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

The structure of [C:Ag+:T] Metal-Mediated Dna Base Pair in A Self-Assembling Rhombohedral Lattice, PDB code: 7sds 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)	32.67 / 3.70
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	106.361, 106.361, 92.685, 90, 90, 120
R / Rfree (%)	25.9 / 28.8

The binding sites of Silver atom in the [C:Ag+:T] Metal-Mediated Dna Base Pair in A Self-Assembling Rhombohedral Lattice (pdb code 7sds). 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+:T] Metal-Mediated Dna Base Pair in A Self-Assembling Rhombohedral Lattice, PDB code: 7sds:
Jump to Silver binding site number: 1; 2;

Silver binding site 1 out of 2 in the [C:Ag+:T] 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+:T] 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:73.8 occ:0.80 C7 B:DT4 2.1 222.4 1.0 O4 B:DT4 2.2 220.2 1.0 C5 B:DT4 2.8 226.0 1.0 C4 B:DT4 2.8 224.0 1.0 N7 B:DA3 3.4 224.1 1.0 C5 B:DA3 3.6 220.0 1.0 N6 B:DA3 3.8 213.0 1.0 C6 B:DA3 3.8 214.3 1.0 N6 B:DA5 3.9 305.2 1.0 C8 B:DA3 4.0 227.1 1.0 N1 B:DA5 4.1 297.5 1.0 C6 B:DT4 4.1 224.9 1.0 N3 B:DT4 4.2 227.3 1.0 O4 A:DT11 4.2 279.3 1.0 C6 B:DA5 4.3 297.7 1.0 N4 A:DC12 4.3 309.6 1.0 C4 B:DA3 4.4 220.5 1.0 AG B:AG102 4.6 73.8 0.5 N9 B:DA3 4.6 225.9 1.0 N1 B:DA3 4.7 209.2 1.0 C2 B:DA5 5.0 295.2 1.0

Silver binding site 2 out of 2 in the [C:Ag+:T] 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+:T] 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:73.8 occ:0.48 N4 A:DC12 2.0 309.6 1.0 N3 B:DT4 2.1 227.3 1.0 N3 A:DC12 2.1 292.0 1.0 O4 B:DT4 2.4 220.2 1.0 C4 A:DC12 2.4 293.1 1.0 C4 B:DT4 2.6 224.0 1.0 C2 B:DT4 3.3 230.3 1.0 C2 B:DA5 3.3 295.2 1.0 C2 A:DC12 3.4 273.4 1.0 O2 B:DT4 3.6 232.3 1.0 N1 B:DA3 3.6 209.2 1.0 N3 B:DA5 3.7 279.7 1.0 C5 A:DC12 3.8 276.7 1.0 N1 B:DA5 3.9 297.5 1.0 N3 A:DT13 3.9 326.9 1.0 C2 B:DA3 4.0 211.3 1.0 O2 A:DC12 4.0 269.9 1.0 C5 B:DT4 4.0 226.0 1.0 C6 B:DA3 4.2 214.3 1.0 C2 A:DT13 4.3 320.2 1.0 O2 A:DT13 4.4 330.2 1.0 N1 B:DT4 4.4 229.0 1.0 C4 B:DA5 4.4 286.5 1.0 C4 A:DT13 4.5 316.3 1.0 N6 B:DA3 4.5 213.0 1.0 N1 A:DC12 4.5 257.1 1.0 AG B:AG101 4.6 73.8 0.8 C6 B:DA5 4.6 297.7 1.0 C6 A:DC12 4.6 259.9 1.0 C6 B:DT4 4.7 224.9 1.0 O4 A:DT13 4.7 322.4 1.0 N3 A:DT11 4.7 252.2 1.0 N3 B:DA3 4.8 218.5 1.0 O4 A:DT11 4.8 279.3 1.0 C5 B:DA5 4.9 294.7 1.0 C5 B:DA3 4.9 220.0 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.