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Iodine in PDB 7uyg: Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota

Protein crystallography data

The structure of Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota, PDB code: 7uyg was solved by J.N.Pruneda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.80 / 1.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 86.245, 86.245, 92.304, 90, 90, 90
R / Rfree (%) 19.5 / 22.1

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota (pdb code 7uyg). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota, PDB code: 7uyg:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 7uyg

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Iodine binding site 1 out of 7 in the Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:23.9
occ:0.81
 O A:HOH602 3.6 29.6 1.0
NH1 A:ARG145 3.8 23.6 1.0
CB A:PHE120 3.9 17.0 1.0
N A:PHE120 4.0 15.8 1.0
CA A:PHE120 4.1 14.1 1.0
CD1 A:TRP119 4.1 17.1 1.0
CD2 A:LEU141 4.4 21.2 1.0
CB A:TRP119 4.4 17.0 1.0
CD1 A:LEU141 4.5 22.0 1.0
C A:TRP119 4.6 16.4 1.0
CG A:TRP119 4.7 17.4 1.0
CZ A:ARG145 4.9 20.5 1.0

Iodine binding site 2 out of 7 in 7uyg

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Iodine binding site 2 out of 7 in the Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:24.4
occ:0.58
 O A:HOH675 3.1 38.3 1.0
NH1 A:ARG165 3.5 20.5 1.0
O A:HOH679 3.7 30.9 1.0
N A:GLU166 3.8 21.9 1.0
CA A:GLU166 3.8 18.9 1.0
CB A:GLU166 4.0 25.7 1.0
CG A:ARG165 4.1 19.0 1.0
CD A:ARG165 4.1 19.2 1.0
C A:ARG165 4.2 17.7 1.0
CB A:ARG165 4.2 19.7 1.0
O A:HOH606 4.4 26.8 1.0
O A:ARG165 4.5 17.8 1.0
CZ A:ARG165 4.6 18.3 1.0
CA A:ARG165 4.8 16.4 1.0
NE A:ARG165 4.9 16.8 1.0
CD A:LYS169 5.0 21.0 1.0

Iodine binding site 3 out of 7 in 7uyg

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Iodine binding site 3 out of 7 in the Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:21.7
occ:0.42
 O A:HOH590 3.3 24.4 1.0
N A:LEU179 3.6 16.9 1.0
CB A:LEU179 3.9 17.2 1.0
CE A:LYS151 4.0 23.1 1.0
O A:LYS175 4.1 27.7 1.0
CB A:GLU178 4.1 18.7 1.0
CA A:ALA176 4.1 18.5 1.0
CD1 A:ILE155 4.2 22.7 1.0
N A:GLU178 4.2 19.1 1.0
CA A:LEU179 4.3 14.9 1.0
C A:ALA176 4.4 19.4 1.0
C A:GLU178 4.4 17.5 1.0
CA A:GLU178 4.5 17.8 1.0
O A:ALA176 4.6 17.2 1.0
O A:HOH524 4.6 32.0 1.0
NZ A:LYS151 4.6 21.1 1.0
CG1 A:ILE155 4.7 19.6 1.0
N A:LYS177 4.8 21.9 1.0
CB A:ALA176 4.9 18.5 1.0
C A:LYS175 5.0 24.9 1.0

Iodine binding site 4 out of 7 in 7uyg

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Iodine binding site 4 out of 7 in the Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:33.4
occ:0.38
 O A:HOH655 3.0 54.2 1.0
N A:TRP119 3.5 17.1 1.0
CD1 A:LEU149 3.8 23.2 1.0
CA A:ALA146 4.0 19.3 1.0
CB A:ALA146 4.0 25.3 1.0
CA A:ALA118 4.1 18.6 1.0
CB A:TRP119 4.1 17.0 1.0
C A:ALA118 4.3 18.2 1.0
O A:HOH516 4.3 28.8 1.0
CA A:TRP119 4.3 16.8 1.0
CB A:ALA118 4.4 20.8 1.0
N A:ALA146 4.4 19.9 1.0
CD1 A:LEU141 4.6 22.0 1.0
O A:HOH572 4.6 44.9 1.0
O A:HOH423 4.7 40.6 1.0
CG A:LEU149 4.8 17.9 1.0
C A:ARG145 4.9 17.3 1.0
O A:ARG145 4.9 18.6 1.0

Iodine binding site 5 out of 7 in 7uyg

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Iodine binding site 5 out of 7 in the Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I307

b:44.6
occ:0.35
 N A:TRP59 3.6 19.4 1.0
CA A:SER58 3.9 20.3 1.0
CD1 A:TRP59 4.0 23.8 1.0
CD2 A:LEU44 4.0 23.1 1.0
CB A:SER58 4.2 22.9 1.0
C A:SER58 4.3 20.2 1.0
O A:HOH611 4.3 34.1 1.0
NE2 A:GLN41 4.3 31.9 1.0
CB A:TRP59 4.4 20.7 1.0
CG A:TRP59 4.6 21.9 1.0
CA A:TRP59 4.6 16.6 1.0
O A:LYS57 4.8 27.5 1.0

Iodine binding site 6 out of 7 in 7uyg

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Iodine binding site 6 out of 7 in the Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I308

b:37.8
occ:0.30
 O A:HOH583 3.1 42.0 1.0
OD1 A:ASN124 3.3 16.7 1.0
N A:ASN124 3.4 15.1 1.0
N A:THR125 3.7 15.7 1.0
CA A:GLN123 3.8 15.1 1.0
CB A:THR125 3.8 18.8 1.0
CG A:GLN123 3.9 16.6 1.0
OG1 A:THR125 3.9 21.1 1.0
C A:GLN123 4.1 14.4 1.0
O A:HOH626 4.1 32.6 1.0
O A:THR125 4.3 18.7 1.0
CA A:THR125 4.3 16.5 1.0
CB A:GLN123 4.3 16.1 1.0
CA A:ASN124 4.4 13.8 1.0
C A:ASN124 4.5 14.1 1.0
CG A:ASN124 4.5 14.9 1.0
O A:LEU122 4.6 22.1 1.0
C A:THR125 4.7 16.2 1.0
N A:GLN123 4.9 15.1 1.0

Iodine binding site 7 out of 7 in 7uyg

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Iodine binding site 7 out of 7 in the Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of the First Otu Domain From Legionella Pneumophila Effector Protein Lota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I309

b:185.2
occ:0.84
 OE1 A:GLU174 3.2 56.7 1.0
O A:HOH546 3.4 44.5 1.0
CA A:PHE171 4.0 18.1 1.0
O A:HOH530 4.0 43.3 1.0
CD1 A:PHE171 4.0 23.2 1.0
CD1 A:LEU161 4.1 49.9 1.0
CB A:PHE171 4.2 19.7 1.0
CD A:GLU174 4.3 40.9 1.0
N A:PHE171 4.4 19.6 1.0
CG A:PHE171 4.6 18.8 1.0
OE2 A:GLU174 4.8 48.7 1.0
CD A:LYS175 4.8 46.5 1.0
C A:GLN170 4.9 20.2 1.0
O A:GLN170 4.9 20.8 1.0
CG A:LEU161 4.9 39.7 1.0

Reference:

G.D.Warren, T.Kitao, T.G.Franklin, J.V.Nguyen, P.P.Geurink, T.Kubori, H.Nagai, J.N.Pruneda. Mechanism of LYS6 Poly-Ubiquitin Specificity By the L. Pneumophila Deubiquitinase Lota. Mol.Cell 2022.
ISSN: ISSN 1097-2765
PubMed: 36538933
DOI: 10.1016/J.MOLCEL.2022.11.022
Page generated: Wed Apr 5 09:25:22 2023

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