Calcium in PDB 6d2s: Mycobacterium Tuberculosis Transcriptional Regulator

Protein crystallography data

The structure of Mycobacterium Tuberculosis Transcriptional Regulator, PDB code: 6d2s was solved by S.Tang, J.Sacchettini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.10 / 1.82
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 74.999, 81.724, 95.365, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.9

Other elements in 6d2s:

The structure of Mycobacterium Tuberculosis Transcriptional Regulator also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Mycobacterium Tuberculosis Transcriptional Regulator (pdb code 6d2s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Mycobacterium Tuberculosis Transcriptional Regulator, PDB code: 6d2s:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6d2s

Go back to Calcium Binding Sites List in 6d2s
Calcium binding site 1 out of 2 in the Mycobacterium Tuberculosis Transcriptional Regulator


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mycobacterium Tuberculosis Transcriptional Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:15.0
occ:0.50
OD1 A:ASP164 2.4 15.7 1.0
OD1 A:ASP160 2.4 17.4 1.0
OD2 A:ASP164 2.5 18.0 1.0
OD2 A:ASP160 2.5 18.8 1.0
CG A:ASP164 2.8 20.4 1.0
CG A:ASP160 2.8 20.7 1.0
O A:HOH633 4.2 35.8 1.0
CB A:ASP164 4.3 17.8 1.0
CB A:ASP160 4.3 18.5 1.0
O A:HOH700 4.5 37.8 1.0
O A:ASP160 4.5 15.9 1.0
O A:HOH653 4.8 24.4 1.0
CD2 A:TYR163 4.8 16.5 1.0
C A:ASP160 5.0 18.5 1.0
CA A:ASP160 5.0 20.2 1.0

Calcium binding site 2 out of 2 in 6d2s

Go back to Calcium Binding Sites List in 6d2s
Calcium binding site 2 out of 2 in the Mycobacterium Tuberculosis Transcriptional Regulator


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mycobacterium Tuberculosis Transcriptional Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:24.2
occ:1.00
O A:LEU403 2.3 30.1 1.0
O A:ALA399 2.3 35.5 1.0
O A:HOH630 2.3 27.5 1.0
O A:HOH641 2.4 27.8 1.0
OD2 A:ASP401 2.4 40.3 1.0
O A:HOH608 2.6 39.7 1.0
O A:HOH618 3.0 50.2 1.0
C A:LEU403 3.4 27.2 1.0
C A:ALA399 3.5 48.6 1.0
CG A:ASP401 3.6 46.5 1.0
N A:ALA399 4.1 39.2 1.0
N A:ASP401 4.1 48.7 1.0
OD1 A:ASP401 4.1 49.5 1.0
N A:LEU403 4.1 29.8 1.0
CA A:LEU403 4.2 27.8 1.0
CA A:ALA399 4.2 43.3 1.0
OE2 A:GLU315 4.3 18.7 1.0
N A:GLY404 4.3 25.4 1.0
CA A:GLY404 4.4 24.7 1.0
OE1 A:GLU315 4.5 18.7 1.0
CB A:ALA399 4.5 47.1 1.0
N A:ALA400 4.5 53.8 1.0
CB A:LEU403 4.6 33.4 1.0
CB A:THR398 4.6 40.4 1.0
C A:THR398 4.6 40.0 1.0
O A:HOH640 4.7 29.5 1.0
C A:ASP401 4.7 51.5 1.0
O A:ASP401 4.7 51.7 1.0
O A:HOH735 4.7 24.2 1.0
CB A:ASP401 4.7 47.1 1.0
CA A:ASP401 4.7 49.3 1.0
CA A:ALA400 4.8 59.1 1.0
CD A:GLU315 4.8 22.6 1.0
C A:ALA400 4.9 54.2 1.0
O A:GLY404 5.0 27.3 1.0
OG1 A:THR398 5.0 47.6 1.0

Reference:

S.Tang, N.D.Hicks, Y.S.Cheng, A.Silva, S.M.Fortune, J.C.Sacchettini. Structural and Functional Insight Into the Mycobacterium Tuberculosis Protein Prpr Reveals A Novel Type of Transcription Factor. Nucleic Acids Res. V. 47 9934 2019.
ISSN: ESSN 1362-4962
PubMed: 31504787
DOI: 10.1093/NAR/GKZ724
Page generated: Sat Dec 12 06:02:14 2020

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