Silver in PDB 5xjz: Structure of DNA1-Ag Complex

The structure of Structure of DNA1-Ag Complex, PDB code: 5xjz was solved by H.H.Liu, J.H.Gan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.23 / 0.98
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	40.236, 42.546, 25.301, 90.00, 90.00, 90.00
R / Rfree (%)	12.4 / 13.1

The binding sites of Silver atom in the Structure of DNA1-Ag Complex (pdb code 5xjz). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 3 binding sites of Silver where determined in the Structure of DNA1-Ag Complex, PDB code: 5xjz:
Jump to Silver binding site number: 1; 2; 3;

Silver binding site 1 out of 3 in the Structure of DNA1-Ag Complex


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of Structure of DNA1-Ag Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag101 b:9.0 occ:0.90 N7 B:DG7 2.1 8.2 1.0 N7 A:DG7 2.2 9.1 1.0 O6 A:DG7 3.0 10.3 1.0 C5 A:DG7 3.0 8.7 1.0 C5 B:DG7 3.0 8.2 1.0 O6 B:DG7 3.0 10.1 1.0 AG A:AG102 3.2 7.8 0.9 O2 B:DC6 3.2 8.8 1.0 C8 B:DG7 3.2 8.3 1.0 C8 A:DG7 3.3 9.0 1.0 C6 A:DG7 3.3 9.0 1.0 C6 B:DG7 3.4 8.8 1.0 O2 A:DC6 3.4 8.5 1.0 N2 A:DG1 3.6 8.5 1.0 C2 B:DC6 3.8 8.0 1.0 N2 B:DG1 3.8 8.5 1.0 C2 A:DC6 3.9 8.0 1.0 N3 A:DC8 4.0 7.8 1.0 N3 B:DC8 4.1 7.1 1.0 N3 B:DC6 4.2 8.0 1.0 N4 A:DC8 4.2 8.3 1.0 C4 B:DG7 4.3 7.9 1.0 C4 A:DG7 4.3 8.5 1.0 N4 B:DC8 4.3 7.6 1.0 C2 A:DG1 4.4 8.1 1.0 N9 B:DG7 4.4 8.1 1.0 N9 A:DG7 4.4 8.8 1.0 N3 A:DC6 4.4 7.9 1.0 C4 A:DC8 4.5 7.7 1.0 N1 B:DC6 4.5 7.7 1.0 N1 A:DC6 4.6 8.0 1.0 C4 B:DC8 4.6 7.6 1.0 C2 B:DG1 4.6 7.6 1.0 C2' A:DC6 4.7 8.5 1.0 N1 A:DG7 4.7 9.5 1.0 N1 A:DG1 4.7 8.4 1.0 N1 B:DG7 4.8 8.9 1.0 C2' B:DC6 4.8 7.7 1.0 C1' A:DC6 4.8 7.8 1.0 C1' B:DC6 4.9 7.8 1.0 C2 A:DC8 4.9 8.0 1.0 N1 B:DG1 5.0 7.8 1.0 C2 B:DC8 5.0 7.8 1.0

Silver binding site 2 out of 3 in the Structure of DNA1-Ag Complex


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of Structure of DNA1-Ag Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag102 b:7.8 occ:0.95 N3 B:DC8 2.1 7.1 1.0 N3 A:DC8 2.1 7.8 1.0 C2 A:DC8 2.9 8.0 1.0 O2 A:DC8 2.9 8.8 1.0 C2 B:DC8 2.9 7.8 1.0 O2 B:DC8 3.0 8.5 1.0 C4 B:DC8 3.1 7.6 1.0 C4 A:DC8 3.2 7.7 1.0 AG A:AG101 3.2 9.0 0.9 O6 A:DG7 3.3 10.3 1.0 O6 B:DG7 3.3 10.1 1.0 N4 B:DC8 3.3 7.6 1.0 N4 A:DC8 3.3 8.3 1.0 C6 B:DG7 3.6 8.8 1.0 N7 B:DG7 3.6 8.2 1.0 C6 A:DG7 3.6 9.0 1.0 N7 A:DG7 3.6 9.1 1.0 C5 B:DG7 3.7 8.2 1.0 C5 A:DG7 3.8 8.7 1.0 N1 A:DC8 4.3 8.3 1.0 N1 B:DC8 4.3 7.9 1.0 C5 B:DC8 4.5 7.7 1.0 C5 A:DC8 4.5 8.6 1.0 C8 B:DG7 4.5 8.3 1.0 N1 B:DG7 4.5 8.9 1.0 C8 A:DG7 4.6 9.0 1.0 N1 A:DG7 4.6 9.5 1.0 C4 B:DG7 4.6 7.9 1.0 C4 A:DG7 4.8 8.5 1.0 C6 A:DC8 4.9 8.7 1.0 C6 B:DC8 4.9 7.5 1.0

Silver binding site 3 out of 3 in the Structure of DNA1-Ag Complex


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of Structure of DNA1-Ag Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag103 b:7.4 occ:0.89 N3 A:DC4 2.1 8.6 1.0 O2 A:DC4 2.8 9.3 1.0 C2 A:DC4 2.8 8.5 1.0 C4 A:DC4 3.2 8.0 1.0 N4 A:DC4 3.5 8.5 1.0 N1 A:DC4 4.2 8.5 1.0 O A:HOH229 4.5 19.1 1.0 C5 A:DC4 4.5 9.1 1.0 C6 A:DC4 4.9 9.6 1.0 O A:HOH211 4.9 22.4 1.0

H.H.Liu, F.S.Shen, P.Haruehanroengra, Q.Q.Yao, Y.S.Cheng, Y.Q.Chen, C.Yang, J.Zhang, B.X.Wu, Q.Luo, R.X.Cui, J.X.Li, J.B.Ma, J.Sheng, J.H.Gan. A Dna Structure Containing Agi -Mediated G:G and C:C Base Pairs Angew. Chem. Int. Ed. Engl. V. 56 9430 2017.
ISSN: ESSN 1521-3773
PubMed: 28635152
DOI: 10.1002/ANIE.201704891