Iodine in PDB 5y9o: The Apo Structure of Legionella Pneumophila Wipa

The structure of The Apo Structure of Legionella Pneumophila Wipa, PDB code: 5y9o was solved by W.Xie, Q.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.61 / 2.55
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.608, 95.976, 106.635, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 28.2

The binding sites of Iodine atom in the The Apo Structure of Legionella Pneumophila Wipa (pdb code 5y9o). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the The Apo Structure of Legionella Pneumophila Wipa, PDB code: 5y9o:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the The Apo Structure of Legionella Pneumophila Wipa


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The Apo Structure of Legionella Pneumophila Wipa within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:62.5 occ:1.00 NE2 A:GLN248 3.6 45.2 1.0 N A:PHE230 3.6 52.3 1.0 OE1 A:GLU252 4.0 73.4 1.0 CB A:PHE230 4.1 42.0 1.0 CD A:GLU252 4.3 67.2 1.0 CA A:PHE230 4.4 43.2 1.0 CB A:GLU252 4.4 56.1 1.0 CA A:PRO229 4.4 40.2 1.0 C A:PRO229 4.5 43.8 1.0 CB A:PRO229 4.6 38.6 1.0 CD A:GLN248 4.6 45.7 1.0 CG A:GLU252 4.6 58.8 1.0 CD2 A:LEU251 4.7 44.7 1.0 CE A:LYS231 4.7 40.7 1.0 CG A:GLN248 4.8 43.2 1.0 O A:PHE230 4.8 51.1 1.0 C A:PHE230 4.8 49.9 1.0 OE2 A:GLU252 4.9 62.2 1.0 CA A:GLU252 4.9 48.7 1.0

Iodine binding site 2 out of 5 in the The Apo Structure of Legionella Pneumophila Wipa


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The Apo Structure of Legionella Pneumophila Wipa within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:71.5 occ:0.81 NE A:ARG44 3.5 83.7 1.0 O A:THR410 3.6 68.3 1.0 NH2 A:ARG44 3.9 92.8 1.0 CD2 A:HIS40 3.9 42.0 1.0 CA A:PHE41 3.9 44.7 1.0 CB A:PHE41 4.0 43.7 1.0 N A:PHE41 4.1 52.4 1.0 CZ A:ARG44 4.2 88.8 1.0 CD1 A:PHE41 4.2 44.7 1.0 C A:THR410 4.4 75.0 1.0 CD1 A:ILE10 4.5 75.2 1.0 CD A:ARG44 4.5 60.9 1.0 O A:LYS37 4.5 47.4 1.0 CG A:PHE41 4.6 42.6 1.0 C A:HIS40 4.6 52.2 1.0 CG2 A:ILE12 4.6 36.4 1.0 CG A:HIS40 4.7 46.9 1.0 CG A:LYS37 4.8 47.2 1.0 NE2 A:HIS40 4.9 40.4 1.0 O A:HIS40 4.9 49.7 1.0 CB A:HIS40 4.9 43.4 1.0

Iodine binding site 3 out of 5 in the The Apo Structure of Legionella Pneumophila Wipa


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of The Apo Structure of Legionella Pneumophila Wipa within 5.0Å range: probe atom residue distance (Å) B Occ A:I503 b:42.6 occ:0.75 OG A:SER137 3.6 47.2 1.0 CA A:ALA134 3.8 47.9 1.0 N A:ALA134 3.9 46.7 1.0 C A:MET133 4.1 43.8 1.0 O A:MET133 4.1 52.6 1.0 CB A:ALA134 4.3 31.6 1.0 CD1 A:ILE88 4.4 45.1 1.0 CB A:MET133 4.5 46.7 1.0 CB A:SER137 4.5 48.9 1.0 CA A:MET133 4.9 46.7 1.0

Iodine binding site 4 out of 5 in the The Apo Structure of Legionella Pneumophila Wipa


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of The Apo Structure of Legionella Pneumophila Wipa within 5.0Å range: probe atom residue distance (Å) B Occ B:I501 b:70.5 occ:0.75 OH B:TYR364 3.3 58.1 1.0 CD B:LYS374 3.5 69.9 1.0 CE B:LYS374 3.5 65.2 1.0 CD B:ARG294 3.5 78.7 1.0 CE1 B:TYR364 3.7 62.8 1.0 CG B:LYS374 3.8 71.5 1.0 ND2 B:ASN368 3.9 67.8 1.0 CZ B:TYR364 4.0 59.0 1.0 CG B:ARG294 4.1 78.0 1.0 CZ3 B:TRP370 4.2 69.8 1.0 OD1 B:ASN368 4.3 62.4 1.0 CG B:ASN368 4.4 67.7 1.0 NE B:ARG357 4.4 88.1 1.0 CH2 B:TRP370 4.5 73.7 1.0 CB B:LYS374 4.5 73.1 1.0 NH1 B:ARG357 4.6 85.5 1.0 CZ B:ARG357 4.7 77.6 1.0 CE3 B:TRP370 4.8 71.1 1.0 NE B:ARG294 4.8 74.9 1.0 CD1 B:TYR364 5.0 52.2 1.0

Iodine binding site 5 out of 5 in the The Apo Structure of Legionella Pneumophila Wipa


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of The Apo Structure of Legionella Pneumophila Wipa within 5.0Å range: probe atom residue distance (Å) B Occ B:I503 b:0.6 occ:1.00 OE1 B:GLU252 3.3 83.0 1.0 NE2 B:GLN248 3.7 70.1 1.0 CB B:PHE230 4.0 70.4 1.0 N B:PHE230 4.4 74.2 1.0 CB B:GLU252 4.4 78.5 1.0 CD2 B:LEU251 4.5 68.0 1.0 CD B:GLU252 4.5 84.1 1.0 CA B:GLU252 4.6 71.7 1.0 CG B:GLN248 4.6 62.0 1.0 CD B:GLN248 4.6 69.8 1.0 N B:GLU252 4.7 79.2 1.0 CG B:LEU251 4.7 76.5 1.0 CA B:PHE230 4.8 69.1 1.0 O B:PHE230 4.9 71.3 1.0 CG B:GLU252 4.9 77.8 1.0

Q.Jia, Y.Lin, X.Gou, L.He, D.Shen, D.Chen, W.Xie, Y.Lu. Legionella Pneumophila Effector Wipa, A Bacterial Ppp Protein Phosphatase with Ptp Activity Acta Biochim. Biophys. Sin. V. 50 547 2018(Shanghai).
ISSN: ESSN 1745-7270
PubMed: 29701815
DOI: 10.1093/ABBS/GMY042