8 cuboctahedra that share corners with four equivalent Zr(2)Cu4Si8 cuboctahedra, edges with four equivalent Zr(2)Cu4Si8 cuboctahedra, edges with eight equivalent Cu(1)Zr4Cu4Si4 cuboctahedra, faces with four equivalent Zr(2)Cu4Si8 cuboctahedra, and faces with four equivalent Cu(1)Zr4Cu4Si4 cuboctahedra. There are two shorter (3.01 Å) and two longer (3.02 Å) Zr(2)-Cu(1) bond lengths. All Zr(2)-Si(1) bond lengths are 2.82 Å. All Zr(2)-Si(3) bond lengths are 2.75 Å. Cu(1) is bonded to two equivalent Zr(1), two equivalent Zr(2), four equivalent Cu(1), two equivalent Si(2), and two equivalent Si(3) atoms to form CuZr4Cu4Si4 cuboctahedra that share corners with ten equivalent Cu(1)Zr4Cu4Si4 cuboctahedra,  an edgeedge with one Cu(1)Zr4Cu4Si4 cuboctahedra, edges with four equivalent Zr(2)Cu4Si8 cuboctahedra, faces with two equivalent Zr(2)Cu4Si8 cuboctahedra, and faces with eight equivalent Cu(1)Zr4Cu4Si4 cuboctahedra. All Cu(1)-Cu(1) bond lengths are 2.63 Å. There is one shorter (2.31 Å) and one longer (2.32 Å) Cu(1)-Si(2) bond length. There is one shorter (2.41 Å) and one longer (2.42 Å) Cu(1)-Si(3) bond length. There are three inequivalent Si sites. In the first Si site, Si(1) is bonded in a 8-coordinate geometry to four equivalent Zr(2) and four equivalent Si(1) atoms. All Si(1)-Si(1) bond lengths are 2.63 Å. In the second Si site, Si(2) is bonded in a 9-coordinate geometry to four equivalent Zr(1), four equivalent Cu(1), and one Si(2) atom. The Si(2)-Si(2) bond length is 2.31 Å. In the third Si site, Si(3) is bonded in a 8-coordinate geometry to four equivalent Zr(2) and four equivalent Cu(1) atoms.