Atomistry » Chlorine » PDB 6o0v-6o8o » 6o5f
Atomistry »
  Chlorine »
    PDB 6o0v-6o8o »
      6o5f »

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

Go back to Chlorine Binding Sites List in 6o5f
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

Go back to Chlorine Binding Sites List in 6o5f
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

Go back to Chlorine Binding Sites List in 6o5f
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

Go back to Chlorine Binding Sites List in 6o5f
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

Go back to Chlorine Binding Sites List in 6o5f
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

Go back to Chlorine Binding Sites List in 6o5f
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

Go back to Chlorine Binding Sites List in 6o5f
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy