Iodine in PDB 5d2r: Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori

The structure of Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori, PDB code: 5d2r was solved by A.C.Chan, M.E.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.03 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.840, 66.610, 144.480, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 21.9

The structure of Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Iodine atom in the Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori (pdb code 5d2r). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 19 binding sites of Iodine where determined in the Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori, PDB code: 5d2r:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 19 in the Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:31.1 occ:0.75 HD22 A:LEU229 3.1 20.1 1.0 HB2 A:ASN328 3.2 23.3 1.0 O A:HOH844 3.3 51.5 1.0 O A:HOH736 3.4 14.2 1.0 HG3 A:LYS329 3.4 22.8 1.0 HG3 A:PRO50 3.5 18.3 1.0 HZ3 A:LYS329 3.5 28.0 1.0 HG2 A:LYS329 3.8 22.8 1.0 HE2 A:LYS329 4.0 23.7 1.0 HB2 A:PRO50 4.0 20.4 1.0 HD13 A:LEU229 4.1 20.0 1.0 CD2 A:LEU229 4.1 16.7 1.0 CG A:LYS329 4.1 19.0 1.0 CB A:ASN328 4.1 19.4 1.0 HB2 A:LEU229 4.1 22.5 1.0 HB3 A:PRO50 4.1 20.4 1.0 CG A:PRO50 4.1 15.3 1.0 NZ A:LYS329 4.2 23.3 1.0 CB A:PRO50 4.3 17.0 1.0 HB3 A:ASN328 4.3 23.3 1.0 HZ1 A:LYS329 4.3 28.0 1.0 HG2 A:PRO50 4.3 18.3 1.0 H A:ASN328 4.3 21.2 1.0 HD21 A:LEU229 4.5 20.1 1.0 CE A:LYS329 4.5 19.7 1.0 HD23 A:LEU229 4.5 20.1 1.0 O A:HOH620 4.7 25.8 1.0 C A:ASN328 4.7 25.2 1.0 N A:LYS329 4.7 21.1 1.0 CG A:LEU229 4.8 16.8 1.0 H A:LYS329 4.8 25.4 1.0 O A:HOH825 4.8 48.8 1.0 CA A:ASN328 4.8 21.1 1.0 CD1 A:LEU229 4.8 16.6 1.0 OD1 A:ASN328 4.8 18.0 1.0 CB A:LEU229 4.8 18.7 1.0 CD A:LYS329 4.9 18.7 1.0 HD21 A:ASN54 4.9 18.5 1.0 HZ2 A:LYS329 4.9 28.0 1.0 N A:ASN328 4.9 17.6 1.0 HA A:LYS329 5.0 28.7 1.0 CG A:ASN328 5.0 18.8 1.0

Iodine binding site 2 out of 19 in the Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:39.2 occ:0.85 HE1 A:PHE170 3.0 43.1 1.0 H A:ASN166 3.0 31.5 1.0 HD2 A:PRO165 3.0 39.4 1.0 HA A:PHE164 3.2 39.6 1.0 HB2 A:ASN166 3.4 40.5 1.0 HD1 A:PHE164 3.4 43.0 1.0 HB3 A:ASN166 3.4 40.5 1.0 HB3 A:PHE164 3.6 35.6 1.0 N A:ASN166 3.8 26.3 1.0 CB A:ASN166 3.8 33.8 1.0 CE1 A:PHE170 3.8 35.9 1.0 CD A:PRO165 3.8 32.9 1.0 CA A:PHE164 3.9 33.0 1.0 N A:PRO165 4.0 26.7 1.0 HG2 A:PRO165 4.0 44.2 1.0 C A:PHE164 4.1 31.4 1.0 CB A:PHE164 4.2 29.7 1.0 CD1 A:PHE164 4.3 35.9 1.0 CA A:ASN166 4.4 26.9 1.0 CG A:PRO165 4.5 36.9 1.0 HD1 A:PHE170 4.5 38.1 1.0 HZ A:PHE170 4.6 41.5 1.0 HD3 A:PRO165 4.6 39.4 1.0 CD1 A:PHE170 4.7 31.7 1.0 CZ A:PHE170 4.7 34.6 1.0 O A:PHE164 4.8 27.6 1.0 CG A:PHE164 4.8 31.9 1.0 HD22 A:ASN166 4.8 54.4 1.0 C A:PRO165 4.8 24.4 1.0 CA A:PRO165 4.9 27.1 1.0

Iodine binding site 3 out of 19 in the Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:39.0 occ:0.85 HZ1 A:LYS329 2.7 28.0 1.0 HD21 A:ASN267 2.7 35.0 1.0 HD23 A:LEU229 3.2 20.1 1.0 O A:HOH807 3.3 23.0 1.0 HB3 A:LEU229 3.4 22.5 1.0 HD2 A:HIS263 3.4 32.9 1.0 HG21 A:ILE266 3.5 22.8 1.0 NZ A:LYS329 3.5 23.3 1.0 ND2 A:ASN267 3.5 29.1 1.0 HZ2 A:LYS329 3.6 28.0 1.0 HD22 A:ASN267 3.9 35.0 1.0 CD2 A:HIS263 3.9 27.4 1.0 HE3 A:LYS329 4.0 23.7 1.0 HD13 A:ILE266 4.0 21.8 1.0 HZ3 A:LYS329 4.1 28.0 1.0 HB2 A:ALA230 4.1 24.9 1.0 O A:HOH703 4.1 40.3 1.0 CD2 A:LEU229 4.1 16.7 1.0 HG22 A:ILE266 4.1 22.8 1.0 HE2 A:HIS263 4.1 36.1 1.0 H A:ALA230 4.2 20.6 1.0 CG2 A:ILE266 4.2 19.0 1.0 CE A:LYS329 4.3 19.7 1.0 HB A:ILE266 4.3 21.1 1.0 NE2 A:HIS263 4.3 30.1 1.0 CB A:LEU229 4.3 18.7 1.0 HD12 A:ILE266 4.3 21.8 1.0 HD22 A:LEU229 4.4 20.1 1.0 HE2 A:LYS329 4.5 23.7 1.0 CG A:ASN267 4.5 27.9 1.0 HA A:HIS263 4.6 24.4 1.0 OD1 A:ASN267 4.6 29.1 1.0 CD1 A:ILE266 4.6 18.2 1.0 CG A:LEU229 4.7 16.8 1.0 HG A:LEU229 4.7 20.2 1.0 N A:ALA230 4.7 17.1 1.0 HB2 A:LEU229 4.7 22.5 1.0 HD21 A:LEU229 4.7 20.1 1.0 CB A:ILE266 4.8 17.6 1.0 CG A:HIS263 4.9 26.8 1.0 H A:LEU229 5.0 26.6 1.0 CB A:ALA230 5.0 20.7 1.0

Iodine binding site 4 out of 19 in the Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I507 b:31.6 occ:0.80 HH11 A:ARG83 2.9 54.6 1.0 HD3 A:ARG83 3.2 43.1 1.0 O A:HOH734 3.2 33.9 1.0 HB3 A:ARG83 3.4 31.3 1.0 NH1 A:ARG83 3.7 45.5 1.0 O A:HOH796 3.7 36.5 1.0 HG2 A:ARG83 3.8 36.3 1.0 HD22 A:ASN318 4.0 31.2 1.0 CD A:ARG83 4.0 35.9 1.0 HH12 A:ARG83 4.0 54.6 1.0 CB A:ARG83 4.1 26.1 1.0 CG A:ARG83 4.2 30.3 1.0 HA A:ARG83 4.2 23.2 1.0 HD21 A:ASN318 4.2 31.2 1.0 ND2 A:ASN318 4.5 26.0 1.0 O A:ARG83 4.5 18.1 1.0 O A:HOH728 4.6 38.1 1.0 HD2 A:ARG83 4.6 43.1 1.0 CA A:ARG83 4.7 19.3 1.0 CZ A:ARG83 4.7 44.9 1.0 NE A:ARG83 4.8 40.2 1.0 HB2 A:ARG83 4.9 31.3 1.0

Iodine binding site 5 out of 19 in the Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I508 b:49.4 occ:0.70 H A:LYS317 2.9 33.2 1.0 HD3 A:PRO302 3.0 61.0 1.0 HB2 A:LYS317 3.0 60.8 1.0 HG3 A:PRO302 3.1 53.2 1.0 HB A:ILE301 3.1 47.9 1.0 O A:HOH685 3.3 29.3 1.0 HA A:VAL316 3.6 34.1 1.0 HG23 A:VAL316 3.6 32.5 1.0 N A:LYS317 3.7 27.6 1.0 CD A:PRO302 3.7 50.8 1.0 CG A:PRO302 3.7 44.4 1.0 HD2 A:LYS317 3.8 86.6 1.0 HH21 A:ARG83 3.9 59.1 1.0 HD3 A:LYS317 3.9 86.6 1.0 CB A:LYS317 3.9 50.7 1.0 HG2 A:PRO302 4.0 53.2 1.0 CB A:ILE301 4.0 39.9 1.0 HG21 A:ILE301 4.1 38.4 1.0 CD A:LYS317 4.2 72.2 1.0 HG22 A:ILE301 4.3 38.4 1.0 HD2 A:PRO302 4.4 61.0 1.0 CG2 A:ILE301 4.4 32.0 1.0 CG2 A:VAL316 4.4 27.1 1.0 NH2 A:ARG83 4.4 49.2 1.0 HG22 A:VAL316 4.4 32.5 1.0 CA A:LYS317 4.4 39.8 1.0 HH22 A:ARG83 4.4 59.1 1.0 CA A:VAL316 4.5 28.4 1.0 CG A:LYS317 4.5 61.9 1.0 HB3 A:LYS317 4.5 60.8 1.0 O A:HOH880 4.5 27.1 1.0 HG3 A:LYS317 4.6 74.3 1.0 HG13 A:ILE301 4.6 55.2 1.0 N A:PRO302 4.6 47.0 1.0 C A:VAL316 4.6 34.9 1.0 HG12 A:ILE301 4.7 55.2 1.0 CG1 A:ILE301 4.7 46.0 1.0 H A:ILE301 4.9 61.6 1.0

Iodine binding site 6 out of 19 in the Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I509 b:55.0 occ:0.75 HD2 A:PRO145 3.0 53.3 1.0 HD2 A:TYR138 3.1 47.2 1.0 HG2 A:LYS146 3.1 56.7 1.0 HB2 A:TYR138 3.5 51.1 1.0 HG3 A:LYS146 3.6 56.7 1.0 CG A:LYS146 3.8 47.3 1.0 HB2 A:ASN144 3.9 49.7 1.0 CD2 A:TYR138 3.9 39.3 1.0 CD A:PRO145 3.9 44.4 1.0 HG2 A:PRO145 3.9 52.8 1.0 HE2 A:LYS146 4.0 60.0 1.0 HB2 A:PRO145 4.0 44.6 1.0 H A:LYS146 4.2 43.8 1.0 CG A:PRO145 4.4 44.0 1.0 HD3 A:LYS146 4.4 53.2 1.0 CB A:TYR138 4.4 42.6 1.0 HZ3 A:LYS146 4.5 58.1 1.0 HD3 A:PRO145 4.5 53.3 1.0 CD A:LYS146 4.5 44.4 1.0 CE A:LYS146 4.6 50.0 1.0 CG A:TYR138 4.6 45.0 1.0 CB A:PRO145 4.6 37.1 1.0 N A:PRO145 4.7 36.9 1.0 OD1 A:ASN144 4.7 33.6 1.0 HE2 A:TYR138 4.7 50.9 1.0 N A:LYS146 4.7 36.5 1.0 CB A:ASN144 4.8 41.4 1.0 CE2 A:TYR138 4.8 42.4 1.0 CB A:LYS146 5.0 41.6 1.0 HB2 A:LYS146 5.0 49.9 1.0 HB3 A:TYR138 5.0 51.1 1.0

Iodine binding site 7 out of 19 in the Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I510 b:58.5 occ:0.70 HG2 A:MET358 3.2 65.3 1.0 HE3 A:LYS349 3.3 62.6 1.0 HA A:GLN357 3.4 66.8 1.0 HG3 A:LYS349 3.6 54.8 1.0 HB3 A:ASP356 4.0 63.6 1.0 CA A:GLN357 4.1 55.7 1.0 CG A:MET358 4.1 54.4 1.0 H A:MET358 4.2 52.3 1.0 N A:GLN357 4.2 54.7 1.0 C A:GLN357 4.2 55.2 1.0 SD A:MET358 4.3 62.4 1.0 CE A:LYS349 4.3 52.1 1.0 N A:MET358 4.3 43.6 1.0 C A:ASP356 4.4 43.3 1.0 HD2 A:LYS349 4.4 61.4 1.0 O A:ASP356 4.5 42.9 1.0 CG A:LYS349 4.5 45.6 1.0 H A:GLN357 4.5 65.6 1.0 HG3 A:MET358 4.6 65.3 1.0 CD A:LYS349 4.6 51.2 1.0 HE2 A:LYS349 4.7 62.6 1.0 O A:GLN357 4.8 53.5 1.0 CB A:ASP356 4.8 53.0 1.0 HB2 A:ASP356 4.8 63.6 1.0 HG2 A:LYS349 4.9 54.8 1.0

Iodine binding site 8 out of 19 in the Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I511 b:43.8 occ:0.70 HG3 A:GLN198 2.9 76.5 1.0 HA A:ARG195 3.1 31.6 1.0 O A:HOH826 3.3 27.1 1.0 HB3 A:GLN156 3.3 30.9 1.0 HB3 A:ARG195 3.5 37.9 1.0 HG2 A:ARG195 3.6 39.8 1.0 OE1 A:GLN198 3.7 67.7 1.0 HB3 A:ALA197 3.7 39.0 1.0 HB2 A:GLN156 3.8 30.9 1.0 CG A:GLN198 3.8 63.7 1.0 CA A:ARG195 3.8 26.4 1.0 CD A:GLN198 4.0 69.1 1.0 CB A:GLN156 4.0 25.7 1.0 CB A:ARG195 4.0 31.5 1.0 O A:HOH678 4.0 29.1 1.0 H A:GLN198 4.1 56.0 1.0 HH21 A:ARG195 4.1 62.2 1.0 C A:ARG195 4.1 27.3 1.0 HA A:GLN156 4.1 27.2 1.0 CG A:ARG195 4.3 33.2 1.0 H A:ALA197 4.3 30.3 1.0 HB2 A:GLN198 4.3 71.0 1.0 O A:ARG195 4.4 31.0 1.0 O A:ASP155 4.4 28.3 1.0 HG2 A:GLN198 4.4 76.5 1.0 N A:GLN198 4.6 46.7 1.0 CA A:GLN156 4.6 22.7 1.0 OE1 A:GLN156 4.6 34.4 1.0 CB A:GLN198 4.6 59.1 1.0 H A:THR196 4.7 28.4 1.0 CB A:ALA197 4.7 32.5 1.0 N A:THR196 4.7 23.7 1.0 NH2 A:ARG195 4.8 51.9 1.0 HD3 A:ARG195 4.8 50.8 1.0 N A:ALA197 4.8 25.3 1.0 HB2 A:ARG195 4.9 37.9 1.0 HH22 A:ARG195 5.0 62.2 1.0 NE2 A:GLN198 5.0 75.3 1.0

Iodine binding site 9 out of 19 in the Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I512 b:43.9 occ:0.50 HB2 A:SER260 2.9 39.7 1.0 H A:SER260 2.9 30.3 1.0 HD2 A:PRO259 2.9 33.9 1.0 HB2 A:ASN258 3.0 35.1 1.0 HB3 A:SER260 3.6 39.7 1.0 CB A:SER260 3.6 33.1 1.0 N A:SER260 3.7 25.3 1.0 CD A:PRO259 3.8 28.3 1.0 CB A:ASN258 3.9 29.3 1.0 HB2 A:PRO259 3.9 32.1 1.0 OD1 A:ASN258 4.0 28.7 1.0 CG A:ASN258 4.1 30.1 1.0 N A:PRO259 4.2 23.6 1.0 CA A:SER260 4.3 25.2 1.0 HG2 A:PRO259 4.3 34.3 1.0 HB3 A:ASN258 4.4 35.1 1.0 HD3 A:PRO259 4.5 33.9 1.0 CG A:PRO259 4.5 28.6 1.0 CB A:PRO259 4.6 26.7 1.0 C A:PRO259 4.7 23.4 1.0 C A:ASN258 4.7 20.3 1.0 CA A:PRO259 4.7 23.2 1.0 HA A:SER260 4.8 30.3 1.0 OG A:SER260 4.8 38.1 1.0 HG A:SER260 4.8 45.7 1.0 CA A:ASN258 4.9 23.6 1.0

Iodine binding site 10 out of 19 in the Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I513 b:52.9 occ:0.50 HZ2 A:LYS325 2.8 38.8 1.0 HB2 A:LEU330 3.2 34.7 1.0 HE3 A:LYS325 3.4 34.5 1.0 NZ A:LYS325 3.5 32.4 1.0 HD21 A:ASN84 3.6 33.1 1.0 HZ1 A:LYS325 3.6 38.8 1.0 HD22 A:LEU330 3.7 52.2 1.0 HD2 A:PHE323 3.8 41.6 1.0 HD3 A:LYS325 3.9 38.1 1.0 CE A:LYS325 3.9 28.8 1.0 HE2 A:PHE323 3.9 48.9 1.0 O A:HOH728 3.9 38.1 1.0 HD13 A:LEU330 4.0 41.6 1.0 ND2 A:ASN84 4.0 27.6 1.0 CB A:LEU330 4.2 28.9 1.0 HD22 A:ASN84 4.2 33.1 1.0 HZ3 A:LYS325 4.3 38.8 1.0 CD2 A:PHE323 4.3 34.7 1.0 CE2 A:PHE323 4.4 40.8 1.0 CD A:LYS325 4.4 31.7 1.0 HB3 A:LEU330 4.5 34.7 1.0 O A:HOH796 4.5 36.5 1.0 CD2 A:LEU330 4.6 43.5 1.0 CG A:ASN84 4.6 24.3 1.0 HD2 A:LYS325 4.7 38.1 1.0 CG A:LEU330 4.7 35.3 1.0 OD1 A:ASN84 4.8 21.1 1.0 CD1 A:LEU330 4.8 34.6 1.0 HE2 A:LYS325 4.8 34.5 1.0 O A:ASN328 4.8 29.9 1.0 HD23 A:LEU330 5.0 52.2 1.0

Y.Liu, E.Frirdich, J.A.Taylor, A.C.Chan, K.M.Blair, J.Vermeulen, R.Ha, M.E.Murphy, N.R.Salama, E.C.Gaynor, M.E.Tanner. A Bacterial Cell Shape-Determining Inhibitor. Acs Chem.Biol. V. 11 981 2016.
ISSN: ESSN 1554-8937
PubMed: 26735022
DOI: 10.1021/ACSCHEMBIO.5B01039