Mercury in PDB 5ydc: Crystal Structure of Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis

The structure of Crystal Structure of Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis, PDB code: 5ydc was solved by S.Singh, S.Karthikeyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.89 / 1.91
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.355, 31.511, 77.901, 90.00, 98.21, 90.00
R / Rfree (%)	20.6 / 26

The binding sites of Mercury atom in the Crystal Structure of Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis (pdb code 5ydc). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the Crystal Structure of Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis, PDB code: 5ydc:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in the Crystal Structure of Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis


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 Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg301 b:52.0 occ:0.40 HG A:HG301 0.0 52.0 0.4 HG A:HG301 2.7 38.9 0.3 O A:HOH426 2.9 40.9 1.0 O A:GLN170 3.6 18.3 1.0 CD2 B:LEU228 3.6 25.9 1.0 C A:GLN170 3.7 19.7 1.0 N A:CYS171 3.7 19.4 1.0 HG A:HG301 3.7 63.0 0.3 CA A:CYS171 3.9 20.6 1.0 CB A:GLN170 4.0 21.2 1.0 O A:HOH408 4.1 27.0 1.0 SG A:CYS171 4.2 25.4 1.0 CB A:ALA174 4.4 19.6 1.0 CA A:GLN170 4.5 20.2 1.0 CB A:CYS171 4.7 22.9 1.0

Mercury binding site 2 out of 6 in the Crystal Structure of Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis


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 Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg301 b:38.9 occ:0.30 HG A:HG301 0.0 38.9 0.3 SG A:CYS171 2.2 25.4 1.0 HG A:HG301 2.6 63.0 0.3 HG A:HG301 2.7 52.0 0.4 N A:CYS171 3.2 19.4 1.0 CB A:CYS171 3.4 22.9 1.0 CA A:CYS171 3.4 20.6 1.0 O A:VAL167 3.5 16.2 1.0 C A:GLN170 4.0 19.7 1.0 CB A:GLN170 4.1 21.2 1.0 CG1 A:VAL167 4.1 19.2 1.0 CG2 B:THR231 4.3 24.1 1.0 CD2 B:LEU228 4.3 25.9 1.0 C A:VAL167 4.5 17.2 1.0 O A:GLN170 4.6 18.3 1.0 CA A:GLN170 4.7 20.2 1.0 CA A:VAL167 4.7 16.9 1.0 OE1 A:GLN170 4.8 25.0 1.0 O A:HOH426 4.8 40.9 1.0 C A:CYS171 5.0 19.6 1.0 CB B:THR231 5.0 23.5 1.0

Mercury binding site 3 out of 6 in the Crystal Structure of Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis


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 Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg301 b:63.0 occ:0.30 HG A:HG301 0.0 63.0 0.3 HG A:HG301 2.6 38.9 0.3 OE1 A:GLN170 2.9 25.0 1.0 CD A:GLN170 3.7 24.2 1.0 HG A:HG301 3.7 52.0 0.4 CB A:GLN170 3.8 21.2 1.0 O A:HOH426 4.1 40.9 1.0 CG1 A:VAL167 4.2 19.2 1.0 CA A:VAL167 4.2 16.9 1.0 CG2 A:VAL167 4.3 19.4 1.0 CG A:GLN170 4.4 22.1 1.0 O A:VAL167 4.4 16.2 1.0 CB A:VAL167 4.5 18.6 1.0 NE2 A:GLN170 4.6 25.2 1.0 SG A:CYS171 4.7 25.4 1.0 C A:VAL167 4.8 17.2 1.0 N A:CYS171 4.9 19.4 1.0

Mercury binding site 4 out of 6 in the Crystal Structure of Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis


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 Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg301 b:34.5 occ:0.40 HG B:HG301 0.0 34.5 0.4 SG B:CYS171 2.3 27.3 1.0 O B:HOH422 2.5 27.3 1.0 HG B:HG301 2.7 61.6 0.2 HG B:HG301 2.8 44.8 0.3 N B:CYS171 3.4 18.6 1.0 CB B:CYS171 3.5 21.4 1.0 O B:VAL167 3.5 17.2 1.0 CA B:CYS171 3.5 19.6 1.0 CG1 B:VAL167 3.9 21.3 1.0 C B:GLN170 4.1 19.1 1.0 CB B:GLN170 4.3 21.9 1.0 CG2 A:THR231 4.4 23.2 1.0 C B:VAL167 4.5 17.6 1.0 CD2 A:LEU228 4.6 22.6 1.0 O A:HOH424 4.7 30.7 1.0 O B:GLN170 4.7 17.4 1.0 CA B:VAL167 4.7 19.2 1.0 CA B:GLN170 4.8 19.8 1.0 CB B:VAL167 4.9 20.4 1.0 OE1 B:GLN170 5.0 32.2 1.0

Mercury binding site 5 out of 6 in the Crystal Structure of Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg301 b:44.8 occ:0.35 HG B:HG301 0.0 44.8 0.3 HG B:HG301 2.8 34.5 0.4 HG B:HG301 3.5 61.6 0.2 O B:GLN170 3.6 17.4 1.0 O B:HOH422 3.7 27.3 1.0 C B:GLN170 3.8 19.1 1.0 CD2 A:LEU228 3.9 22.6 1.0 N B:CYS171 3.9 18.6 1.0 CA B:CYS171 4.0 19.6 1.0 CB B:GLN170 4.1 21.9 1.0 SG B:CYS171 4.3 27.3 1.0 CB B:ALA174 4.3 21.9 1.0 CA B:GLN170 4.6 19.8 1.0 CB B:CYS171 4.7 21.4 1.0

Mercury binding site 6 out of 6 in the Crystal Structure of Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of Mercury Soaked C-Terminal Domain of RV1828 From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Hg301 b:61.6 occ:0.25 HG B:HG301 0.0 61.6 0.2 O A:HOH424 2.7 30.7 1.0 HG B:HG301 2.7 34.5 0.4 HG B:HG301 3.5 44.8 0.3 O B:HOH422 3.7 27.3 1.0 SG B:CYS171 3.9 27.3 1.0 CD2 A:LEU228 4.2 22.6 1.0 CG2 A:THR231 4.3 23.2 1.0 OG1 A:THR231 4.6 23.0 1.0 CB A:THR231 4.7 22.7 1.0

S.Singh, R.R.Sevalkar, D.Sarkar, S.Karthikeyan. Characteristics of the Essential Pathogenicity Factor RV1828, A Merr Family Transcription Regulator From Mycobacterium Tuberculosis. Febs J. V. 285 4424 2018.
ISSN: ISSN 1742-4658
PubMed: 30306715
DOI: 10.1111/FEBS.14676