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Silver in PDB 2m54: Refined uc(Nmr) Solution Structure of Metal-Modified Dna

Silver Binding Sites:

The binding sites of Silver atom in the Refined uc(Nmr) Solution Structure of Metal-Modified Dna (pdb code 2m54). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 3 binding sites of Silver where determined in the Refined uc(Nmr) Solution Structure of Metal-Modified Dna, PDB code: 2m54:
Jump to Silver binding site number: 1; 2; 3;

Silver binding site 1 out of 3 in 2m54

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Silver binding site 1 out of 3 in the Refined uc(Nmr) Solution Structure of Metal-Modified Dna


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of Refined uc(Nmr) Solution Structure of Metal-Modified Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag101

b:0.0
occ:1.00
N3 B:D3327 2.1 0.0 1.0
N3 A:D338 2.1 0.0 1.0
C2 B:D3327 3.1 0.0 1.0
C2 A:D338 3.1 0.0 1.0
C4 B:D3327 3.1 0.0 1.0
C4 A:D338 3.2 0.0 1.0
H44 B:D3327 3.3 0.0 1.0
H44 A:D338 3.3 0.0 1.0
H22 A:D338 3.4 0.0 1.0
H22 B:D3327 3.4 0.0 1.0
AG A:AG102 3.5 0.0 1.0
N3 A:D339 3.6 0.0 1.0
C4 A:D339 4.0 0.0 1.0
H2 B:DA28 4.0 0.0 1.0
C2 A:D339 4.1 0.0 1.0
H44 A:D339 4.2 0.0 1.0
C2 B:DA28 4.3 0.0 1.0
N1 B:D3327 4.3 0.0 1.0
N1 A:D338 4.3 0.0 1.0
C5 B:D3327 4.3 0.0 1.0
C5 A:D338 4.3 0.0 1.0
N1 B:DA28 4.4 0.0 1.0
H22 A:D339 4.5 0.0 1.0
N3 B:D3326 4.5 0.0 1.0
N3 B:DA28 4.8 0.0 1.0
C5 A:D339 4.8 0.0 1.0
H3 A:DT7 4.8 0.0 1.0
N1 A:D339 4.8 0.0 1.0
H44 B:D3326 5.0 0.0 1.0

Silver binding site 2 out of 3 in 2m54

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Silver binding site 2 out of 3 in the Refined uc(Nmr) Solution Structure of Metal-Modified Dna


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of Refined uc(Nmr) Solution Structure of Metal-Modified Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag102

b:0.0
occ:1.00
N3 A:D339 2.1 0.0 1.0
N3 B:D3326 2.1 0.0 1.0
C2 B:D3326 3.1 0.0 1.0
C2 A:D339 3.1 0.0 1.0
C4 A:D339 3.2 0.0 1.0
C4 B:D3326 3.2 0.0 1.0
H44 A:D339 3.3 0.0 1.0
H44 B:D3326 3.3 0.0 1.0
H22 B:D3326 3.4 0.0 1.0
H22 A:D339 3.4 0.0 1.0
AG A:AG101 3.5 0.0 1.0
AG A:AG103 3.5 0.0 1.0
N3 B:D3327 3.6 0.0 1.0
N3 A:D3310 3.6 0.0 1.0
C2 B:D3327 4.1 0.0 1.0
C2 A:D3310 4.1 0.0 1.0
C4 B:D3327 4.1 0.0 1.0
C4 A:D3310 4.1 0.0 1.0
H44 A:D3310 4.3 0.0 1.0
H44 B:D3327 4.3 0.0 1.0
N1 A:D339 4.3 0.0 1.0
N1 B:D3326 4.3 0.0 1.0
H22 B:D3327 4.3 0.0 1.0
C5 A:D339 4.3 0.0 1.0
C5 B:D3326 4.3 0.0 1.0
H22 A:D3310 4.3 0.0 1.0
N3 A:D338 4.6 0.0 1.0
N3 B:D3325 4.6 0.0 1.0
N1 B:D3327 4.9 0.0 1.0
N1 A:D3310 4.9 0.0 1.0
C5 B:D3327 4.9 0.0 1.0
C5 A:D3310 4.9 0.0 1.0

Silver binding site 3 out of 3 in 2m54

Go back to Silver Binding Sites List in 2m54
Silver binding site 3 out of 3 in the Refined uc(Nmr) Solution Structure of Metal-Modified Dna


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of Refined uc(Nmr) Solution Structure of Metal-Modified Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag103

b:0.0
occ:1.00
N3 A:D3310 2.1 0.0 1.0
N3 B:D3325 2.1 0.0 1.0
C2 A:D3310 3.1 0.0 1.0
C2 B:D3325 3.1 0.0 1.0
C4 A:D3310 3.2 0.0 1.0
C4 B:D3325 3.2 0.0 1.0
H44 A:D3310 3.3 0.0 1.0
H44 B:D3325 3.3 0.0 1.0
H22 B:D3325 3.4 0.0 1.0
H22 A:D3310 3.4 0.0 1.0
AG A:AG102 3.5 0.0 1.0
N3 B:D3326 3.6 0.0 1.0
C4 B:D3326 4.0 0.0 1.0
H2 A:DA11 4.1 0.0 1.0
C2 B:D3326 4.1 0.0 1.0
H44 B:D3326 4.2 0.0 1.0
C2 A:DA11 4.3 0.0 1.0
N1 A:D3310 4.3 0.0 1.0
N1 B:D3325 4.3 0.0 1.0
C5 A:D3310 4.3 0.0 1.0
C5 B:D3325 4.3 0.0 1.0
N1 A:DA11 4.4 0.0 1.0
H22 B:D3326 4.5 0.0 1.0
N3 A:D339 4.5 0.0 1.0
N3 A:DA11 4.8 0.0 1.0
C5 B:D3326 4.8 0.0 1.0
H3 B:DT24 4.8 0.0 1.0
N1 B:D3326 4.9 0.0 1.0
H44 A:D339 5.0 0.0 1.0

Reference:

S.Kumbhar, S.Johannsen, R.K.Sigel, M.P.Waller, J.Muller. A Qm/Mm Refinement of An Experimental Dna Structure with Metal-Mediated Base Pairs. J.Inorg.Biochem. V. 127 203 2013.
ISSN: ISSN 0162-0134
PubMed: 23622950
DOI: 10.1016/J.JINORGBIO.2013.03.009
Page generated: Sat Dec 12 01:21:14 2020

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