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

Enzymatic activity of 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;

Protein crystallography data

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

Magnesium Binding Sites:

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 6l5n

Go back to Magnesium Binding Sites List in 6l5n
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 6l5n

Go back to Magnesium Binding Sites List in 6l5n
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 6l5n

Go back to Magnesium Binding Sites List in 6l5n
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

Reference:

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
Page generated: Tue Oct 1 10:21:15 2024

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