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Chlorine in PDB 4qik: Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex

Protein crystallography data

The structure of Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex, PDB code: 4qik was solved by D.Tan, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.68 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.800, 93.100, 100.200, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.2

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex (pdb code 4qik). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 14 binding sites of Chlorine where determined in the Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex, PDB code: 4qik:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 14 in 4qik

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Chlorine binding site 1 out of 14 in the Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex


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 the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:20.1
occ:1.00
 O A:HOH773 2.6 34.6 1.0
N A:PHE194 3.2 8.8 1.0
O A:HOH639 3.4 20.6 1.0
CD A:ARG188 3.5 21.4 1.0
O A:PHE194 3.7 12.2 1.0
CE3 A:TRP184 3.7 16.6 1.0
CG A:ARG188 3.7 14.0 1.0
CB A:TRP184 3.8 13.9 1.0
CA A:GLN193 3.8 10.1 1.0
O A:HOH728 3.9 31.0 1.0
CG A:GLN193 3.9 17.5 1.0
C A:GLN193 4.0 9.4 1.0
O A:HOH689 4.0 30.1 1.0
CA A:PHE194 4.1 9.3 1.0
CG1 A:VAL187 4.1 8.2 1.0
CD2 A:TRP184 4.1 15.0 1.0
O A:TRP184 4.1 12.0 1.0
CB A:PHE194 4.1 9.7 1.0
CG A:TRP184 4.2 16.0 1.0
C A:PHE194 4.2 11.2 1.0
CA A:TRP184 4.3 13.3 1.0
CB A:VAL187 4.3 9.3 1.0
CB A:GLN193 4.4 13.2 1.0
CZ3 A:TRP184 4.6 15.4 1.0
C A:TRP184 4.6 11.2 1.0
O A:CYS192 4.8 12.1 1.0
N A:ARG188 4.9 9.4 1.0
NE A:ARG188 4.9 25.2 1.0
CD A:GLN193 5.0 22.0 1.0
N A:GLN193 5.0 10.9 1.0

Chlorine binding site 2 out of 14 in 4qik

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Chlorine binding site 2 out of 14 in the Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex


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 the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:22.5
occ:1.00
 O A:HOH742 2.6 29.5 1.0
N A:MSE199 3.2 9.8 1.0
N A:ALA198 3.3 10.8 1.0
C A:GLY196 3.5 10.6 1.0
CA A:GLY196 3.6 13.3 1.0
N A:PRO197 3.7 11.2 1.0
CB A:ALA198 3.7 15.7 1.0
CB A:MSE199 3.8 12.5 1.0
CA A:ALA198 3.9 10.7 1.0
O A:GLY196 3.9 11.7 1.0
C A:ALA198 4.0 11.5 1.0
CE A:MSE199 4.1 17.4 1.0
CD A:PRO197 4.1 14.6 1.0
CA A:MSE199 4.1 10.6 1.0
C A:PRO197 4.2 12.1 1.0
O A:LEU195 4.3 22.2 1.0
CA A:PRO197 4.5 11.0 1.0
N A:GLY196 4.6 14.2 1.0
C A:LEU195 4.8 16.1 1.0
CE1 A:PHE234 4.9 18.9 1.0
O A:HOH696 5.0 32.8 1.0

Chlorine binding site 3 out of 14 in 4qik

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Chlorine binding site 3 out of 14 in the Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex


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 the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:32.8
occ:1.00
 O A:HOH911 2.9 31.9 1.0
N A:GLN144 3.2 24.5 1.0
O A:HOH826 3.3 38.2 1.0
NH1 A:ARG153 3.4 44.2 1.0
CA A:GLY150 3.5 20.1 1.0
CA A:CYS143 3.8 22.0 1.0
CD A:ARG153 3.9 31.1 1.0
CB A:GLN144 3.9 24.1 1.0
C A:CYS143 4.0 21.7 1.0
CG A:GLN144 4.1 27.5 1.0
CA A:GLN144 4.1 22.6 1.0
N A:GLY150 4.2 25.3 1.0
O A:HIS142 4.3 24.5 1.0
CZ A:ARG153 4.5 50.4 1.0
CB A:CYS143 4.6 21.6 1.0
C A:GLY150 4.6 25.4 1.0
NE A:ARG153 4.6 39.0 1.0
O A:GLY150 4.7 20.8 1.0
O A:GLN144 4.7 22.2 1.0
N A:CYS143 4.8 19.6 1.0
O A:HOH919 4.8 40.6 1.0
CB A:ARG153 4.9 23.9 1.0
C A:GLU149 4.9 32.5 1.0
C A:GLN144 4.9 18.7 1.0
O A:GLU149 4.9 29.2 1.0
C A:HIS142 4.9 24.7 0.7
CG A:ARG153 4.9 27.6 1.0
SG A:CYS143 5.0 22.1 1.0

Chlorine binding site 4 out of 14 in 4qik

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Chlorine binding site 4 out of 14 in the Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex


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 the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:36.6
occ:1.00
 NZ A:LYS100 3.2 31.4 1.0
N A:LEU145 3.3 15.9 1.0
OH A:TYR96 3.5 23.2 1.0
N A:VAL146 3.8 21.6 1.0
CE A:LYS100 3.8 33.1 1.0
CG1 A:VAL146 3.9 17.9 1.0
CG2 A:VAL146 4.0 20.6 1.0
OE1 A:GLN144 4.0 35.1 1.0
C A:GLN144 4.0 18.7 1.0
CE1 A:TYR96 4.0 19.3 1.0
CA A:GLN144 4.1 22.6 1.0
CA A:LEU145 4.1 15.3 1.0
O A:HOH801 4.2 28.8 1.0
CZ A:TYR96 4.2 22.9 1.0
CD A:LYS100 4.3 32.7 1.0
CB A:LEU145 4.3 18.3 1.0
C A:LEU145 4.4 19.7 1.0
CB A:VAL146 4.4 17.4 1.0
CD A:GLN144 4.4 36.6 1.0
O A:CYS143 4.6 20.4 1.0
CA A:VAL146 4.7 19.7 1.0
NE2 A:GLN144 4.7 32.0 1.0
CB A:GLN144 4.8 24.1 1.0
CG A:LEU145 4.9 22.4 1.0
O A:HOH771 5.0 33.8 1.0

Chlorine binding site 5 out of 14 in 4qik

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Chlorine binding site 5 out of 14 in the Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex


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 the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:28.6
occ:1.00
 OG A:SER305 2.8 16.7 0.5
NE2 A:GLN311 3.3 24.3 1.0
O A:HOH976 3.4 35.3 1.0
O A:HOH895 3.5 37.0 1.0
C A:ASP310 3.6 21.9 1.0
CA A:ASP310 3.6 21.5 1.0
O A:ASP310 3.7 18.9 1.0
CB A:SER305 3.7 19.3 0.5
OG A:SER305 3.7 16.7 0.5
CB A:SER305 3.8 19.3 0.5
CG A:GLN311 3.8 23.9 1.0
N A:ASP310 3.8 17.5 1.0
CD A:GLN311 4.0 26.6 1.0
CA A:SER305 4.1 16.2 0.5
CA A:SER305 4.1 16.2 0.5
C A:GLY309 4.1 22.7 1.0
N A:GLN311 4.1 22.6 1.0
O A:GLY309 4.2 19.7 1.0
O A:HOH763 4.3 35.4 1.0
N A:SER305 4.8 13.5 1.0
CA A:GLN311 4.8 19.6 1.0
CB A:GLN311 4.8 28.4 1.0
CA A:GLY309 5.0 19.1 1.0

Chlorine binding site 6 out of 14 in 4qik

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Chlorine binding site 6 out of 14 in the Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex


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 the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:36.4
occ:1.00
 O A:HOH918 2.6 38.8 1.0
O A:HOH659 3.0 28.2 1.0
N A:ASN175 3.1 23.7 1.0
O A:HOH611 3.2 18.0 1.0
O A:HOH743 3.2 37.8 1.0
CB A:ASN175 3.7 21.5 1.0
CA A:GLN174 3.9 19.5 1.0
CA A:ASN175 4.0 23.4 1.0
C A:GLN174 4.0 26.1 1.0
ND2 A:ASN182 4.1 19.7 1.0
CD A:ARG343 4.1 34.8 1.0
O A:HIS173 4.2 22.2 1.0
CE1 A:HIS173 4.4 27.6 1.0
ND1 A:HIS173 4.5 26.3 1.0
O A:HOH860 4.5 45.9 1.0
O A:ASN175 4.5 22.9 1.0
CG A:GLN174 4.6 17.8 1.0
O A:HOH604 4.6 15.2 1.0
O A:HOH625 4.7 20.9 1.0
C A:ASN175 4.7 25.4 1.0
CB A:GLN174 4.8 17.4 1.0
NH2 A:ARG343 4.8 20.2 1.0
N A:GLN174 4.8 17.1 1.0
C A:HIS173 4.9 25.9 1.0
CG A:ARG343 5.0 34.4 1.0

Chlorine binding site 7 out of 14 in 4qik

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Chlorine binding site 7 out of 14 in the Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex


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 the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl507

b:36.0
occ:1.00
 N A:SER315 3.3 16.7 1.0
N A:LYS314 3.3 15.8 1.0
O A:HOH638 3.3 18.7 1.0
O A:SER312 3.5 22.9 1.0
C A:SER312 3.6 21.0 1.0
O C:HOH101 3.6 43.2 1.0
OG A:SER315 3.7 23.3 1.0
CB A:LYS314 3.8 24.0 1.0
CA A:LYS314 3.9 19.2 1.0
N A:HIS313 3.9 21.3 1.0
CB A:SER315 4.0 25.6 1.0
C A:HIS313 4.0 15.1 1.0
O A:HOH833 4.1 39.1 1.0
C A:LYS314 4.1 18.4 1.0
O A:GLN311 4.1 31.7 1.0
CA A:SER312 4.1 21.3 1.0
CA A:HIS313 4.2 12.7 1.0
O A:HOH963 4.2 33.2 1.0
CA A:SER315 4.3 17.8 1.0
O A:HOH995 4.5 40.2 1.0
CG A:LYS314 4.7 27.4 1.0
CE A:LYS314 4.8 37.8 1.0
C A:GLN311 4.9 24.2 1.0
N A:SER312 5.0 21.8 1.0
O A:HIS313 5.0 15.8 1.0

Chlorine binding site 8 out of 14 in 4qik

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Chlorine binding site 8 out of 14 in the Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl508

b:34.8
occ:1.00
 O A:HOH770 2.7 22.3 1.0
O A:ALA186 2.8 11.4 1.0
NE A:ARG190 2.9 19.3 1.0
O A:HOH676 3.1 30.2 1.0
CG A:ARG190 3.4 18.9 1.0
C A:ALA186 3.5 11.3 1.0
CD A:ARG190 3.6 22.9 1.0
CA A:ALA186 3.6 11.2 1.0
CB A:ALA186 3.7 7.8 1.0
CZ A:ARG190 3.9 28.8 1.0
NH2 A:ARG190 4.0 26.7 1.0
CG2 A:ILE290 4.2 9.5 1.0
CB A:ALA189 4.5 11.4 1.0
N A:VAL187 4.7 9.1 1.0
CB A:ARG190 4.8 15.1 1.0
N A:ARG190 4.8 14.6 1.0
O A:HOH755 4.9 30.3 1.0

Chlorine binding site 9 out of 14 in 4qik

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Chlorine binding site 9 out of 14 in the Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:23.8
occ:1.00
 N B:PHE194 3.1 12.6 1.0
O B:HOH924 3.3 37.1 1.0
O B:HOH649 3.5 23.8 1.0
CD B:ARG188 3.5 24.1 1.0
O B:PHE194 3.6 14.4 1.0
CG B:ARG188 3.7 15.3 1.0
CA B:GLN193 3.7 11.5 1.0
CE3 B:TRP184 3.8 17.1 1.0
CG B:GLN193 3.9 22.4 1.0
C B:GLN193 3.9 11.9 1.0
O B:HOH772 3.9 40.1 1.0
CA B:PHE194 3.9 11.0 1.0
CB B:TRP184 4.0 15.1 1.0
CB B:PHE194 4.1 13.4 1.0
CG1 B:VAL187 4.1 10.0 1.0
C B:PHE194 4.2 15.3 1.0
O B:TRP184 4.2 11.9 1.0
CD2 B:TRP184 4.2 13.2 1.0
CG B:TRP184 4.3 15.5 1.0
CB B:GLN193 4.3 17.4 1.0
CB B:VAL187 4.4 11.6 1.0
CA B:TRP184 4.4 15.8 1.0
CZ3 B:TRP184 4.7 15.3 1.0
O B:HOH919 4.7 38.0 1.0
C B:TRP184 4.7 10.7 1.0
O B:CYS192 4.9 13.7 1.0
N B:GLN193 4.9 15.8 1.0
N B:ARG188 4.9 8.3 1.0
CD B:GLN193 4.9 26.8 1.0
NE B:ARG188 4.9 31.6 1.0

Chlorine binding site 10 out of 14 in 4qik

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Chlorine binding site 10 out of 14 in the Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of the Roq Domain of Human Roquin in Complex with the TNF23 Rna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:25.7
occ:1.00
 O B:HOH775 3.2 37.3 1.0
N B:GLU148 3.2 22.8 1.0
NH2 B:ARG151 3.3 26.5 1.0
CA B:GLU147 3.6 23.3 1.0
C B:GLU147 3.9 27.6 1.0
CB B:GLU148 4.0 28.7 1.0
CB B:GLU147 4.1 31.8 1.0
CA B:GLU148 4.2 26.6 1.0
O B:VAL146 4.2 25.3 1.0
CZ B:ARG151 4.2 24.8 1.0
NH1 B:ARG151 4.3 18.2 1.0
O B:HOH871 4.6 45.2 1.0
N B:GLU147 4.7 22.8 1.0
C B:VAL146 4.9 22.7 1.0
O B:HOH752 4.9 32.7 1.0

Reference:

D.Tan, M.Zhou, M.Kiledjian, L.Tong. The Roq Domain of Roquin Recognizes Mrna Constitutive-Decay Element and Double-Stranded Rna. Nat.Struct.Mol.Biol. V. 21 679 2014.
ISSN: ISSN 1545-9993
PubMed: 25026078
DOI: 10.1038/NSMB.2857
Page generated: Fri Jul 26 00:31:09 2024

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