Magnesium in PDB 5vhc: DHX36 with An N-Terminal Truncation Bound to Adp-BEF3

The structure of DHX36 with An N-Terminal Truncation Bound to Adp-BEF3, PDB code: 5vhc was solved by M.Chen, A.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.50 / 2.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.878, 111.516, 62.966, 90.00, 110.67, 90.00
R / Rfree (%)	19.4 / 23.3

The structure of DHX36 with An N-Terminal Truncation Bound to Adp-BEF3 also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Magnesium atom in the DHX36 with An N-Terminal Truncation Bound to Adp-BEF3 (pdb code 5vhc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the DHX36 with An N-Terminal Truncation Bound to Adp-BEF3, PDB code: 5vhc:

Magnesium binding site 1 out of 1 in the DHX36 with An N-Terminal Truncation Bound to Adp-BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of DHX36 with An N-Terminal Truncation Bound to Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1101 b:47.4 occ:1.00 F1 D:BEF1102 2.0 48.5 1.0 OG1 D:THR239 2.0 45.2 1.0 OE1 D:GLU337 2.3 45.9 1.0 O1B D:ADP1103 2.5 41.0 1.0 BE D:BEF1102 2.9 45.4 1.0 O3B D:ADP1103 3.1 41.3 1.0 CD D:GLU337 3.3 50.8 1.0 PB D:ADP1103 3.3 40.3 1.0 CB D:THR239 3.3 46.9 1.0 OE2 D:GLU337 3.5 61.3 1.0 F2 D:BEF1102 3.6 50.1 1.0 OD2 D:ASP336 3.8 56.4 1.0 N D:THR239 4.0 40.2 1.0 O2A D:ADP1103 4.1 41.5 1.0 OD1 D:ASP336 4.1 53.5 1.0 CA D:THR239 4.2 46.2 1.0 CG2 D:THR239 4.3 35.0 1.0 F3 D:BEF1102 4.3 40.8 1.0 O2B D:ADP1103 4.4 38.1 1.0 CG D:ASP336 4.4 52.5 1.0 O3A D:ADP1103 4.4 41.3 1.0 CA D:SER559 4.4 48.8 1.0 O D:HOH1260 4.5 41.6 1.0 CG D:GLU337 4.6 44.7 1.0 CE D:LYS238 4.6 47.2 1.0 OG D:SER559 4.7 47.7 1.0 PA D:ADP1103 4.7 35.5 1.0 CB D:LYS238 4.8 51.7 1.0 CB D:SER559 4.8 45.0 1.0 NZ D:LYS238 4.9 41.7 1.0 NH2 D:ARG607 5.0 67.8 1.0

M.C.Chen, R.Tippana, N.A.Demeshkina, P.Murat, S.Balasubramanian, S.Myong, A.R.Ferre-D'amare. Structural Basis of G-Quadruplex Unfolding By the Deah/Rha Helicase DHX36. Nature V. 558 465 2018.
ISSN: ESSN 1476-4687
PubMed: 29899445
DOI: 10.1038/S41586-018-0209-9