Magnesium in PDB 6uv2: Crystal Structure of Apo Core Domain of Rna Helicase DDX17

All present enzymatic activity of Crystal Structure of Apo Core Domain of Rna Helicase DDX17:
3.6.4.13;

The structure of Crystal Structure of Apo Core Domain of Rna Helicase DDX17, PDB code: 6uv2 was solved by T.D.Ngo, A.C.Partin, Y.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.81 / 1.89
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.722, 112.722, 99.426, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 19.1

The structure of Crystal Structure of Apo Core Domain of Rna Helicase DDX17 also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Apo Core Domain of Rna Helicase DDX17 (pdb code 6uv2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Apo Core Domain of Rna Helicase DDX17, PDB code: 6uv2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Apo Core Domain of Rna Helicase DDX17


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Apo Core Domain of Rna Helicase DDX17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:22.9 occ:1.00 F1 A:BEF502 2.0 21.5 1.0 O A:HOH697 2.1 21.2 1.0 O1B A:ADP501 2.1 19.7 1.0 O A:HOH735 2.1 20.9 1.0 O A:HOH736 2.2 21.7 1.0 O A:HOH726 2.2 21.4 1.0 BE A:BEF502 3.1 22.3 1.0 PB A:ADP501 3.3 22.8 1.0 O3B A:ADP501 3.5 21.9 1.0 OE2 A:GLU247 3.9 23.5 1.0 OG1 A:THR143 3.9 22.2 1.0 OD2 A:ASP246 3.9 23.7 1.0 F3 A:BEF502 4.0 22.2 1.0 OD1 A:ASP246 4.1 21.9 1.0 CA A:GLY402 4.2 21.7 1.0 O3A A:ADP501 4.3 22.9 1.0 F2 A:BEF502 4.3 23.9 1.0 O1A A:ADP501 4.4 24.6 1.0 O2B A:ADP501 4.4 21.8 1.0 O A:GLY402 4.4 22.1 1.0 CG A:ASP246 4.4 23.9 1.0 O A:HOH787 4.5 22.7 1.0 O2A A:ADP501 4.5 23.4 1.0 PA A:ADP501 4.5 23.9 1.0 CE A:LYS142 4.6 19.9 1.0 CB A:LYS142 4.8 22.3 1.0 C A:GLY402 4.8 23.5 1.0 NZ A:LYS142 4.9 22.7 1.0 N A:THR143 4.9 21.1 1.0 CD A:GLU247 4.9 23.1 1.0 NH2 A:ARG432 5.0 23.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Apo Core Domain of Rna Helicase DDX17


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Apo Core Domain of Rna Helicase DDX17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:39.7 occ:1.00 O A:HOH786 2.6 44.2 1.0 N A:ASP131 3.0 24.3 1.0 O A:ASP294 3.0 32.1 1.0 O A:ARG293 3.1 32.7 1.0 O A:HOH892 3.1 48.7 1.0 MG A:MG505 3.1 35.9 1.0 CG A:ARG130 3.6 36.0 1.0 CA A:ARG130 3.6 23.6 1.0 CB A:ASP131 3.7 22.5 1.0 C A:ARG130 3.8 22.7 1.0 C A:ASP294 3.8 31.3 1.0 OD1 A:ASP131 3.9 25.6 1.0 CB A:ASP294 3.9 33.9 1.0 CG A:ASP131 3.9 27.3 1.0 CA A:ASP131 4.0 23.0 1.0 C A:ARG293 4.2 31.0 1.0 CB A:ARG130 4.2 26.1 1.0 NH1 A:ARG130 4.2 36.5 1.0 O A:HOH621 4.3 45.7 1.0 CA A:ASP294 4.3 31.8 1.0 O A:GLY129 4.3 27.5 1.0 CZ A:ARG130 4.7 39.6 1.0 CD A:ARG130 4.7 34.3 1.0 OD2 A:ASP131 4.7 26.6 1.0 N A:ASP294 4.7 32.1 1.0 N A:TYR295 4.7 25.1 1.0 O A:ASP131 4.8 22.1 1.0 N A:ARG130 4.8 24.1 1.0 NE A:ARG130 4.8 39.4 1.0 C A:ASP131 4.9 23.8 1.0 CA A:TYR295 4.9 22.7 1.0 O A:HOH718 5.0 38.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Apo Core Domain of Rna Helicase DDX17


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Apo Core Domain of Rna Helicase DDX17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:35.9 occ:1.00 OD1 A:ASP131 2.7 25.6 1.0 NZ A:LYS53 2.7 40.0 1.0 O A:GLY129 2.7 27.5 1.0 O A:HOH786 3.0 44.2 1.0 MG A:MG504 3.1 39.7 1.0 CE A:LYS53 3.3 44.7 1.0 CD A:LYS53 3.4 44.9 1.0 N A:ASP131 3.5 24.3 1.0 CA A:GLN272 3.6 25.6 1.0 O A:HOH718 3.6 38.2 1.0 CG A:ASP131 3.7 27.3 1.0 O A:ARG271 3.8 28.5 1.0 CB A:GLN272 3.8 24.5 1.0 CG A:GLN272 3.9 24.2 1.0 C A:GLY129 3.9 26.0 1.0 C A:ARG130 4.0 22.7 1.0 CA A:ARG130 4.1 23.6 1.0 O A:HOH892 4.2 48.7 1.0 N A:GLN272 4.3 24.9 1.0 CA A:ASP131 4.3 23.0 1.0 C A:ARG271 4.4 28.9 1.0 CB A:ASP131 4.4 22.5 1.0 N A:ARG130 4.5 24.1 1.0 CG A:LYS53 4.6 47.7 1.0 OD2 A:ASP131 4.6 26.6 1.0 O A:ARG130 4.8 24.6 1.0 C A:GLN272 4.8 26.1 1.0 N A:THR273 4.8 23.0 1.0 CD A:GLN272 4.9 26.4 1.0 O A:ASP270 4.9 34.7 1.0 O A:ARG293 5.0 32.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Apo Core Domain of Rna Helicase DDX17


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Apo Core Domain of Rna Helicase DDX17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:32.6 occ:0.84 O A:HOH776 2.3 36.4 1.0 O A:GLU304 2.3 24.6 1.0 OG A:SER306 2.4 32.6 1.0 O A:ASN302 2.5 29.1 1.0 O A:HOH775 2.8 23.8 1.0 CB A:SER306 3.4 27.8 1.0 C A:GLU304 3.5 29.0 1.0 N A:SER306 3.5 25.0 1.0 C A:ASN302 3.6 28.9 1.0 CA A:SER306 4.1 27.6 1.0 C A:LEU305 4.1 24.1 1.0 C A:LEU303 4.2 32.0 1.0 CA A:LEU305 4.2 24.7 1.0 N A:LEU305 4.3 24.6 1.0 N A:GLU304 4.3 26.0 1.0 O A:LEU303 4.3 32.5 1.0 N A:ASN302 4.4 26.8 1.0 CA A:ASN302 4.4 32.1 1.0 N A:LEU303 4.5 28.0 1.0 O A:SER306 4.5 28.1 1.0 CA A:GLU304 4.6 29.5 1.0 ND2 A:ASN299 4.6 34.1 1.0 O A:HOH822 4.6 26.5 1.0 OD1 A:ASN299 4.6 37.9 1.0 CA A:LEU303 4.6 29.5 1.0 CB A:ASN302 4.6 34.0 1.0 O A:VAL300 4.8 25.1 1.0 C A:SER306 4.8 28.8 1.0 O A:LEU305 4.9 26.0 1.0 C A:GLY301 4.9 25.9 1.0 O A:HOH708 4.9 40.6 1.0

T.D.Ngo, A.C.Partin, Y.Nam. Rna Specificity and Autoregulation of DDX17, A Modulator of Microrna Biogenesis. Cell Rep V. 29 4024 2019.
ISSN: ESSN 2211-1247
PubMed: 31851931
DOI: 10.1016/J.CELREP.2019.11.059