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

The structure of [C:Ag+:C] Metal-Mediated Dna Base Pair in A Self-Assembling Rhombohedral Lattice, PDB code: 7sdg was solved by S.Vecchioni, B.Lu, 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)	32.38 / 3.63
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	105.984, 105.984, 90.264, 90, 90, 120
R / Rfree (%)	18.8 / 20.7

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

Silver binding site 1 out of 2 in the [C:Ag+:C] 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 [C:Ag+:C] 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:154.7 occ:0.30 N4 B:DC4 1.9 208.2 1.0 C4 B:DC4 2.8 221.5 1.0 N3 B:DC4 3.0 227.2 1.0 AG B:AG102 3.1 243.5 1.0 N6 B:DA3 3.1 218.3 1.0 O4 A:DT11 3.2 274.1 1.0 N4 A:DC12 3.3 289.4 1.0 C6 B:DA3 3.5 236.4 1.0 N1 B:DA5 3.7 267.9 1.0 N6 B:DA5 3.9 269.6 1.0 C5 B:DA3 3.9 242.0 1.0 C4 A:DT11 4.0 272.6 1.0 N7 B:DA3 4.1 232.9 1.0 C5 B:DC4 4.1 232.9 1.0 C6 B:DA5 4.2 268.9 1.0 N1 B:DA3 4.2 248.2 1.0 C2 B:DC4 4.4 241.3 1.0 C4 A:DC12 4.5 283.4 1.0 C7 A:DT11 4.6 286.6 1.0 C5 A:DT11 4.6 279.3 1.0 C2 B:DA5 4.7 271.5 1.0 N3 A:DT11 4.7 267.0 1.0 C4 B:DA3 4.8 258.3 1.0 N3 A:DC12 4.9 280.6 1.0

Silver binding site 2 out of 2 in the [C:Ag+:C] 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 [C:Ag+:C] 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:243.5 occ:1.00 N3 A:DC12 2.6 280.6 1.0 N3 B:DC4 2.6 227.2 1.0 N4 A:DC12 2.8 289.4 1.0 C2 B:DA5 2.8 271.5 1.0 N1 B:DA5 2.8 267.9 1.0 AG B:AG101 3.1 154.7 0.3 C4 A:DC12 3.1 283.4 1.0 O2 B:DC4 3.1 243.7 1.0 C2 B:DC4 3.3 241.3 1.0 N1 B:DA3 3.4 248.2 1.0 N3 B:DA5 3.7 257.6 1.0 C4 B:DC4 3.7 221.5 1.0 C2 A:DC12 3.7 274.8 1.0 C6 B:DA5 3.8 268.9 1.0 C6 B:DA3 3.8 236.4 1.0 N4 B:DC4 3.9 208.2 1.0 C2 B:DA3 3.9 262.2 1.0 N3 A:DT11 4.0 267.0 1.0 O4 A:DT11 4.0 274.1 1.0 N6 B:DA3 4.0 218.3 1.0 O2 A:DC12 4.0 273.2 1.0 C4 A:DT11 4.2 272.6 1.0 N3 A:DT13 4.2 275.6 1.0 C4 B:DA5 4.4 264.2 1.0 O4 A:DT13 4.4 281.9 1.0 C4 A:DT13 4.4 278.1 1.0 N6 B:DA5 4.4 269.6 1.0 C5 B:DA5 4.5 270.5 1.0 C5 A:DC12 4.5 276.6 1.0 C5 B:DA3 4.6 242.0 1.0 N1 B:DC4 4.6 250.4 1.0 N3 B:DA3 4.7 267.9 1.0 C2 A:DT11 4.8 267.0 1.0 C2 A:DT13 4.8 272.0 1.0 C4 B:DA3 4.9 258.3 1.0 N1 A:DC12 5.0 267.6 1.0 C5 B:DC4 5.0 232.9 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.