Zinc 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:

Iodine

(I)

19 atoms

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc where determined in the Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori, PDB code: 5d2r:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn501 b:23.0 occ:1.00 OE1 A:GLN46 2.1 18.7 1.0 ND1 A:HIS128 2.1 20.9 1.0 OE1 A:GLU49 2.2 12.7 1.0 O6 A:56W523 2.3 22.0 1.0 O2 A:56W523 2.4 21.5 1.0 OE2 A:GLU49 2.5 14.3 1.0 HB3 A:HIS128 2.6 22.0 1.0 CD A:GLU49 2.7 14.2 1.0 P A:56W523 2.8 18.1 1.0 CG A:HIS128 3.0 19.0 1.0 CD A:GLN46 3.0 18.9 1.0 CE1 A:HIS128 3.1 22.5 1.0 CB A:HIS128 3.3 18.4 1.0 HE1 A:HIS128 3.3 27.0 1.0 HE22 A:GLN46 3.4 22.5 1.0 HH12 A:ARG86 3.6 46.0 1.0 NE2 A:GLN46 3.6 18.8 1.0 HB2 A:GLN46 3.6 23.4 1.0 H9 A:56W523 3.7 30.2 1.0 HA A:HIS128 3.7 18.9 1.0 O A:HOH756 3.9 18.5 1.0 H15 A:56W523 3.9 26.8 1.0 H A:ASP129 4.0 18.6 1.0 HB2 A:HIS128 4.0 22.0 1.0 CA A:HIS128 4.1 15.8 1.0 C7 A:56W523 4.1 22.4 1.0 O1 A:56W523 4.1 23.9 1.0 O A:ASP129 4.1 23.5 1.0 CG A:GLU49 4.2 13.4 1.0 CD2 A:HIS128 4.2 18.3 1.0 NE2 A:HIS128 4.2 20.5 1.0 C6 A:56W523 4.2 20.4 1.0 CG A:GLN46 4.2 19.4 1.0 NH1 A:ARG86 4.3 38.3 1.0 HG22 A:ILE45 4.3 18.3 1.0 CB A:GLN46 4.4 19.5 1.0 HE21 A:GLN46 4.4 22.5 1.0 C5 A:56W523 4.4 28.1 1.0 OE2 A:GLU222 4.4 25.1 1.0 N A:ASP129 4.5 15.5 1.0 HH22 A:ARG86 4.5 49.0 1.0 HG3 A:GLU49 4.6 16.1 1.0 C4 A:56W523 4.6 25.6 1.0 C3 A:56W523 4.6 25.2 1.0 HG2 A:GLU49 4.6 16.1 1.0 HH11 A:ARG86 4.6 46.0 1.0 HG2 A:GLN46 4.7 23.3 1.0 H12 A:56W523 4.7 24.4 1.0 H18 A:56W523 4.7 31.5 1.0 C A:HIS128 4.8 15.4 1.0 HB2 A:GLU49 4.8 16.7 1.0 HB3 A:GLU49 4.8 16.7 1.0 H16 A:56W523 4.8 26.8 1.0 HB3 A:GLN46 4.8 23.4 1.0 CB A:GLU49 4.9 13.9 1.0 HG3 A:GLN46 4.9 23.3 1.0 HG23 A:ILE45 5.0 18.3 1.0 H A:GLN46 5.0 22.3 1.0 HE2 A:HIS128 5.0 24.6 1.0

Zinc binding site 2 out of 3 in the Inhibitor Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn502 b:24.0 occ:0.80 OD2 A:ASP254 1.7 17.7 1.0 ND1 A:HIS62 2.0 28.5 1.0 CG A:ASP254 2.5 24.6 1.0 OD1 A:ASP254 2.6 27.0 1.0 CE1 A:HIS62 2.9 27.8 1.0 HE1 A:HIS62 3.0 33.4 1.0 CG A:HIS62 3.1 22.6 1.0 HB3 A:HIS62 3.2 22.8 1.0 HA A:HIS62 3.3 25.6 1.0 CB A:HIS62 3.6 19.0 1.0 CA A:HIS62 3.9 21.3 1.0 CB A:ASP254 4.0 27.3 1.0 NE2 A:HIS62 4.1 24.0 1.0 CD2 A:HIS62 4.2 21.4 1.0 O A:MET61 4.2 23.9 1.0 HB2 A:ASP254 4.2 32.8 1.0 HB3 A:ASP254 4.3 32.8 1.0 HB2 A:HIS62 4.5 22.8 1.0 HD22 A:LEU265 4.6 31.1 1.0 HD1 A:PHE255 4.7 22.3 1.0 H A:ASP254 4.7 35.1 1.0 O A:HIS62 4.8 21.9 1.0 HE2 A:HIS62 4.8 28.8 1.0 N A:HIS62 4.8 21.6 1.0 C A:MET61 4.8 22.1 1.0 HD21 A:LEU265 4.9 31.1 1.0 C A:HIS62 4.9 21.7 1.0 O A:HOH658 4.9 50.6 1.0 O A:HOH719 5.0 54.7 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn503 b:37.3 occ:0.50 OD1 A:ASP157 2.1 42.2 1.0 OE1 A:GLU158 2.1 52.3 1.0 CG A:ASP157 2.7 40.9 1.0 OD2 A:ASP157 2.8 47.7 1.0 CD A:GLU158 3.2 44.9 0.1 HG2 A:GLU158 3.3 49.6 1.0 O A:HOH604 3.8 45.3 1.0 CG A:GLU158 3.8 41.3 1.0 CB A:ASP157 4.2 32.8 1.0 H A:ASP157 4.3 31.7 1.0 OE2 A:GLU158 4.3 39.7 1.0 H A:GLU158 4.4 29.9 1.0 HB2 A:ASP157 4.5 39.3 1.0 HB3 A:GLU158 4.5 41.6 1.0 HG3 A:GLU158 4.5 49.6 1.0 N A:GLU158 4.7 24.9 1.0 HB3 A:ASP157 4.7 39.3 1.0 O A:HOH826 4.7 27.1 1.0 CB A:GLU158 4.8 34.7 1.0 CA A:ASP157 4.9 27.4 1.0 N A:ASP157 4.9 26.4 1.0 C A:ASP157 4.9 26.8 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