Mercury in PDB 6vpr: Crystal Structure of the C-Terminal Domain of Denr

The structure of Crystal Structure of the C-Terminal Domain of Denr, PDB code: 6vpr was solved by I.B.Lomakin, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.98 / 2.20
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	116.600, 116.600, 75.230, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 28.8

The binding sites of Mercury atom in the Crystal Structure of the C-Terminal Domain of Denr (pdb code 6vpr). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the Crystal Structure of the C-Terminal Domain of Denr, PDB code: 6vpr:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in the Crystal Structure of the C-Terminal Domain of Denr


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 the C-Terminal Domain of Denr within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg206 b:0.7 occ:1.00 SG A:CYS132 2.7 97.4 1.0 OE2 A:GLU163 2.9 99.9 1.0 CB A:CYS132 3.2 74.4 1.0 CB A:GLU163 3.8 77.4 1.0 CD A:GLU163 4.0 98.7 1.0 O A:ASP162 4.4 64.2 1.0 CG A:GLU163 4.4 86.0 1.0 CA A:CYS132 4.5 63.0 1.0 NE A:ARG130 4.5 60.5 1.0 CD A:ARG130 4.6 59.6 1.0 CZ A:ARG130 4.9 71.2 1.0 OE1 A:GLU163 5.0 0.2 1.0

Mercury binding site 2 out of 4 in the Crystal Structure of the C-Terminal Domain of Denr


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 the C-Terminal Domain of Denr within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg207 b:0.4 occ:1.00 SG A:CYS154 2.7 91.2 1.0 O11 A:TLA201 3.2 90.6 1.0 CB A:CYS154 3.2 81.6 1.0 O A:ACT205 3.2 0.5 1.0 O1 A:TLA201 3.3 0.2 1.0 O A:GLN167 3.5 58.6 1.0 C1 A:TLA201 3.6 0.1 1.0 CA A:CYS154 3.8 70.8 1.0 OXT A:ACT205 3.8 81.8 1.0 C A:ACT205 3.9 0.0 1.0 O A:SER153 4.1 78.9 1.0 C A:GLN167 4.3 63.3 1.0 CZ A:PHE170 4.7 63.8 1.0 CB A:GLN167 4.7 54.9 1.0 C A:CYS154 4.8 80.0 1.0 N A:GLY155 4.8 70.4 1.0 N A:CYS154 4.8 78.5 1.0 C A:SER153 4.9 83.2 1.0 O3 A:TLA201 4.9 0.8 1.0 N A:GLY168 4.9 62.3 1.0 CA A:GLY168 4.9 58.6 1.0

Mercury binding site 3 out of 4 in the Crystal Structure of the C-Terminal Domain of Denr


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of the C-Terminal Domain of Denr within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg307 b:0.4 occ:1.00 SG B:CYS132 2.5 66.8 1.0 OXT B:ACT306 2.6 67.5 1.0 OE2 B:GLU163 3.3 77.7 1.0 CB B:CYS132 3.4 40.3 1.0 C B:ACT306 3.6 0.4 1.0 CD B:GLU163 4.2 62.5 1.0 CD B:ARG130 4.2 69.3 1.0 CB B:GLU163 4.2 69.4 1.0 CH3 B:ACT306 4.3 88.1 1.0 NE B:ARG130 4.3 80.5 1.0 CG B:GLU163 4.4 56.6 1.0 O B:ACT306 4.5 98.4 1.0 O11 A:TLA202 4.6 0.0 1.0 CZ B:ARG130 4.6 81.8 1.0 CA B:CYS132 4.7 62.2 1.0 NH2 B:ARG130 4.8 79.2 1.0 CG B:ARG130 4.8 58.9 1.0 O B:ASP162 4.9 52.1 1.0

Mercury binding site 4 out of 4 in the Crystal Structure of the C-Terminal Domain of Denr


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of the C-Terminal Domain of Denr within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg308 b:0.7 occ:1.00 SG B:CYS154 2.8 90.7 1.0 OXT B:ACT305 2.9 99.8 1.0 O B:GLN167 3.2 64.0 1.0 CB B:CYS154 3.2 75.4 1.0 O2 B:SO4304 3.9 83.9 1.0 C B:GLN167 4.0 64.7 1.0 CA B:CYS154 4.0 79.7 1.0 C B:ACT305 4.1 94.3 1.0 O B:SER153 4.5 78.5 1.0 CB B:GLN167 4.5 63.7 1.0 N B:GLY168 4.5 56.3 1.0 CA B:GLY168 4.6 61.5 1.0 CZ B:PHE170 4.6 62.3 1.0 N B:GLY155 4.7 84.0 1.0 CA B:GLN167 4.8 58.0 1.0 C B:CYS154 4.8 83.6 1.0 CE2 B:PHE170 4.9 67.6 1.0 O B:ACT305 4.9 92.3 1.0

I.B.Lomakin, S.De, J.Wang, A.Borkar, T.A.Steitz. Crystal Structure of the C-Terminal Domain of Denr. Comp.Stuct.Biol.J 2020.
DOI: 10.1016/J.CSBJ.2020.03.009