Mercury in PDB 6iue: Dna Helical Wire Containing Hg(II)

The structure of Dna Helical Wire Containing Hg(II), PDB code: 6iue was solved by A.Ono, H.Kanazawa, H.Ito, M.Goto, K.Nakamura, H.Saneyoshi, J.Kondo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.62 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.929, 28.215, 88.844, 90.00, 94.97, 90.00
R / Rfree (%)	29.4 / 34.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Mercury atom in the Dna Helical Wire Containing Hg(II) (pdb code 6iue). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 48 binding sites of Mercury where determined in the Dna Helical Wire Containing Hg(II), PDB code: 6iue:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 48 in the Dna Helical Wire Containing Hg(II)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Dna Helical Wire Containing Hg(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg301 b:23.3 occ:1.00 N3 A:DT1 2.1 13.5 1.0 N1 M:DG9 2.3 12.8 1.0 O A:HOH401 2.6 10.7 1.0 O2 A:DT2 2.8 6.2 1.0 C4 A:DT1 2.9 7.3 1.0 O4 A:DT1 3.0 6.8 1.0 C2 A:DT1 3.0 10.9 1.0 O2 A:DT1 3.1 11.5 1.0 O C:HOH201 3.1 25.5 1.0 N2 M:DG9 3.2 6.4 1.0 C6 M:DG9 3.2 5.9 1.0 C2 M:DG9 3.2 8.6 1.0 O6 M:DG9 3.2 2.6 1.0 O4 M:DT8 3.3 5.8 1.0 C2 A:DT2 3.5 7.7 1.0 N4 C:DC25 3.5 6.0 1.0 C4 M:DT8 4.0 10.2 1.0 N3 C:DC25 4.0 6.1 1.0 N3 A:DT2 4.1 10.4 1.0 C4 C:DC25 4.1 8.5 1.0 N1 A:DT2 4.2 9.2 1.0 HG A:HG303 4.3 13.8 1.0 N1 A:DT1 4.3 8.1 1.0 C5 A:DT1 4.3 8.7 1.0 N3 M:DC10 4.3 5.8 1.0 C1' A:DT2 4.4 7.7 1.0 HG A:HG302 4.5 16.3 1.0 C5 M:DG9 4.5 11.7 1.0 N4 M:DC10 4.5 4.4 1.0 N3 M:DG9 4.5 11.7 1.0 N3 M:DT8 4.6 11.9 1.0 C6 A:DT1 4.8 5.7 1.0 C5 M:DT8 4.9 10.8 1.0 C4 M:DC10 4.9 6.0 1.0 C4 M:DG9 4.9 7.4 1.0 O4' A:DT2 4.9 10.9 1.0 O M:HOH205 5.0 10.0 1.0

Mercury binding site 2 out of 48 in the Dna Helical Wire Containing Hg(II)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Dna Helical Wire Containing Hg(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg302 b:16.3 occ:1.00 N3 A:DT3 1.9 8.0 1.0 N3 M:DT8 2.0 11.9 1.0 C4 A:DT3 2.7 8.7 1.0 O4 A:DT3 2.8 6.7 1.0 N2 A:DG4 2.8 4.2 1.0 C4 M:DT8 2.8 10.2 1.0 C2 A:DT3 2.8 8.9 1.0 O4 M:DT8 2.9 5.8 1.0 C2 M:DT8 2.9 8.7 1.0 O2 A:DT3 3.0 8.8 1.0 N2 M:DG9 3.1 6.4 1.0 O2 M:DT8 3.1 11.0 1.0 O2 M:DT7 3.2 8.4 1.0 O2 A:DT2 3.2 6.2 1.0 C2 A:DG4 3.4 9.9 1.0 C2 M:DG9 3.5 8.6 1.0 N1 A:DG4 3.9 4.7 1.0 HG A:HG303 4.0 13.8 1.0 N1 M:DG9 4.0 12.8 1.0 N3 A:DG4 4.0 18.6 1.0 N3 M:DG9 4.0 11.7 1.0 C5 A:DT3 4.1 8.8 1.0 N1 A:DT3 4.1 10.9 1.0 C2 M:DT7 4.1 7.3 1.0 N1 M:DT8 4.2 11.7 1.0 C5 M:DT8 4.2 10.8 1.0 C2 A:DT2 4.2 7.7 1.0 HG M:HG101 4.4 18.2 1.0 HG A:HG301 4.5 23.3 1.0 C6 A:DT3 4.6 8.3 1.0 N3 M:DT7 4.6 9.3 1.0 C6 M:DT8 4.7 11.9 1.0 N3 A:DT2 4.7 10.4 1.0 O M:HOH204 4.8 10.6 1.0 C4 M:DG9 4.9 7.4 1.0 C4 A:DG4 4.9 8.6 1.0 C6 A:DG4 4.9 6.7 1.0 C6 M:DG9 5.0 5.9 1.0

Mercury binding site 3 out of 48 in the Dna Helical Wire Containing Hg(II)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Dna Helical Wire Containing Hg(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg303 b:13.8 occ:1.00 N3 A:DT2 2.1 10.4 1.0 N3 M:DT7 2.2 9.3 1.0 O4 A:DT1 2.7 6.8 1.0 O4 M:DT6 2.8 5.8 1.0 O4 A:DT3 2.9 6.7 1.0 C2 A:DT2 2.9 7.7 1.0 O2 A:DT2 3.0 6.2 1.0 C4 A:DT2 3.0 12.5 1.0 C4 M:DT7 3.0 5.8 1.0 C2 M:DT7 3.0 7.3 1.0 O4 M:DT8 3.0 5.8 1.0 O4 M:DT7 3.0 10.5 1.0 O2 M:DT7 3.1 8.4 1.0 O4 A:DT2 3.1 6.0 1.0 C4 A:DT1 3.5 7.3 1.0 C4 M:DT6 3.5 12.1 1.0 C4 A:DT3 3.9 8.7 1.0 HG A:HG302 4.0 16.3 1.0 C4 M:DT8 4.1 10.2 1.0 N3 M:DT6 4.2 10.6 1.0 N1 A:DT2 4.2 9.2 1.0 N3 A:DT1 4.3 13.5 1.0 HG M:HG101 4.3 18.2 1.0 HG A:HG301 4.3 23.3 1.0 N1 M:DT7 4.3 11.3 1.0 C5 A:DT2 4.3 8.8 1.0 C5 M:DT7 4.3 10.0 1.0 C5 A:DT1 4.3 8.7 1.0 C5 M:DT6 4.4 11.2 1.0 C7 A:DT1 4.4 6.2 1.0 N3 A:DT3 4.5 8.0 1.0 O M:HOH205 4.5 10.0 1.0 C7 M:DT6 4.6 4.3 1.0 N3 M:DT8 4.7 11.9 1.0 C6 A:DT2 4.7 8.9 1.0 C6 M:DT7 4.8 7.9 1.0 C5 A:DT3 5.0 8.8 1.0

Mercury binding site 4 out of 48 in the Dna Helical Wire Containing Hg(II)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Dna Helical Wire Containing Hg(II) within 5.0Å range: probe atom residue distance (Å) B Occ M:Hg101 b:18.2 occ:1.00 N1 A:DG4 2.1 4.7 1.0 N3 M:DT6 2.3 10.6 1.0 O M:HOH203 2.4 11.0 1.0 O2 M:DT7 2.6 8.4 1.0 O6 A:DG4 2.9 7.4 1.0 C6 A:DG4 2.9 6.7 1.0 O4 A:DT3 3.0 6.7 1.0 O B:HOH203 3.0 2.8 1.0 C4 M:DT6 3.1 12.1 1.0 C2 A:DG4 3.1 9.9 1.0 O4 M:DT6 3.1 5.8 1.0 C2 M:DT6 3.1 12.1 1.0 O2 M:DT6 3.2 9.8 1.0 N2 A:DG4 3.2 4.2 1.0 C2 M:DT7 3.4 7.3 1.0 N4 B:DC15 3.6 6.8 1.0 C4 A:DT3 3.7 8.7 1.0 N3 B:DC15 3.8 7.0 1.0 N3 M:DT7 4.1 9.3 1.0 C4 B:DC15 4.1 8.7 1.0 C5 A:DG4 4.2 9.5 1.0 N1 M:DT7 4.3 11.3 1.0 HG A:HG303 4.3 13.8 1.0 N3 A:DG4 4.4 18.6 1.0 N1 M:DT6 4.4 10.6 1.0 HG A:HG302 4.4 16.3 1.0 C1' M:DT7 4.4 9.0 1.0 N3 A:DT3 4.5 8.0 1.0 C5 M:DT6 4.5 11.2 1.0 C5 A:DT3 4.5 8.8 1.0 N3 A:DC5 4.5 11.6 1.0 C7 A:DT3 4.6 5.6 1.0 C4 A:DG4 4.7 8.6 1.0 C2 B:DC15 4.9 8.2 1.0 C6 M:DT6 4.9 8.8 1.0 N4 A:DC5 4.9 19.6 1.0

Mercury binding site 5 out of 48 in the Dna Helical Wire Containing Hg(II)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Dna Helical Wire Containing Hg(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg101 b:16.3 occ:1.00 N3 B:DT12 2.1 11.6 1.0 N3 N:DT17 2.2 16.2 1.0 O4 B:DT12 2.7 10.8 1.0 O4 N:DT17 2.7 10.3 1.0 O4 B:DT13 2.8 8.5 1.0 C4 B:DT12 2.8 10.2 1.0 C4 N:DT17 2.8 10.3 1.0 O4 B:DT11 2.8 9.7 1.0 O4 N:DT18 2.9 16.6 1.0 O4 N:DT16 3.1 13.4 1.0 C2 B:DT12 3.2 8.2 1.0 C2 N:DT17 3.2 12.5 1.0 O2 N:DT17 3.4 14.1 1.0 O2 B:DT12 3.4 4.2 1.0 C4 B:DT11 3.7 13.0 1.0 C4 N:DT16 3.8 18.0 1.0 C4 B:DT13 3.9 7.1 1.0 C4 N:DT18 3.9 15.9 1.0 HG B:HG102 3.9 15.3 1.0 C5 B:DT12 4.2 14.5 1.0 C5 N:DT17 4.2 19.7 1.0 HG N:HG101 4.3 23.1 1.0 N3 B:DT11 4.3 13.0 1.0 N3 N:DT16 4.4 14.7 1.0 HG B:HG103 4.4 60.1 1.0 N1 B:DT12 4.4 11.6 1.0 N3 N:DT18 4.4 10.8 1.0 N1 N:DT17 4.4 10.2 1.0 C5 B:DT11 4.5 18.2 1.0 C5 N:DT16 4.6 13.1 1.0 C7 B:DT11 4.6 10.3 1.0 N3 B:DT13 4.6 8.1 1.0 C6 B:DT12 4.7 11.6 1.0 C6 N:DT17 4.8 17.1 1.0 C7 N:DT16 4.8 17.4 1.0 C5 B:DT13 4.8 8.4 1.0 C7 B:DT13 4.9 5.2 1.0

Mercury binding site 6 out of 48 in the Dna Helical Wire Containing Hg(II)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Dna Helical Wire Containing Hg(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg102 b:15.3 occ:1.00 N3 B:DT13 1.9 8.1 1.0 N3 N:DT18 2.0 10.8 1.0 C4 B:DT13 2.6 7.1 1.0 O4 B:DT13 2.6 8.5 1.0 N2 B:DG14 2.7 3.4 1.0 N2 N:DG19 2.7 3.2 1.0 C2 N:DT18 2.8 12.7 1.0 O2 N:DT18 2.8 12.1 1.0 C2 B:DT13 2.9 6.8 1.0 C4 N:DT18 3.0 15.9 1.0 C2 B:DG14 3.2 8.4 1.0 O4 N:DT18 3.2 16.6 1.0 O2 B:DT13 3.2 2.0 1.0 O2 N:DT17 3.2 14.1 1.0 C2 N:DG19 3.2 5.8 1.0 O2 B:DT12 3.3 4.2 1.0 N1 B:DG14 3.6 3.8 1.0 N1 N:DG19 3.8 15.4 1.0 N3 B:DG14 3.8 9.7 1.0 N3 N:DG19 3.9 12.7 1.0 HG B:HG101 3.9 16.3 1.0 C5 B:DT13 4.0 8.4 1.0 N1 N:DT18 4.1 6.5 1.0 N1 B:DT13 4.1 8.0 1.0 C2 N:DT17 4.1 12.5 1.0 C2 B:DT12 4.2 8.2 1.0 C5 N:DT18 4.3 6.9 1.0 HG B:HG103 4.4 60.1 1.0 N3 N:DT17 4.4 16.2 1.0 HG N:HG101 4.4 23.1 1.0 N3 B:DT12 4.5 11.6 1.0 C6 B:DT13 4.5 5.3 1.0 C6 B:DG14 4.6 4.5 1.0 C6 N:DT18 4.7 10.9 1.0 C4 B:DG14 4.7 8.5 1.0 C4 N:DG19 4.8 8.4 1.0 C6 N:DG19 4.8 7.5 1.0

Mercury binding site 7 out of 48 in the Dna Helical Wire Containing Hg(II)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Dna Helical Wire Containing Hg(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg103 b:60.1 occ:1.00 N1 N:DG19 2.2 15.4 1.0 N3 B:DT11 2.2 13.0 1.0 O2 B:DT12 2.8 4.2 1.0 O6 N:DG19 2.8 4.5 1.0 C6 N:DG19 2.9 7.5 1.0 O N:HOH203 3.0 1.6 1.0 C4 B:DT11 3.1 13.0 1.0 O4 B:DT11 3.1 9.7 1.0 C2 B:DT11 3.1 7.8 1.0 O4 N:DT18 3.1 16.6 1.0 O2 B:DT11 3.2 7.1 1.0 C2 N:DG19 3.2 5.8 1.0 N2 N:DG19 3.3 3.2 1.0 N4 R:DC60 3.4 11.8 1.0 C2 B:DT12 3.5 8.2 1.0 C4 N:DT18 3.8 15.9 1.0 N3 B:DT12 3.9 11.6 1.0 C5 N:DG19 4.2 9.9 1.0 C4 R:DC60 4.3 7.2 1.0 N3 N:DT18 4.3 10.8 1.0 O2 N:DC20 4.3 12.9 1.0 HG B:HG101 4.4 16.3 1.0 N1 B:DT11 4.4 14.4 1.0 N1 B:DT12 4.4 11.6 1.0 N3 N:DC20 4.4 4.6 1.0 C5 B:DT11 4.4 18.2 1.0 N3 N:DG19 4.4 12.7 1.0 HG B:HG102 4.4 15.3 1.0 C5 N:DT18 4.7 6.9 1.0 C2 N:DC20 4.7 6.8 1.0 C1' B:DT12 4.7 8.5 1.0 C4 N:DG19 4.7 8.4 1.0 N3 R:DC60 4.8 10.0 1.0 C6 B:DT11 4.9 12.7 1.0 C7 N:DT18 4.9 12.4 1.0

Mercury binding site 8 out of 48 in the Dna Helical Wire Containing Hg(II)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Dna Helical Wire Containing Hg(II) within 5.0Å range: probe atom residue distance (Å) B Occ N:Hg101 b:23.1 occ:1.00 N1 B:DG14 2.2 3.8 1.0 N3 N:DT16 2.3 14.7 1.0 O2 N:DT17 2.7 14.1 1.0 O6 B:DG14 3.0 7.2 1.0 C6 B:DG14 3.0 4.5 1.0 O B:HOH203 3.0 2.8 1.0 C2 N:DT16 3.1 9.8 1.0 O4 B:DT13 3.1 8.5 1.0 O2 N:DT16 3.1 6.1 1.0 C2 B:DG14 3.2 8.4 1.0 C4 N:DT16 3.2 18.0 1.0 N2 B:DG14 3.2 3.4 1.0 O4 N:DT16 3.2 13.4 1.0 C2 N:DT17 3.3 12.5 1.0 N3 N:DT17 3.8 16.2 1.0 C4 B:DT13 3.8 7.1 1.0 N1 N:DT17 4.2 10.2 1.0 N4 A:DC5 4.2 19.6 1.0 C5 B:DG14 4.3 5.6 1.0 HG B:HG101 4.3 16.3 1.0 N1 N:DT16 4.4 15.3 1.0 N3 B:DG14 4.4 9.7 1.0 HG B:HG102 4.4 15.3 1.0 N3 A:DC5 4.5 11.6 1.0 C5 N:DT16 4.5 13.1 1.0 O2 B:DC15 4.5 4.7 1.0 C1' N:DT17 4.5 10.1 1.0 C5 B:DT13 4.6 8.4 1.0 N3 B:DT13 4.6 8.1 1.0 C7 B:DT13 4.6 5.2 1.0 N3 B:DC15 4.7 7.0 1.0 C4 A:DC5 4.7 12.9 1.0 C4 B:DG14 4.8 8.5 1.0 O B:HOH202 4.8 9.5 1.0 C4 N:DT17 4.9 10.3 1.0 C2 B:DC15 4.9 8.2 1.0 C6 N:DT16 4.9 14.6 1.0

Mercury binding site 9 out of 48 in the Dna Helical Wire Containing Hg(II)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Dna Helical Wire Containing Hg(II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Hg101 b:13.4 occ:1.00 N3 O:DT28 2.0 4.5 1.0 N3 C:DT23 2.0 7.8 1.0 C4 O:DT28 2.7 7.8 1.0 O4 O:DT28 2.8 1.5 1.0 C2 C:DT23 2.8 6.9 1.0 O2 C:DT23 2.8 6.7 1.0 N2 C:DG24 2.9 2.1 1.0 N2 O:DG29 2.9 7.5 1.0 C2 O:DT28 3.0 7.6 1.0 C4 C:DT23 3.0 10.0 1.0 O2 O:DT27 3.1 4.4 1.0 O2 O:DT28 3.2 3.6 1.0 O4 C:DT23 3.2 4.6 1.0 C2 C:DG24 3.3 4.3 1.0 O2 C:DT22 3.3 2.6 1.0 C2 O:DG29 3.4 10.1 1.0 N1 C:DG24 3.7 7.6 1.0 N1 O:DG29 3.9 10.7 1.0 HG O:HG102 4.0 12.3 1.0 N3 O:DG29 4.0 6.7 1.0 N3 C:DG24 4.0 5.9 1.0 N1 C:DT23 4.1 11.9 1.0 C5 O:DT28 4.1 5.8 1.0 C2 O:DT27 4.1 8.2 1.0 N1 O:DT28 4.2 7.3 1.0 C2 C:DT22 4.2 9.6 1.0 C5 C:DT23 4.3 7.6 1.0 HG O:HG101 4.4 16.4 1.0 HG C:HG102 4.5 36.0 1.0 N3 O:DT27 4.5 7.3 1.0 C6 O:DT28 4.6 7.3 1.0 C6 C:DT23 4.7 9.7 1.0 C6 C:DG24 4.7 4.8 1.0 N3 C:DT22 4.7 11.0 1.0 C4 C:DG24 4.9 3.5 1.0 C4 O:DG29 4.9 7.0 1.0 C6 O:DG29 4.9 10.5 1.0

Mercury binding site 10 out of 48 in the Dna Helical Wire Containing Hg(II)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Dna Helical Wire Containing Hg(II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Hg102 b:36.0 occ:1.00 N1 O:DG29 2.3 10.7 1.0 N3 C:DT21 2.4 16.4 1.0 O6 O:DG29 2.8 5.4 1.0 O2 C:DT22 2.9 2.6 1.0 O4 O:DT28 2.9 1.5 1.0 C6 O:DG29 3.0 10.5 1.0 O4 C:DT21 3.1 7.0 1.0 C4 C:DT21 3.1 13.6 1.0 C2 C:DT21 3.3 11.4 1.0 C2 O:DG29 3.3 10.1 1.0 O2 C:DT21 3.4 21.3 1.0 N2 O:DG29 3.4 7.5 1.0 C4 O:DT28 3.6 7.8 1.0 C2 C:DT22 3.7 9.6 1.0 N3 C:DT22 4.3 11.0 1.0 C5 O:DT28 4.3 5.8 1.0 C5 O:DG29 4.3 9.7 1.0 C7 O:DT28 4.3 8.6 1.0 HG O:HG102 4.4 12.3 1.0 N3 O:DT28 4.4 4.5 1.0 C5 C:DT21 4.5 11.9 1.0 HG C:HG101 4.5 13.4 1.0 N1 C:DT21 4.6 18.8 1.0 N3 O:DG29 4.6 6.7 1.0 N1 C:DT22 4.6 9.0 1.0 O C:HOH202 4.7 9.3 1.0 C4 O:DG29 4.9 7.0 1.0 C1' C:DT22 4.9 12.8 1.0

A.Ono, H.Kanazawa, H.Ito, M.Goto, K.Nakamura, H.Saneyoshi, J.Kondo. A Novel Dna Helical Wire Containing Hgii-Mediated T:T and T:G Pairs. Angew.Chem.Int.Ed.Engl. V. 58 16835 2019.
ISSN: ESSN 1521-3773
PubMed: 31507027
DOI: 10.1002/ANIE.201910029