Magnesium in PDB 6l5n: Crystal Structure of Human Dead-Box Rna Helicase DDX21 at Post-Unwound State

All present enzymatic activity of Crystal Structure of Human Dead-Box Rna Helicase DDX21 at Post-Unwound State:
3.6.4.13;

The structure of Crystal Structure of Human Dead-Box Rna Helicase DDX21 at Post-Unwound State, PDB code: 6l5n was solved by Z.J.Chen, X.J.Hu, Z.Zhou, J.X.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.52 / 2.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.360, 89.230, 79.690, 90.00, 115.60, 90.00
R / Rfree (%)	17.5 / 23.3

The binding sites of Magnesium atom in the Crystal Structure of Human Dead-Box Rna Helicase DDX21 at Post-Unwound State (pdb code 6l5n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Dead-Box Rna Helicase DDX21 at Post-Unwound State, PDB code: 6l5n:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Human Dead-Box Rna Helicase DDX21 at Post-Unwound State


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 Human Dead-Box Rna Helicase DDX21 at Post-Unwound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:15.0 occ:1.00 O1G A:ANP601 1.9 15.4 1.0 O A:HOH716 2.0 14.7 1.0 O2B A:ANP601 2.0 12.7 1.0 O A:HOH718 2.1 15.8 1.0 O A:HOH723 2.1 13.0 1.0 O A:HOH743 2.3 17.0 1.0 PG A:ANP601 3.2 19.6 1.0 PB A:ANP601 3.3 18.7 1.0 N3B A:ANP601 3.6 20.4 1.0 OE1 A:GLU340 3.7 20.2 1.0 OD2 A:ASP339 3.7 19.1 1.0 OD1 A:ASP339 3.9 20.2 1.0 OG1 A:THR237 4.0 13.8 1.0 O3G A:ANP601 4.0 20.5 1.0 CA A:GLY500 4.1 18.7 1.0 CG A:ASP339 4.2 19.6 1.0 O1B A:ANP601 4.3 18.5 1.0 O2G A:ANP601 4.4 14.2 1.0 O2A A:ANP601 4.4 17.1 1.0 O3A A:ANP601 4.4 19.9 1.0 O A:GLY500 4.4 17.5 1.0 O A:HOH747 4.5 19.2 1.0 CE A:LYS236 4.5 18.6 1.0 O1A A:ANP601 4.6 17.8 1.0 PA A:ANP601 4.7 17.6 1.0 CB A:LYS236 4.8 15.6 1.0 C A:GLY500 4.8 20.0 1.0 CD A:GLU340 4.8 24.0 1.0 O A:HOH760 4.9 16.5 1.0 N A:THR237 4.9 15.8 1.0 N A:GLY500 5.0 18.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Dead-Box Rna Helicase DDX21 at Post-Unwound State


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 Human Dead-Box Rna Helicase DDX21 at Post-Unwound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:20.2 occ:1.00 O B:HOH713 2.0 18.2 1.0 O B:HOH739 2.0 19.6 1.0 O1G B:ANP601 2.0 21.7 1.0 O2B B:ANP601 2.1 20.2 1.0 O B:HOH717 2.1 20.3 1.0 O B:HOH726 2.2 17.3 1.0 PG B:ANP601 3.3 21.2 1.0 PB B:ANP601 3.5 18.6 1.0 OD2 B:ASP339 3.6 23.4 1.0 OE1 B:GLU340 3.7 26.5 1.0 N3B B:ANP601 3.8 20.0 1.0 OD1 B:ASP339 3.9 26.1 1.0 OG1 B:THR237 3.9 21.8 1.0 CA B:GLY500 4.1 21.4 1.0 O3G B:ANP601 4.1 22.3 1.0 CG B:ASP339 4.2 31.6 1.0 O2A B:ANP601 4.3 20.5 1.0 O1B B:ANP601 4.4 21.6 1.0 O B:HOH724 4.4 21.0 1.0 CE B:LYS236 4.5 18.9 1.0 O3A B:ANP601 4.5 19.6 1.0 O2G B:ANP601 4.5 12.7 1.0 O B:GLY500 4.6 22.3 1.0 PA B:ANP601 4.7 19.5 1.0 O1A B:ANP601 4.7 18.5 1.0 CD B:GLU340 4.8 29.6 1.0 CB B:LYS236 4.8 19.8 1.0 C B:GLY500 4.9 20.3 1.0 N B:THR237 4.9 20.1 1.0 NZ B:LYS236 4.9 20.6 1.0 O B:HOH731 5.0 16.1 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Dead-Box Rna Helicase DDX21 at Post-Unwound State


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 Human Dead-Box Rna Helicase DDX21 at Post-Unwound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:57.3 occ:1.00 O B:HOH753 2.0 51.0 1.0 O2A B:ANP602 2.1 61.4 1.0 O2G B:ANP602 2.1 49.2 1.0 O B:HOH742 2.2 55.4 1.0 O B:HOH704 2.4 43.0 1.0 O2B B:ANP602 2.4 53.2 1.0 PG B:ANP602 3.3 59.8 1.0 PA B:ANP602 3.4 48.4 1.0 PB B:ANP602 3.4 54.0 1.0 O3A B:ANP602 3.7 54.9 1.0 OD1 B:ASP517 3.7 66.2 1.0 O1G B:ANP602 3.7 61.5 1.0 N3B B:ANP602 3.9 52.3 1.0 O B:HOH752 4.1 39.9 1.0 OE1 B:GLU519 4.1 44.8 1.0 NZ A:LYS474 4.2 43.9 1.0 O5' B:ANP602 4.3 54.9 1.0 C8 B:ANP602 4.4 33.4 1.0 O1A B:ANP602 4.4 63.2 1.0 O3G B:ANP602 4.6 44.8 1.0 OE2 B:GLU519 4.7 47.6 1.0 O1B B:ANP602 4.7 65.1 1.0 CD B:GLU519 4.8 55.6 1.0 C2' B:ANP602 4.8 45.6 1.0 CG B:ASP517 4.9 59.1 1.0

Z.Chen, Z.Li, X.Hu, F.Xie, S.Kuang, B.Zhan, W.Gao, X.Chen, S.Gao, Y.Li, Y.Wang, F.Qian, C.Ding, J.Gan, C.Ji, X.Xu, Z.Zhou, J.Huang, H.H.He, J.Li. Structural Basis of Human Helicase DDX21 in Rna Binding, Unwinding, and Antiviral Signal Activation. Adv Sci 2020.
DOI: 10.1002/ADVS.202000532