Atomistry » Mercury » PDB 5lf8-6bvg » 5ydc
Atomistry »
  Mercury »
    PDB 5lf8-6bvg »
      5ydc »

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

Protein crystallography data

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

Mercury Binding Sites:

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 5ydc

Go back to Mercury Binding Sites List in 5ydc
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 5ydc

Go back to Mercury Binding Sites List in 5ydc
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 5ydc

Go back to Mercury Binding Sites List in 5ydc
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 5ydc

Go back to Mercury Binding Sites List in 5ydc
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 5ydc

Go back to Mercury Binding Sites List in 5ydc
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 5ydc

Go back to Mercury Binding Sites List in 5ydc
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

Reference:

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
Page generated: Sun Dec 13 19:13:24 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy