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

The structure of [Iu:Ag+:C] Metal-Mediated Dna Base Pair in A Self-Assembling Rhombohedral Lattice, PDB code: 7sdo 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)	32.37 / 3.62
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	105.823, 105.823, 91.006, 90, 90, 120
R / Rfree (%)	26.5 / 34.5

The structure of [Iu:Ag+:C] Metal-Mediated Dna Base Pair in A Self-Assembling Rhombohedral Lattice also contains other interesting chemical elements:

Iodine

(I)

1 atom

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

Silver binding site 1 out of 2 in the [Iu: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 [Iu: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:258.7 occ:1.00 N3 A:5IU12 1.9 292.2 1.0 N3 B:DC4 2.1 245.6 1.0 O4 A:5IU12 2.1 305.5 1.0 C4 A:5IU12 2.3 297.9 1.0 O2 B:DC4 2.6 251.5 1.0 C2 B:DC4 2.7 252.1 1.0 C2 A:5IU12 3.1 285.4 1.0 N6 B:DA3 3.1 238.1 1.0 C6 B:DA3 3.2 247.8 1.0 C4 B:DC4 3.2 247.1 1.0 N1 B:DA3 3.3 251.3 1.0 N4 B:DC4 3.5 241.4 1.0 O2 A:5IU12 3.5 281.0 1.0 C5 A:5IU12 3.7 296.4 1.0 O4 A:DT11 3.8 302.4 1.0 N1 B:DA5 3.9 236.2 1.0 C5 B:DA3 3.9 255.9 1.0 AG B:AG102 4.0 255.5 0.9 O4 A:DT13 4.0 286.8 1.0 N1 B:DC4 4.0 260.6 1.0 N3 A:DT13 4.1 273.1 1.0 C2 B:DA3 4.1 262.6 1.0 C2 B:DA5 4.2 240.5 1.0 N1 A:5IU12 4.2 283.1 1.0 C4 A:DT11 4.3 300.5 1.0 C4 A:DT13 4.3 277.6 1.0 C5 B:DC4 4.4 255.4 1.0 C6 A:5IU12 4.5 288.6 1.0 C4 B:DA3 4.6 267.2 1.0 C6 B:DA5 4.6 243.1 1.0 N7 B:DA3 4.6 255.9 1.0 C6 B:DC4 4.7 262.0 1.0 N3 B:DA3 4.8 271.4 1.0 N3 A:DT11 4.8 293.1 1.0 N6 B:DA5 4.9 242.4 1.0 C2 A:DT13 4.9 266.3 1.0 C5 A:DT11 5.0 305.8 1.0

Silver binding site 2 out of 2 in the [Iu: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 [Iu: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:255.5 occ:0.86 O2 B:DC4 1.9 251.5 1.0 C2' B:DC4 2.8 267.9 1.0 C2 B:DC4 2.9 252.1 1.0 N3 B:DA5 3.0 254.2 1.0 C1' B:DC4 3.1 269.6 1.0 C2 B:DA5 3.2 240.5 1.0 C4 B:DA5 3.3 262.4 1.0 N1 B:DC4 3.4 260.6 1.0 N1 B:DA5 3.7 236.2 1.0 C5 B:DA5 3.8 257.8 1.0 N9 B:DA5 3.9 278.2 1.0 AG B:AG101 4.0 258.7 1.0 N3 B:DC4 4.0 245.6 1.0 C6 B:DA5 4.0 243.1 1.0 C3' B:DC4 4.1 280.8 1.0 O3' B:DC4 4.3 288.1 1.0 O4' B:DA5 4.3 304.5 1.0 C1' B:DA5 4.4 289.7 1.0 O4' B:DC4 4.5 279.6 1.0 O2 A:5IU12 4.5 281.0 1.0 C2 B:DA3 4.5 262.6 1.0 N3 B:DA3 4.6 271.4 1.0 N7 B:DA5 4.6 270.2 1.0 C8 B:DA5 4.6 282.1 1.0 C6 B:DC4 4.7 262.0 1.0 N3 A:5IU12 4.8 292.2 1.0 C4' B:DC4 4.9 288.2 1.0 N1 B:DA3 4.9 251.3 1.0 N6 B:DA5 5.0 242.4 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.