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Mercury in PDB 5gsk: Crystal Structure of Duplex DNA3 in Complex with Hg(II) and Sr(II)

Protein crystallography data

The structure of Crystal Structure of Duplex DNA3 in Complex with Hg(II) and Sr(II), PDB code: 5gsk was solved by H.H.Liu, R.Wang, Q.Q.Yao, Y.Q.Cheng, C.Yang, Q.Luo, B.X.Wu, J.X.Li, J.B.Ma, J.Sheng, J.H.Gan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.80 / 1.05
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 40.318, 40.318, 24.980, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 15.6

Other elements in 5gsk:

The structure of Crystal Structure of Duplex DNA3 in Complex with Hg(II) and Sr(II) also contains other interesting chemical elements:

Strontium (Sr) 1 atom

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Duplex DNA3 in Complex with Hg(II) and Sr(II) (pdb code 5gsk). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total only one binding site of Mercury was determined in the Crystal Structure of Duplex DNA3 in Complex with Hg(II) and Sr(II), PDB code: 5gsk:

Mercury binding site 1 out of 1 in 5gsk

Go back to Mercury Binding Sites List in 5gsk
Mercury binding site 1 out of 1 in the Crystal Structure of Duplex DNA3 in Complex with Hg(II) and Sr(II)


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 Duplex DNA3 in Complex with Hg(II) and Sr(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg101

b:17.7
occ:0.60
N3 A:DT6 2.0 19.1 1.0
O A:HOH201 2.3 25.3 1.0
C4 A:DT6 2.8 19.1 1.0
O4 A:DT6 2.9 20.4 1.0
C2 A:DT6 3.0 18.0 1.0
O2 A:DT6 3.2 21.2 1.0
N3 A:DC7 3.4 19.1 1.0
C2 A:DC7 3.5 20.8 1.0
O2 A:DC7 3.6 24.0 1.0
N1 A:DG5 3.8 16.9 1.0
C4 A:DC7 4.0 18.6 1.0
N1 A:DC7 4.2 18.4 1.0
O6 A:DG5 4.2 17.2 1.0
C5 A:DT6 4.2 18.5 1.0
N1 A:DT6 4.2 18.6 1.0
C6 A:DG5 4.3 16.4 1.0
SR A:SR102 4.3 18.8 0.8
C2 A:DG5 4.4 16.2 1.0
N2 A:DG5 4.5 17.2 1.0
N4 A:DC7 4.5 18.4 1.0
C5 A:DC7 4.7 18.8 1.0
C6 A:DT6 4.7 18.2 1.0
C6 A:DC7 4.7 19.2 1.0
C1' A:DC7 4.9 19.4 1.0

Reference:

H.H.Liu, C.Cai, P.Haruehanroengra, Q.Q.Yao, Y.Q.Chen, C.Yang, Q.Luo, B.X.Wu, J.X.Li, J.B.Ma, J.Sheng, J.H.Gan. Flexibility and Stabilization of Hgii-Mediated C:T and T:T Base Pairs in Dna Duplex Nucleic Acids Res. V. 45 2910 2017.
ISSN: ESSN 1362-4962
PubMed: 27998930
DOI: 10.1093/NAR/GKW1296
Page generated: Sun Dec 13 19:12:42 2020

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