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Silver in PDB 6lbw: Crystal Structure of Ag-Mediated Base Pairs in Uncanonical Dna Duplex

Protein crystallography data

The structure of Crystal Structure of Ag-Mediated Base Pairs in Uncanonical Dna Duplex, PDB code: 6lbw was solved by H.A.Aoyama, S.O.Obika, O.N.Nakagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.06 / 1.50
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 28.560, 68.110, 118.850, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 24.3

Other elements in 6lbw:

The structure of Crystal Structure of Ag-Mediated Base Pairs in Uncanonical Dna Duplex also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Silver Binding Sites:

The binding sites of Silver atom in the Crystal Structure of Ag-Mediated Base Pairs in Uncanonical Dna Duplex (pdb code 6lbw). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 2 binding sites of Silver where determined in the Crystal Structure of Ag-Mediated Base Pairs in Uncanonical Dna Duplex, PDB code: 6lbw:
Jump to Silver binding site number: 1; 2;

Silver binding site 1 out of 2 in 6lbw

Go back to Silver Binding Sites List in 6lbw
Silver binding site 1 out of 2 in the Crystal Structure of Ag-Mediated Base Pairs in Uncanonical Dna Duplex


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of Crystal Structure of Ag-Mediated Base Pairs in Uncanonical Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag101

b:21.3
occ:1.00
N1 B:DA5 2.2 21.3 1.0
N1 A:DA5 2.2 21.9 1.0
O6 A:DG4 2.9 22.7 1.0
O6 B:DG4 2.9 20.3 1.0
C2 A:DA5 2.9 17.5 1.0
C2 B:DA5 3.0 15.1 1.0
O B:HOH121 3.1 26.8 1.0
O A:HOH210 3.1 28.3 1.0
C6 B:DA5 3.2 21.4 1.0
C6 A:DA5 3.2 19.9 1.0
N6 B:DA5 3.4 21.4 1.0
N6 A:DA5 3.4 21.9 1.0
AG A:AG102 3.5 22.5 1.0
C6 B:DG4 3.6 25.4 1.0
C6 A:DG4 3.6 27.0 1.0
N7 B:DG4 4.0 18.4 1.0
C5 B:DG4 4.0 18.2 1.0
N4 A:DC8 4.1 16.3 1.0
N4 B:DC8 4.1 20.2 1.0
C5 A:DG4 4.2 26.6 1.0
N7 A:DG4 4.2 21.4 1.0
N3 A:DA5 4.3 23.1 1.0
N3 B:DA5 4.3 27.2 1.0
C5 B:DA5 4.5 21.4 1.0
C5 A:DA5 4.5 23.5 1.0
O2 B:LCC6 4.5 23.6 1.0
O2 A:LCC6 4.5 27.3 1.0
N1 B:DG4 4.6 21.0 1.0
N1 A:DG4 4.6 20.7 1.0
N3 A:LCC6 4.8 21.1 1.0
C4 A:DA5 4.8 26.3 1.0
C4 B:DA5 4.8 23.1 1.0
N3 B:LCC6 4.8 22.7 1.0
O A:HOH214 4.8 26.0 1.0
C2 A:LCC6 4.9 25.4 1.0
C2 B:LCC6 4.9 21.8 1.0
O B:HOH129 5.0 23.1 1.0

Silver binding site 2 out of 2 in 6lbw

Go back to Silver Binding Sites List in 6lbw
Silver binding site 2 out of 2 in the Crystal Structure of Ag-Mediated Base Pairs in Uncanonical Dna Duplex


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of Crystal Structure of Ag-Mediated Base Pairs in Uncanonical Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag102

b:22.5
occ:1.00
N7 B:DG4 2.1 18.4 1.0
N7 A:DG4 2.1 21.4 1.0
O B:HOH129 3.0 23.1 1.0
O A:HOH214 3.0 26.0 1.0
C8 B:DG4 3.0 18.6 1.0
C8 A:DG4 3.1 23.1 1.0
C5 A:DG4 3.1 26.6 1.0
C5 B:DG4 3.1 18.2 1.0
O6 A:DG4 3.3 22.7 1.0
O A:HOH223 3.3 36.4 1.0
O6 B:DG4 3.4 20.3 1.0
O B:HOH128 3.4 49.2 1.0
AG A:AG101 3.5 21.3 1.0
C6 A:DG4 3.6 27.0 1.0
C6 B:DG4 3.6 25.4 1.0
C2 A:DA5 3.9 17.5 1.0
N1 A:DA5 4.0 21.9 1.0
C2 B:DA5 4.1 15.1 1.0
N1 B:DA5 4.2 21.3 1.0
N9 B:DG4 4.2 18.8 1.0
N9 A:DG4 4.3 20.5 1.0
C4 B:DG4 4.3 15.3 1.0
C4 A:DG4 4.3 23.2 1.0
N3 A:DA5 4.7 23.1 1.0
O A:HOH219 4.9 27.2 1.0
N1 A:DG4 4.9 20.7 1.0
C6 A:DA5 5.0 19.9 1.0
O B:HOH131 5.0 26.6 1.0
N1 B:DG4 5.0 21.0 1.0

Reference:

H.A.Aoyama, S.O.Obika, O.N.Nakagawa. Crystal Structure of Ag-Mediated Base Pairs in Uncanonical Dna Duplex To Be Published.
Page generated: Sat Dec 12 01:23:10 2020

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