Bromine in PDB 6djh: Crystal Structure of TDP1 Catalytic Domain in Complex with Compound XZ515

The structure of Crystal Structure of TDP1 Catalytic Domain in Complex with Compound XZ515, PDB code: 6djh was solved by G.T.Lountos, X.Z.Zhao, E.Kiselev, J.E.Tropea, D.Needle, T.R.Burke Jr., Y.Pommier, D.S.Waugh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.08 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.074, 105.149, 194.447, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 23

The binding sites of Bromine atom in the Crystal Structure of TDP1 Catalytic Domain in Complex with Compound XZ515 (pdb code 6djh). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of TDP1 Catalytic Domain in Complex with Compound XZ515, PDB code: 6djh:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of TDP1 Catalytic Domain in Complex with Compound XZ515


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of TDP1 Catalytic Domain in Complex with Compound XZ515 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br701 b:85.2 occ:0.73 BR9 A:GNM701 0.0 85.2 0.7 C08 A:GNM701 1.9 40.1 0.7 C07 A:GNM701 2.9 35.9 0.7 C10 A:GNM701 2.9 35.8 0.7 N06 A:GNM701 3.0 33.6 0.7 O A:HOH932 3.5 42.5 1.0 OH A:TYR204 3.9 40.3 1.0 O A:HOH1032 4.1 49.2 1.0 C13 A:GNM701 4.2 29.7 0.7 C11 A:GNM701 4.2 34.4 0.7 C05 A:GNM701 4.3 35.3 0.7 CG A:PRO461 4.4 26.9 1.0 CB A:PRO461 4.5 29.6 1.0 O A:HOH1085 4.6 45.9 1.0 O A:HOH833 4.6 51.6 1.0 C12 A:GNM701 4.7 34.4 0.7 O A:HOH1110 4.7 52.3 1.0 CZ A:TYR204 4.8 40.9 1.0 CH2 A:TRP590 4.9 43.7 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of TDP1 Catalytic Domain in Complex with Compound XZ515


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of TDP1 Catalytic Domain in Complex with Compound XZ515 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br701 b:68.5 occ:0.60 BR9 B:GNM701 0.0 68.5 0.6 C08 B:GNM701 1.9 39.2 0.6 C10 B:GNM701 2.9 36.5 0.6 C07 B:GNM701 2.9 37.1 0.6 N06 B:GNM701 3.1 35.6 0.6 C13 B:GNM701 4.2 36.5 0.6 C11 B:GNM701 4.2 34.1 0.6 OH B:TYR204 4.2 45.3 1.0 CB B:PRO461 4.3 41.7 1.0 CG B:PRO461 4.4 29.2 1.0 C05 B:GNM701 4.4 40.4 0.6 C12 B:GNM701 4.7 31.2 0.6 CH2 B:TRP590 4.8 38.9 1.0

G.T.Lountos, X.Z.Zhao, E.Kiselev, J.E.Tropea, D.Needle, Y.Pommier, T.R.Burke, D.S.Waugh. Identification of A Ligand Binding Hot Spot and Structural Motifs Replicating Aspects of Tyrosyl-Dna Phosphodiesterase I (TDP1) Phosphoryl Recognition By Crystallographic Fragment Cocktail Screening. Nucleic Acids Res. V. 47 10134 2019.
ISSN: ESSN 1362-4962
PubMed: 31199869
DOI: 10.1093/NAR/GKZ515