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Mercury in PDB 4l24: Crystal Structure of Metallo-Dna Duplex Containing Consecutive T- Hg(II)-T Base Pairs

Protein crystallography data

The structure of Crystal Structure of Metallo-Dna Duplex Containing Consecutive T- Hg(II)-T Base Pairs, PDB code: 4l24 was solved by J.Kondo, T.Yamada, C.Hirose, I.Okamoto, Y.Tanaka, A.Ono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.77 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.500, 41.270, 64.560, 90.00, 90.00, 90.00
R / Rfree (%) 25.8 / 26.7

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Metallo-Dna Duplex Containing Consecutive T- Hg(II)-T Base Pairs (pdb code 4l24). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 2 binding sites of Mercury where determined in the Crystal Structure of Metallo-Dna Duplex Containing Consecutive T- Hg(II)-T Base Pairs, PDB code: 4l24:
Jump to Mercury binding site number: 1; 2;

Mercury binding site 1 out of 2 in 4l24

Go back to Mercury Binding Sites List in 4l24
Mercury binding site 1 out of 2 in the Crystal Structure of Metallo-Dna Duplex Containing Consecutive T- Hg(II)-T Base Pairs


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of Metallo-Dna Duplex Containing Consecutive T- Hg(II)-T Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg101

b:0.0
occ:1.00
N3 A:DT7 2.0 66.4 1.0
N3 B:DT18 2.0 51.0 1.0
C2 B:DT18 2.9 55.1 1.0
C4 A:DT7 2.9 78.8 1.0
C2 A:DT7 2.9 79.0 1.0
C4 B:DT18 2.9 74.7 1.0
O4 A:DT7 3.0 90.6 1.0
O2 B:DT18 3.0 71.2 1.0
O4 B:DT18 3.0 74.1 1.0
O2 A:DT7 3.1 0.3 1.0
HG A:HG102 3.3 0.4 1.0
N1 B:DA17 3.6 22.7 1.0
N3 B:DT19 3.8 45.5 1.0
C6 B:DA17 3.8 66.7 1.0
N6 B:DA17 3.9 30.5 1.0
N3 A:DT6 3.9 74.0 1.0
O4 A:DT6 4.0 85.3 1.0
N3 A:DT8 4.0 18.2 1.0
C2 B:DT19 4.1 83.7 1.0
O2 B:DT19 4.2 67.6 1.0
C4 A:DT6 4.2 89.4 1.0
N1 B:DT18 4.2 50.4 1.0
N1 A:DT7 4.2 89.9 1.0
C2 B:DA17 4.2 69.6 1.0
C5 A:DT7 4.2 60.1 1.0
C5 B:DT18 4.3 62.2 1.0
C4 B:DT19 4.3 68.3 1.0
O4 A:DT8 4.5 40.2 1.0
C4 A:DT8 4.5 64.1 1.0
C5 B:DA17 4.6 10.5 1.0
C2 A:DT8 4.6 66.3 1.0
O4 B:DT19 4.6 59.6 1.0
C6 A:DT7 4.7 70.8 1.0
C2 A:DT6 4.7 94.5 1.0
O2 A:DT8 4.7 79.0 1.0
C6 B:DT18 4.7 37.4 1.0
N1 B:DT19 4.9 48.2 1.0
O2 A:DT6 5.0 84.7 1.0
N3 B:DA17 5.0 41.7 1.0

Mercury binding site 2 out of 2 in 4l24

Go back to Mercury Binding Sites List in 4l24
Mercury binding site 2 out of 2 in the Crystal Structure of Metallo-Dna Duplex Containing Consecutive T- Hg(II)-T Base Pairs


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of Metallo-Dna Duplex Containing Consecutive T- Hg(II)-T Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg102

b:0.4
occ:1.00
N3 A:DT6 2.0 74.0 1.0
N3 B:DT19 2.0 45.5 1.0
C4 A:DT6 2.8 89.4 1.0
O4 A:DT6 2.9 85.3 1.0
C2 B:DT19 2.9 83.7 1.0
C2 A:DT6 2.9 94.5 1.0
C4 B:DT19 2.9 68.3 1.0
O4 B:DT19 3.0 59.6 1.0
O2 B:DT19 3.0 67.6 1.0
O2 A:DT6 3.1 84.7 1.0
HG A:HG101 3.3 0.0 1.0
N6 A:DA5 3.7 29.6 1.0
N1 A:DA5 3.7 26.6 1.0
C6 A:DA5 3.7 66.3 1.0
N3 A:DT7 3.8 66.4 1.0
N3 B:DT18 3.9 51.0 1.0
N3 B:DT20 3.9 40.3 1.0
O4 B:DT18 4.1 74.1 1.0
N1 A:DT6 4.1 85.2 1.0
C5 A:DT6 4.2 56.6 1.0
N1 B:DT19 4.2 48.2 1.0
O4 B:DT20 4.2 40.9 1.0
C4 B:DT20 4.2 56.6 1.0
C5 B:DT19 4.2 65.8 1.0
C4 B:DT18 4.3 74.7 1.0
C2 A:DT7 4.3 79.0 1.0
O2 A:DT7 4.4 0.3 1.0
C4 A:DT7 4.5 78.8 1.0
C2 A:DA5 4.5 73.4 1.0
C2 B:DT20 4.5 40.6 1.0
C5 A:DA5 4.5 39.1 1.0
O4 A:DT7 4.6 90.6 1.0
C6 A:DT6 4.6 66.2 1.0
C6 B:DT19 4.7 74.0 1.0
C2 B:DT18 4.7 55.1 1.0
O2 B:DT20 4.8 67.8 1.0
O2 B:DT18 4.8 71.2 1.0

Reference:

J.Kondo, T.Yamada, C.Hirose, I.Okamoto, Y.Tanaka, A.Ono. Crystal Structure of Metallo Dna Duplex Containing Consecutive Watson-Crick-Like T-Hg(II) -T Base Pairs Angew.Chem.Int.Ed.Engl. V. 53 2385 2014.
ISSN: ISSN 1433-7851
PubMed: 24478025
DOI: 10.1002/ANIE.201309066
Page generated: Sun Dec 13 19:11:21 2020

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