Silver in PDB 7sdq: [Mc:Ag+:U] Metal-Mediated Dna Base Pair in A Self-Assembling Rhombohedral Lattice

The structure of [Mc:Ag+:U] Metal-Mediated Dna Base Pair in A Self-Assembling Rhombohedral Lattice, PDB code: 7sdq was solved by B.Lu, S.Vecchioni, N.C.Seeman, R.Sha, Y.P.Ohayon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.65 / 4.30
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	105.465, 105.465, 93.608, 90, 90, 120
R / Rfree (%)	20 / 20.9

The binding sites of Silver atom in the [Mc:Ag+:U] Metal-Mediated Dna Base Pair in A Self-Assembling Rhombohedral Lattice (pdb code 7sdq). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 2 binding sites of Silver where determined in the [Mc:Ag+:U] Metal-Mediated Dna Base Pair in A Self-Assembling Rhombohedral Lattice, PDB code: 7sdq:
Jump to Silver binding site number: 1; 2;

Silver binding site 1 out of 2 in the [Mc:Ag+:U] Metal-Mediated Dna Base Pair in A Self-Assembling Rhombohedral Lattice


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of [Mc:Ag+:U] Metal-Mediated Dna Base Pair in A Self-Assembling Rhombohedral Lattice within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag101 b:249.7 occ:1.00 N3 B:DU4 2.1 223.8 1.0 N3 A:5CM12 2.1 244.9 1.0 N4 A:5CM12 2.6 262.6 1.0 O2 B:DU4 2.6 229.5 1.0 C4 A:5CM12 2.7 244.6 1.0 C2 B:DU4 2.8 230.5 1.0 N1 B:DA3 3.3 219.8 1.0 C2 A:5CM12 3.3 234.3 1.0 C4 B:DU4 3.4 225.5 1.0 O2 A:5CM12 3.6 239.9 1.0 C2 B:DA5 3.6 232.5 1.0 C2 B:DA3 3.6 226.5 1.0 N3 B:DA5 3.8 223.8 1.0 N3 A:DT13 3.8 223.8 1.0 O4 B:DU4 3.8 225.3 1.0 C6 B:DA3 3.9 219.5 1.0 AG B:AG102 4.0 119.9 0.6 C5 A:5CM12 4.1 230.3 1.0 C2 A:DT13 4.1 227.7 1.0 O2 A:DT13 4.2 246.2 1.0 N1 B:DA5 4.2 237.7 1.0 N1 B:DU4 4.2 238.7 1.0 N6 B:DA3 4.2 213.2 1.0 C4 A:DT13 4.4 204.5 1.0 N3 B:DA3 4.4 233.4 1.0 N1 A:5CM12 4.5 215.5 1.0 C4 B:DA5 4.5 231.3 1.0 O4 A:DT13 4.6 204.5 1.0 C5 B:DA3 4.7 226.3 1.0 C5 B:DU4 4.7 233.4 1.0 C6 A:5CM12 4.8 215.8 1.0 C4 B:DA3 4.8 232.8 1.0 C6 B:DA5 5.0 231.7 1.0 N1 A:DT13 5.0 208.6 1.0

Silver binding site 2 out of 2 in the [Mc:Ag+:U] Metal-Mediated Dna Base Pair in A Self-Assembling Rhombohedral Lattice


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of [Mc:Ag+:U] Metal-Mediated Dna Base Pair in A Self-Assembling Rhombohedral Lattice within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag102 b:119.9 occ:0.62 O4 B:DU4 2.1 225.3 1.0 N4 A:5CM12 2.2 262.6 1.0 N6 B:DA3 2.7 213.2 1.0 C4 B:DU4 3.1 225.5 1.0 O4 A:DT11 3.3 277.0 1.0 C6 B:DA3 3.4 219.5 1.0 N3 B:DU4 3.5 223.8 1.0 C4 A:5CM12 3.6 244.6 1.0 C4 A:DT11 3.9 261.7 1.0 C5 B:DA3 3.9 226.3 1.0 AG B:AG101 4.0 249.7 1.0 N7 B:DA3 4.1 228.2 1.0 N1 B:DA3 4.2 219.8 1.0 C5A A:5CM12 4.2 241.1 1.0 C5 B:DU4 4.3 233.4 1.0 C5 A:5CM12 4.4 230.3 1.0 C7 A:DT11 4.4 262.3 1.0 N1 B:DA5 4.4 237.7 1.0 C5 A:DT11 4.5 258.7 1.0 N3 A:5CM12 4.5 244.9 1.0 N3 A:DT11 4.7 253.0 1.0 C2 B:DA5 4.7 232.5 1.0 O4 A:DT13 4.8 204.5 1.0

S.Vecchioni, B.Lu, R.Sha, Y.P.Ohayon, J.Yoder, K.Woloszyn, W.Bernfeld, W.Hendrickson, L.Rothschild, C.Mao, S.Wind, N.C.Seeman. Metal-Mediated Dna Nanotechnology in 3D: Reengineering the Semantomorphic Alphabet To Be Published.