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Chlorine in PDB 6o5f: Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State

Enzymatic activity of Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State

All present enzymatic activity of Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State:
3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State, PDB code: 6o5f was solved by H.Song, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.90 / 2.50
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 66.102, 66.102, 230.463, 90.00, 90.00, 120.00
R / Rfree (%) 21.2 / 24.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State (pdb code 6o5f). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State, PDB code: 6o5f:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 6o5f

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Chlorine binding site 1 out of 7 in the Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl701

b:64.8
occ:1.00
 OG1 A:THR323 3.0 52.9 1.0
N A:ARG326 3.1 57.1 1.0
N A:GLY325 3.3 49.5 1.0
CA A:GLY325 3.4 53.7 1.0
CB A:THR323 3.5 52.3 1.0
C A:GLY325 3.7 48.0 1.0
N A:GLY302 3.9 51.7 1.0
CB A:ARG326 4.0 54.1 1.0
C A:THR323 4.1 46.3 1.0
CA A:GLY302 4.1 60.3 1.0
CA A:ARG326 4.1 44.8 1.0
O A:THR323 4.1 49.0 1.0
CZ A:PHE357 4.1 63.3 1.0
CE1 A:PHE357 4.2 59.3 1.0
N A:PRO324 4.3 50.0 1.0
C A:PRO324 4.3 47.0 1.0
CA A:THR323 4.4 52.7 1.0
CG2 A:THR323 4.6 42.0 1.0
CD A:PRO324 4.8 49.2 1.0
O A:GLY325 4.8 50.5 1.0
CA A:PRO324 4.9 49.3 1.0

Chlorine binding site 2 out of 7 in 6o5f

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Chlorine binding site 2 out of 7 in the Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl702

b:65.4
occ:1.00
 N A:ARG478 3.1 48.7 1.0
CB A:ARG478 3.4 45.6 1.0
CB A:SER476 3.6 45.4 1.0
N A:GLN477 3.7 45.6 1.0
CA A:ARG478 3.8 46.8 1.0
OG A:SER476 3.8 49.9 1.0
C A:GLN477 4.0 52.4 1.0
CB A:GLN477 4.1 40.5 1.0
CA A:GLN477 4.1 50.0 1.0
C A:SER476 4.3 45.3 1.0
CA A:SER476 4.5 40.7 1.0
CG A:ARG478 4.7 45.7 1.0

Chlorine binding site 3 out of 7 in 6o5f

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Chlorine binding site 3 out of 7 in the Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl703

b:73.6
occ:1.00
 N A:PHE340 2.8 53.2 1.0
O A:PRO267 2.9 50.7 1.0
O A:GLY337 2.9 41.9 1.0
N A:CYS341 3.3 43.3 1.0
CB A:TYR266 3.3 53.0 1.0
CA A:PHE340 3.3 49.3 1.0
C A:LEU338 3.4 47.3 1.0
C A:PHE340 3.4 42.2 1.0
C A:TYR266 3.4 56.8 1.0
CA A:TYR266 3.5 49.0 1.0
CB A:PHE340 3.5 55.8 1.0
N A:ASP339 3.5 48.8 1.0
N A:PRO267 3.5 53.0 1.0
CA A:LEU338 3.6 48.5 1.0
O A:LEU338 3.8 47.8 1.0
CD A:PRO267 3.8 41.0 1.0
C A:PRO267 3.8 49.6 1.0
C A:GLY337 3.8 42.1 1.0
CD2 A:TYR266 3.9 54.1 1.0
O A:TYR266 3.9 55.7 1.0
C A:ASP339 4.0 54.5 1.0
N A:LEU338 4.1 50.9 1.0
CG A:TYR266 4.1 56.6 1.0
CD2 A:PHE340 4.1 56.9 1.0
O A:PHE340 4.1 44.5 1.0
CA A:CYS341 4.1 46.5 1.0
CG A:PHE340 4.2 50.0 1.0
CB A:CYS341 4.3 51.5 1.0
CA A:PRO267 4.3 45.0 1.0
CA A:ASP339 4.3 52.1 1.0
N A:ILE268 4.8 49.1 1.0
CB A:LEU338 4.9 40.9 1.0
N A:TYR266 4.9 52.4 1.0
CG A:PRO267 5.0 49.9 1.0

Chlorine binding site 4 out of 7 in 6o5f

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Chlorine binding site 4 out of 7 in the Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl704

b:82.9
occ:1.00
 N A:GLY227 2.8 73.8 1.0
N A:LYS230 3.3 49.7 1.0
N A:SER228 3.5 60.8 1.0
N A:GLY229 3.5 49.3 1.0
CA A:GLY227 3.6 63.9 1.0
CE A:LYS230 3.7 47.2 1.0
C A:THR226 3.7 66.3 1.0
CA A:THR226 3.7 73.0 1.0
CB A:LYS230 3.9 51.1 1.0
C A:GLY227 3.9 70.6 1.0
CG A:LYS230 4.1 62.2 1.0
CA A:GLY229 4.1 52.1 1.0
O A:GLN225 4.1 79.0 1.0
CA A:LYS230 4.2 53.2 1.0
C A:GLY229 4.2 55.4 1.0
C A:SER228 4.3 49.4 1.0
OG A:SER228 4.3 72.8 1.0
CA A:SER228 4.4 62.6 1.0
CD A:LYS230 4.5 58.9 1.0
N A:THR231 4.7 44.2 1.0
N A:THR226 4.7 75.1 1.0
CB A:THR226 4.7 69.0 1.0
NZ A:LYS230 4.8 54.5 1.0
C A:GLN225 4.8 69.5 1.0
O A:THR226 4.9 76.9 1.0
O A:GLY227 5.0 67.6 1.0

Chlorine binding site 5 out of 7 in 6o5f

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Chlorine binding site 5 out of 7 in the Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl701

b:62.1
occ:1.00
 OG1 B:THR323 3.0 45.9 1.0
N B:ARG326 3.1 51.7 1.0
N B:GLY325 3.1 50.4 1.0
CA B:GLY325 3.3 57.6 1.0
CB B:THR323 3.4 48.2 1.0
C B:GLY325 3.6 51.3 1.0
C B:THR323 3.9 50.0 1.0
N B:GLY302 3.9 52.3 1.0
O B:THR323 4.0 43.2 1.0
CZ B:PHE357 4.0 50.4 1.0
CB B:ARG326 4.1 55.7 1.0
CE1 B:PHE357 4.1 56.4 1.0
CA B:ARG326 4.2 48.5 1.0
N B:PRO324 4.2 54.4 1.0
C B:PRO324 4.2 55.6 1.0
CA B:GLY302 4.2 64.5 1.0
CA B:THR323 4.3 43.7 1.0
CG2 B:THR323 4.6 43.4 1.0
CD B:PRO324 4.7 49.3 1.0
CA B:PRO324 4.8 55.0 1.0
O B:GLY325 4.8 54.1 1.0

Chlorine binding site 6 out of 7 in 6o5f

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Chlorine binding site 6 out of 7 in the Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl702

b:75.5
occ:1.00
 N B:PHE340 2.9 50.0 1.0
O B:GLY337 2.9 37.8 1.0
O B:PRO267 3.0 47.7 1.0
CB B:TYR266 3.3 53.3 1.0
N B:CYS341 3.4 42.6 1.0
CA B:PHE340 3.4 47.6 1.0
C B:PHE340 3.4 42.4 1.0
C B:LEU338 3.4 47.1 1.0
C B:TYR266 3.4 53.9 1.0
CA B:TYR266 3.4 51.2 1.0
CB B:PHE340 3.5 50.5 1.0
N B:PRO267 3.5 53.1 1.0
CA B:LEU338 3.5 51.5 1.0
N B:ASP339 3.5 53.2 1.0
C B:GLY337 3.8 49.9 1.0
CD B:PRO267 3.8 44.4 1.0
O B:LEU338 3.8 41.2 1.0
C B:PRO267 3.8 48.7 1.0
CD2 B:TYR266 3.9 52.1 1.0
O B:TYR266 3.9 54.4 1.0
C B:ASP339 4.0 51.6 1.0
N B:LEU338 4.0 46.9 1.0
O B:PHE340 4.1 55.1 1.0
CG B:TYR266 4.1 58.4 1.0
CD2 B:PHE340 4.1 58.2 1.0
CA B:CYS341 4.1 47.1 1.0
CG B:PHE340 4.2 53.2 1.0
CA B:PRO267 4.3 45.5 1.0
CB B:CYS341 4.3 53.1 1.0
CA B:ASP339 4.3 49.9 1.0
N B:ILE268 4.9 52.5 1.0
CB B:LEU338 4.9 42.2 1.0
N B:TYR266 4.9 60.7 1.0
CG B:PRO267 5.0 48.6 1.0

Chlorine binding site 7 out of 7 in 6o5f

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Chlorine binding site 7 out of 7 in the Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Dead-Box Rna Helicase DDX3X at Pre-Unwound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl703

b:64.9
occ:1.00
 N B:ARG478 3.0 48.1 1.0
CB B:ARG478 3.3 38.5 1.0
N B:GLN477 3.7 42.6 1.0
CB B:SER476 3.7 43.8 1.0
CA B:ARG478 3.8 47.0 1.0
O B:HOH827 3.8 52.0 1.0
OG B:SER476 3.9 43.4 1.0
C B:GLN477 4.0 52.5 1.0
CA B:GLN477 4.1 48.0 1.0
CB B:GLN477 4.1 42.5 1.0
C B:SER476 4.3 47.8 1.0
CA B:SER476 4.5 49.7 1.0
CG B:ARG478 4.7 44.6 1.0

Reference:

H.Song, X.Ji. The Mechanism of Rna Duplex Recognition and Unwinding By Dead-Box Helicase DDX3X. Nat Commun V. 10 3085 2019.
ISSN: ESSN 2041-1723
PubMed: 31300642
DOI: 10.1038/S41467-019-11083-2
Page generated: Mon Jul 29 12:30:23 2024

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