Arsenic in PDB 5j39: Crystal Structure of the Extended Tudor Domain From TDRD2

The structure of Crystal Structure of the Extended Tudor Domain From TDRD2, PDB code: 5j39 was solved by H.Zhang, W.Tempel, A.Dong, C.Bountra, C.H.Arrowsmith, A.M.Edwards, J.Min, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.11 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.692, 53.798, 108.063, 90.00, 84.26, 90.00
R / Rfree (%)	19 / 22.2

The binding sites of Arsenic atom in the Crystal Structure of the Extended Tudor Domain From TDRD2 (pdb code 5j39). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Crystal Structure of the Extended Tudor Domain From TDRD2, PDB code: 5j39:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in the Crystal Structure of the Extended Tudor Domain From TDRD2


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of the Extended Tudor Domain From TDRD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:As501 b:78.0 occ:0.70 AS A:CAC501 0.0 78.0 0.7 O1 A:CAC501 1.6 79.0 0.7 O2 A:CAC501 1.7 78.9 0.7 C1 A:CAC501 2.0 78.0 0.7 C2 A:CAC501 2.0 76.3 0.7 OD2 A:ASP393 3.5 73.6 1.0 CD2 A:LEU364 4.1 66.0 1.0 CG A:PHE391 4.3 34.3 1.0 CG A:ASP393 4.4 64.9 1.0 CB A:PHE391 4.4 34.1 1.0 CD1 A:PHE391 4.6 35.9 1.0 CD2 A:PHE391 4.7 36.0 1.0 CZ A:TYR371 4.7 45.8 1.0 CB A:ASP393 4.7 44.9 1.0 CE1 A:TYR371 4.8 38.1 1.0 CE2 A:TYR371 4.9 38.8 1.0 OH A:TYR371 5.0 49.9 1.0

Arsenic binding site 2 out of 2 in the Crystal Structure of the Extended Tudor Domain From TDRD2


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of the Extended Tudor Domain From TDRD2 within 5.0Å range: probe atom residue distance (Å) B Occ B:As501 b:63.8 occ:0.80 AS B:CAC501 0.0 63.8 0.8 O1 B:CAC501 1.6 64.1 0.8 O2 B:CAC501 1.7 66.3 0.8 C2 B:CAC501 1.9 64.8 0.8 C1 B:CAC501 2.0 62.9 0.8 OD2 B:ASP393 3.8 60.6 1.0 CD2 B:LEU364 4.2 53.5 1.0 CG B:PHE391 4.4 31.3 1.0 CB B:PHE391 4.4 29.4 1.0 CG B:ASP393 4.4 55.2 1.0 CB B:ASP393 4.5 36.8 1.0 CD1 B:PHE391 4.6 33.2 1.0 CD1 B:LEU364 4.6 49.7 1.0 CZ B:TYR371 4.7 43.1 1.0 CD2 B:PHE388 4.7 34.7 1.0 CG B:PHE388 4.7 30.5 1.0 CE1 B:TYR371 4.7 35.2 1.0 CD2 B:PHE391 4.8 34.8 1.0 CE2 B:TYR371 4.9 32.7 1.0 CB B:PHE388 4.9 27.7 1.0 CD1 B:TYR371 4.9 31.3 1.0 CG B:LEU364 5.0 50.1 1.0

H.Zhang, K.Liu, N.Izumi, H.Huang, D.Ding, Z.Ni, S.S.Sidhu, C.Chen, Y.Tomari, J.Min. Structural Basis For Arginine Methylation-Independent Recognition of PIWIL1 By TDRD2. Proc. Natl. Acad. Sci. V. 114 12483 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29118143
DOI: 10.1073/PNAS.1711486114