Iodine in PDB 4wcn: Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori

The structure of Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori, PDB code: 4wcn 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)	49.15 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.230, 66.830, 145.050, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.8

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

Zinc	(Zn)	1 atom
Sodium	(Na)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 44;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori (pdb code 4wcn). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 44 binding sites of Iodine where determined in the Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori, PDB code: 4wcn:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 44 in the Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein 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 Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:22.5 occ:0.76 HD21 A:LEU229 3.2 20.2 1.0 HB2 A:ASN328 3.2 22.2 1.0 HZ3 A:LYS329 3.2 26.8 1.0 HG3 A:PRO50 3.5 22.3 1.0 O A:HOH676 3.5 12.4 1.0 HG3 A:LYS329 3.6 22.9 1.0 HG2 A:LYS329 3.8 22.9 1.0 O A:HOH875 3.9 49.6 1.0 NZ A:LYS329 3.9 22.4 1.0 HB2 A:PRO50 3.9 19.9 1.0 HZ1 A:LYS329 4.0 26.8 1.0 HE2 A:LYS329 4.0 23.7 1.0 HB3 A:PRO50 4.1 19.9 1.0 CB A:ASN328 4.1 18.5 1.0 CD2 A:LEU229 4.1 16.8 1.0 CG A:LYS329 4.1 19.1 1.0 CG A:PRO50 4.2 18.6 1.0 CB A:PRO50 4.2 16.6 1.0 HB3 A:ASN328 4.3 22.2 1.0 HD13 A:LEU229 4.4 16.6 1.0 H A:ASN328 4.4 19.6 1.0 HG2 A:PRO50 4.4 22.3 1.0 HD23 A:LEU229 4.4 20.2 1.0 HB2 A:LEU229 4.4 22.8 1.0 CE A:LYS329 4.5 19.8 1.0 HD22 A:LEU229 4.6 20.2 1.0 O A:HOH740 4.6 33.5 1.0 HZ2 A:LYS329 4.6 26.8 1.0 C A:ASN328 4.7 17.3 1.0 N A:LYS329 4.8 19.1 1.0 H A:LYS329 4.8 22.9 1.0 CA A:ASN328 4.8 16.8 1.0 HD22 A:ASN54 4.9 18.6 1.0 OD1 A:ASN328 4.9 19.5 1.0 CD A:LYS329 5.0 18.6 1.0 N A:ASN328 5.0 16.3 1.0 CG A:LEU229 5.0 16.2 1.0 HA A:LYS329 5.0 23.6 1.0

Iodine binding site 2 out of 44 in the Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein 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 Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:34.7 occ:1.00 HE A:ARG135 3.0 31.0 1.0 HG21 A:VAL139 3.4 37.7 1.0 NA A:NA544 3.5 26.8 0.5 HD12 A:LEU143 3.7 43.0 1.0 HG11 A:VAL139 3.8 47.1 1.0 NE A:ARG135 3.8 25.8 1.0 HH21 A:ARG135 3.8 27.9 1.0 HG3 A:ARG135 4.1 33.6 1.0 HD2 A:ARG135 4.3 30.9 1.0 CG2 A:VAL139 4.4 31.4 1.0 NH2 A:ARG135 4.5 23.2 1.0 CD A:ARG135 4.5 25.8 1.0 HG22 A:VAL139 4.6 37.7 1.0 CZ A:ARG135 4.6 22.2 1.0 CG1 A:VAL139 4.6 39.2 1.0 CD1 A:LEU143 4.7 35.9 1.0 HG13 A:VAL139 4.8 47.1 1.0 CG A:ARG135 4.8 28.0 1.0 HB3 A:LEU143 4.9 37.3 1.0 HD21 A:LEU143 4.9 29.3 1.0 HG23 A:VAL139 5.0 37.7 1.0 HD11 A:LEU143 5.0 43.0 1.0

Iodine binding site 3 out of 44 in the Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein 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 Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I503 b:38.1 occ:1.00 H A:ASN166 3.0 30.1 1.0 HD2 A:PRO165 3.1 35.1 1.0 HE1 A:PHE170 3.2 31.9 1.0 HB3 A:ASN166 3.2 32.2 1.0 HA A:PHE164 3.2 33.5 1.0 HB2 A:ASN166 3.3 32.2 1.0 HD1 A:PHE164 3.4 35.3 1.0 O A:HOH630 3.5 40.1 1.0 HB3 A:PHE164 3.6 29.1 1.0 CB A:ASN166 3.7 26.8 1.0 N A:ASN166 3.8 25.1 1.0 CD A:PRO165 3.9 29.2 1.0 CA A:PHE164 3.9 27.9 1.0 O A:HOH844 3.9 49.8 1.0 CE1 A:PHE170 4.0 26.6 1.0 N A:PRO165 4.0 24.1 1.0 HG2 A:PRO165 4.1 38.1 1.0 C A:PHE164 4.1 26.6 1.0 CB A:PHE164 4.2 24.3 1.0 CD1 A:PHE164 4.3 29.4 1.0 CA A:ASN166 4.4 24.4 1.0 CG A:PRO165 4.5 31.7 1.0 HD22 A:ASN166 4.5 38.5 1.0 HD1 A:PHE170 4.6 29.0 1.0 HD3 A:PRO165 4.6 35.1 1.0 CD1 A:PHE170 4.7 24.2 1.0 HZ A:PHE170 4.7 31.0 1.0 CG A:PHE164 4.7 26.2 1.0 O A:PHE164 4.8 23.2 1.0 CZ A:PHE170 4.8 25.8 1.0 C A:PRO165 4.9 22.1 1.0 CG A:ASN166 4.9 28.0 1.0 CA A:PRO165 5.0 24.0 1.0 O A:ASN166 5.0 19.0 1.0

Iodine binding site 4 out of 44 in the Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein 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 Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:43.7 occ:0.79 I A:IOD504 0.0 43.7 0.8 I A:IOD504 1.2 14.2 0.2 HD22 A:ASN267 2.7 32.4 1.0 HD1 A:HIS263 2.9 35.6 1.0 HD22 A:LEU229 3.2 20.2 1.0 O A:HOH700 3.3 24.1 1.0 HB3 A:LEU229 3.4 22.8 1.0 ND2 A:ASN267 3.5 27.0 1.0 ND1 A:HIS263 3.5 29.7 1.0 HG22 A:ILE266 3.6 20.8 1.0 HZ1 A:LYS329 3.6 26.8 1.0 HB2 A:ALA230 3.6 27.5 1.0 HD21 A:ASN267 3.7 32.4 1.0 HD11 A:ILE266 3.7 18.4 1.0 HA A:HIS263 3.8 26.1 1.0 HD12 A:ILE266 3.9 18.4 1.0 HB A:ILE266 3.9 21.2 1.0 H A:ALA230 4.0 23.1 1.0 HE1 A:HIS263 4.0 37.5 1.0 CE1 A:HIS263 4.1 31.3 1.0 CD2 A:LEU229 4.1 16.8 1.0 CD1 A:ILE266 4.2 15.4 1.0 CG2 A:ILE266 4.3 17.4 1.0 CB A:LEU229 4.3 19.0 1.0 HG23 A:ILE266 4.3 20.8 1.0 HG A:LEU229 4.4 19.4 1.0 N A:ALA230 4.4 19.2 1.0 NZ A:LYS329 4.4 22.4 1.0 HE3 A:LYS329 4.4 23.7 1.0 CG A:HIS263 4.5 27.4 1.0 CB A:ILE266 4.5 17.7 1.0 CB A:ALA230 4.5 22.9 1.0 CG A:LEU229 4.5 16.2 1.0 HZ2 A:LYS329 4.6 26.8 1.0 HD21 A:LEU229 4.6 20.2 1.0 CG A:ASN267 4.6 25.6 1.0 HB2 A:HIS263 4.6 30.3 1.0 HD23 A:LEU229 4.7 20.2 1.0 CA A:HIS263 4.7 21.7 1.0 HA A:ALA230 4.7 23.4 1.0 HB2 A:LEU229 4.8 22.8 1.0 CB A:HIS263 4.8 25.2 1.0 CA A:ALA230 4.9 19.5 1.0 OD1 A:ASN267 4.9 25.0 1.0 CE A:LYS329 4.9 19.8 1.0 HB3 A:ALA230 4.9 27.5 1.0 O A:HIS263 4.9 22.0 1.0 HE2 A:LYS329 5.0 23.7 1.0

Iodine binding site 5 out of 44 in the Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein 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 Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:14.2 occ:0.21 I A:IOD504 0.0 14.2 0.2 I A:IOD504 1.2 43.7 0.8 HZ1 A:LYS329 2.6 26.8 1.0 HD22 A:ASN267 3.0 32.4 1.0 HD22 A:LEU229 3.1 20.2 1.0 HB3 A:LEU229 3.4 22.8 1.0 NZ A:LYS329 3.4 22.4 1.0 HZ2 A:LYS329 3.5 26.8 1.0 HD1 A:HIS263 3.6 35.6 1.0 O A:HOH700 3.7 24.1 1.0 ND2 A:ASN267 3.8 27.0 1.0 HE3 A:LYS329 3.8 23.7 1.0 HG22 A:ILE266 3.8 20.8 1.0 CD2 A:LEU229 4.0 16.8 1.0 HZ3 A:LYS329 4.1 26.8 1.0 CE A:LYS329 4.1 19.8 1.0 HE1 A:HIS263 4.1 37.5 1.0 ND1 A:HIS263 4.2 29.7 1.0 HD21 A:LEU229 4.2 20.2 1.0 O A:HOH875 4.2 49.6 1.0 HD21 A:ASN267 4.2 32.4 1.0 CB A:LEU229 4.3 19.0 1.0 HE2 A:LYS329 4.4 23.7 1.0 CE1 A:HIS263 4.4 31.3 1.0 HG23 A:ILE266 4.4 20.8 1.0 HD12 A:ILE266 4.5 18.4 1.0 HB2 A:LEU229 4.5 22.8 1.0 CG2 A:ILE266 4.6 17.4 1.0 HB A:ILE266 4.6 21.2 1.0 OD1 A:ASN267 4.6 25.0 1.0 H A:ALA230 4.6 23.1 1.0 HD23 A:LEU229 4.6 20.2 1.0 CG A:LEU229 4.6 16.2 1.0 CG A:ASN267 4.7 25.6 1.0 HD11 A:ILE266 4.7 18.4 1.0 HB2 A:ALA230 4.7 27.5 1.0 HG A:LEU229 4.7 19.4 1.0 O A:HOH871 4.8 46.6 1.0 HA A:HIS263 4.9 26.1 1.0

Iodine binding site 6 out of 44 in the Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein 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 Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:27.3 occ:0.61 H A:LYS317 2.8 27.8 1.0 HD3 A:PRO302 3.0 47.0 1.0 HB2 A:LYS317 3.2 38.1 1.0 HB A:ILE301 3.2 36.8 1.0 HG3 A:PRO302 3.3 44.7 1.0 HG21 A:VAL316 3.4 28.7 1.0 HA A:VAL316 3.6 25.4 1.0 O A:HOH774 3.6 35.6 1.0 HD2 A:LYS317 3.7 47.0 1.0 N A:LYS317 3.7 23.2 1.0 HH21 A:ARG83 3.7 44.3 1.0 HG3 A:LYS317 3.8 39.2 1.0 CD A:PRO302 3.8 39.1 1.0 CG A:PRO302 3.8 37.3 1.0 CB A:LYS317 4.0 31.7 1.0 HG2 A:PRO302 4.0 44.7 1.0 CB A:ILE301 4.2 30.7 1.0 CG A:LYS317 4.2 32.6 1.0 CG2 A:VAL316 4.3 23.9 1.0 NH2 A:ARG83 4.3 36.9 1.0 HG22 A:ILE301 4.3 30.8 1.0 HD2 A:PRO302 4.3 47.0 1.0 HH22 A:ARG83 4.3 44.3 1.0 HG22 A:VAL316 4.4 28.7 1.0 O A:HOH668 4.4 24.6 1.0 CA A:VAL316 4.4 21.2 1.0 CD A:LYS317 4.4 39.1 1.0 CA A:LYS317 4.5 26.5 1.0 HG23 A:ILE301 4.5 30.8 1.0 C A:VAL316 4.6 24.6 1.0 CG2 A:ILE301 4.6 25.7 1.0 HG13 A:ILE301 4.7 41.0 1.0 N A:PRO302 4.7 35.6 1.0 HG12 A:ILE301 4.7 41.0 1.0 HB3 A:LYS317 4.8 38.1 1.0 H A:ILE301 4.8 44.8 1.0 CG1 A:ILE301 4.8 34.2 1.0 CB A:VAL316 4.9 20.0 1.0 HG23 A:VAL316 5.0 28.7 1.0 HD3 A:LYS317 5.0 47.0 1.0

Iodine binding site 7 out of 44 in the Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein 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 Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:48.3 occ:1.00 HE3 A:LYS325 3.3 25.6 1.0 HZ1 A:LYS325 3.3 26.5 1.0 HD2 A:PHE323 3.4 30.3 1.0 O A:HOH666 3.4 31.3 1.0 HD3 A:LYS325 3.6 26.6 1.0 HE2 A:PHE323 3.6 34.8 1.0 HD22 A:ASN84 3.9 25.0 1.0 ND2 A:ASN84 3.9 20.8 1.0 CE A:LYS325 3.9 21.3 1.0 NZ A:LYS325 3.9 22.1 1.0 CG A:ASN84 4.0 19.4 1.0 CD2 A:PHE323 4.1 25.2 1.0 HB2 A:LEU330 4.1 27.4 1.0 OD1 A:ASN84 4.1 17.1 1.0 HB2 A:ASN84 4.1 25.4 1.0 HZ3 A:LYS325 4.1 26.5 1.0 HD21 A:ASN84 4.2 25.0 1.0 CE2 A:PHE323 4.2 29.0 1.0 CD A:LYS325 4.2 22.2 1.0 HD12 A:LEU330 4.3 29.0 1.0 HA A:ARG83 4.4 20.8 1.0 O A:LEU82 4.4 21.6 1.0 HD21 A:LEU330 4.5 34.1 1.0 CB A:ASN84 4.6 21.2 1.0 HD2 A:LYS325 4.7 26.6 1.0 HZ2 A:LYS325 4.7 26.5 1.0 O A:HOH663 4.7 31.3 1.0 O A:HOH723 4.8 44.7 1.0 HE2 A:LYS325 4.8 25.6 1.0 C A:ARG83 4.9 16.9 1.0

Iodine binding site 8 out of 44 in the Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein 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 Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I507 b:54.5 occ:1.00 HD2 A:ARG135 3.1 30.9 1.0 HD2 A:PRO136 3.2 38.9 1.0 HG2 A:PRO136 3.4 42.6 1.0 HB3 A:ARG135 3.6 35.3 1.0 H A:VAL137 3.9 35.0 1.0 CD A:PRO136 4.0 32.4 1.0 CG A:PRO136 4.1 35.5 1.0 CD A:ARG135 4.1 25.8 1.0 HG23 A:VAL137 4.2 46.6 1.0 HB A:VAL137 4.3 47.5 1.0 O A:HOH613 4.4 31.3 1.0 HG3 A:PRO136 4.4 42.6 1.0 CB A:ARG135 4.5 29.4 1.0 HD3 A:ARG135 4.6 30.9 1.0 HG3 A:ARG135 4.6 33.6 1.0 HG21 A:VAL139 4.6 37.7 1.0 HD3 A:PRO136 4.6 38.9 1.0 CG A:ARG135 4.6 28.0 1.0 HE A:ARG135 4.7 31.0 1.0 N A:VAL137 4.7 29.1 1.0 HG23 A:VAL139 4.7 37.7 1.0 N A:PRO136 4.8 33.5 1.0 NE A:ARG135 4.9 25.8 1.0 HA A:ARG135 4.9 29.8 1.0 CG2 A:VAL137 4.9 38.8 1.0 HG22 A:VAL139 4.9 37.7 1.0 CB A:VAL137 4.9 39.5 1.0 CG2 A:VAL139 5.0 31.4 1.0

Iodine binding site 9 out of 44 in the Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein 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 Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I508 b:28.4 occ:0.59 HH11 A:ARG83 2.9 43.1 1.0 HD3 A:ARG83 3.3 33.5 1.0 HD22 A:ASN318 3.5 35.0 1.0 HB3 A:ARG83 3.6 23.6 1.0 NH1 A:ARG83 3.7 35.9 1.0 HD21 A:ASN318 3.8 35.0 1.0 HG2 A:ARG83 4.0 26.9 1.0 ND2 A:ASN318 4.0 29.1 1.0 HH12 A:ARG83 4.0 43.1 1.0 CD A:ARG83 4.2 27.9 1.0 O A:HOH666 4.2 31.3 1.0 CB A:ARG83 4.4 19.7 1.0 CG A:ARG83 4.4 22.4 1.0 HA A:ARG83 4.5 20.8 1.0 O A:ARG83 4.5 18.3 1.0 HD2 A:ARG83 4.8 33.5 1.0 CZ A:ARG83 4.8 34.3 1.0 O A:HOH723 4.8 44.7 1.0 CA A:ARG83 4.9 17.3 1.0 NE A:ARG83 5.0 30.6 1.0

Iodine binding site 10 out of 44 in the Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein 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 Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:I509 b:43.1 occ:0.82 HH11 A:ARG33 2.9 35.0 1.0 HD21 A:ASN120 3.0 39.8 1.0 HD3 A:ARG33 3.3 43.0 1.0 HD22 A:LEU69 3.3 30.9 1.0 HE1 A:HIS38 3.4 42.6 1.0 HB2 A:ASN120 3.5 44.5 1.0 NH1 A:ARG33 3.7 29.2 1.0 O A:HOH896 3.8 31.1 1.0 ND2 A:ASN120 3.9 33.2 1.0 HH12 A:ARG33 4.0 35.0 1.0 CE1 A:HIS38 4.0 35.5 1.0 HD2 A:ARG33 4.0 43.0 1.0 CD A:ARG33 4.1 35.9 1.0 CD2 A:LEU69 4.2 25.8 1.0 HB3 A:ARG33 4.2 45.6 1.0 CB A:ASN120 4.3 37.1 1.0 HD23 A:LEU69 4.3 30.9 1.0 HD1 A:HIS38 4.3 37.1 1.0 HD22 A:ASN120 4.4 39.8 1.0 HB3 A:ASN120 4.4 44.5 1.0 HD21 A:LEU69 4.5 30.9 1.0 ND1 A:HIS38 4.5 30.9 1.0 CG A:ASN120 4.7 33.6 1.0 CZ A:ARG33 4.8 30.5 1.0 NE A:ARG33 4.9 33.4 1.0 CB A:ARG33 5.0 38.0 1.0 NE2 A:HIS38 5.0 35.1 1.0

A.C.Chan, K.M.Blair, Y.Liu, E.Frirdich, E.C.Gaynor, M.E.Tanner, N.R.Salama, M.E.Murphy. Helical Shape of Helicobacter Pylori Requires An Atypical Glutamine As A Zinc Ligand in the Carboxypeptidase CSD4 J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M114.624734