Zinc in PDB 4wcl: Crystal Structure of Product Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori

The structure of Crystal Structure of Product Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori, PDB code: 4wcl 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)	42.76 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.030, 66.770, 144.570, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 19.5

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

Iodine	(I)	33 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Product Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori (pdb code 4wcl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Product Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori, PDB code: 4wcl:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Product 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 Crystal Structure of Product Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:23.5 occ:0.54 OD2 A:ASP254 1.8 21.8 1.0 ND1 A:HIS62 1.9 19.6 1.0 O A:HOH962 2.2 45.2 1.0 O A:HOH778 2.5 44.2 1.0 CG A:ASP254 2.5 21.4 1.0 OD1 A:ASP254 2.6 20.2 1.0 CE1 A:HIS62 2.7 20.3 1.0 HE1 A:HIS62 2.8 24.4 1.0 CG A:HIS62 3.1 17.6 1.0 HA A:HIS62 3.2 19.9 1.0 HB3 A:HIS62 3.4 20.0 1.0 CB A:HIS62 3.6 16.7 1.0 CA A:HIS62 3.9 16.6 1.0 NE2 A:HIS62 3.9 18.8 1.0 CB A:ASP254 3.9 23.1 1.0 CD2 A:HIS62 4.1 17.1 1.0 O A:MET61 4.1 17.7 1.0 HB2 A:ASP254 4.2 27.8 1.0 HB3 A:ASP254 4.3 27.8 1.0 HD22 A:LEU265 4.5 22.2 1.0 HB2 A:HIS62 4.6 20.0 1.0 HE2 A:HIS62 4.7 22.6 1.0 C A:MET61 4.8 15.8 1.0 HD1 A:PHE255 4.8 18.0 1.0 N A:HIS62 4.8 15.5 1.0 H A:ASP254 4.8 24.3 1.0 O A:HIS62 4.9 17.4 1.0 O A:HOH959 4.9 41.2 1.0 HD13 A:LEU265 4.9 18.4 1.0 C A:HIS62 4.9 16.3 1.0 O A:HOH894 4.9 42.3 1.0 HD21 A:LEU265 5.0 22.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Product 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 Crystal Structure of Product Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:21.5 occ:0.90 ND1 A:HIS128 2.0 17.9 1.0 O A:HOH746 2.2 22.3 1.0 OE1 A:GLN46 2.2 14.2 1.0 OE2 A:GLU49 2.3 14.2 1.0 OE1 A:GLU49 2.3 11.1 1.0 O A:HOH702 2.3 22.0 1.0 CD A:GLU49 2.6 12.7 1.0 CE1 A:HIS128 2.9 18.7 1.0 HB3 A:HIS128 3.0 19.6 1.0 HE1 A:HIS128 3.0 22.4 1.0 CG A:HIS128 3.1 17.0 1.0 CD A:GLN46 3.2 16.1 1.0 CB A:HIS128 3.5 16.4 1.0 HB2 A:GLN46 3.6 18.9 1.0 HG2 A:GLN46 3.7 20.4 1.0 H2 A:API535 3.8 28.6 1.0 CG A:GLN46 3.9 17.0 1.0 HA A:HIS128 3.9 17.2 1.0 O A:ASP129 4.0 17.6 1.0 O A:HOH700 4.0 15.8 1.0 NE2 A:HIS128 4.1 18.3 1.0 H A:ASP129 4.1 16.5 1.0 HN22 A:API535 4.1 26.8 1.0 CG A:GLU49 4.1 13.2 1.0 CD2 A:HIS128 4.2 17.2 1.0 NE2 A:GLN46 4.2 17.9 1.0 O A:HOH764 4.2 29.7 1.0 CB A:GLN46 4.2 15.8 1.0 HE22 A:GLN46 4.3 21.5 1.0 O A:HOH754 4.3 26.4 1.0 CA A:HIS128 4.3 14.3 1.0 HG22 A:ILE45 4.3 18.4 1.0 HB2 A:HIS128 4.3 19.6 1.0 OE1 A:GLU222 4.5 22.2 1.0 HG3 A:GLU49 4.5 15.8 1.0 HG2 A:GLU49 4.5 15.8 1.0 N A:ASP129 4.6 13.8 1.0 C2 A:API535 4.6 23.9 1.0 HN21 A:API535 4.6 26.8 1.0 N2 A:API535 4.6 22.3 1.0 HG23 A:ILE45 4.7 18.4 1.0 HB3 A:GLN46 4.7 18.9 1.0 H A:GLN46 4.8 18.4 1.0 HG3 A:GLN46 4.8 20.4 1.0 HE2 A:HIS128 4.8 21.9 1.0 O A:HOH712 4.8 16.4 1.0 HH11 A:ARG86 4.9 28.9 0.5 HE21 A:GLN46 4.9 21.5 1.0 CG2 A:ILE45 4.9 15.3 1.0 C A:ASP129 4.9 16.9 1.0 HB3 A:GLU49 4.9 14.3 1.0 HB2 A:GLU49 4.9 14.3 1.0 C A:HIS128 4.9 14.5 1.0 CB A:GLU49 5.0 11.9 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Product 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 Crystal Structure of Product Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:23.5 occ:0.28 I A:IOD532 2.5 46.7 0.6 SD A:MET358 2.5 35.4 1.0 I A:IOD526 2.6 66.8 0.7 I A:IOD527 2.8 55.6 0.6 HD3 A:LYS349 3.0 40.5 1.0 HG2 A:MET358 3.2 43.9 1.0 HG3 A:MET358 3.2 43.9 1.0 CG A:MET358 3.3 36.6 1.0 I A:IOD532 3.5 48.5 0.5 HE2 A:MET358 3.6 42.4 1.0 CE A:MET358 3.7 35.4 1.0 HE1 A:MET358 3.9 42.4 1.0 CD A:LYS349 3.9 33.7 1.0 HB2 A:LYS349 4.0 36.3 1.0 HZ2 A:LYS349 4.1 46.4 1.0 HG3 A:LYS349 4.3 36.7 1.0 HD2 A:LYS349 4.4 40.5 1.0 HE3 A:MET358 4.5 42.4 1.0 CG A:LYS349 4.5 30.6 1.0 HE2 A:LYS349 4.6 41.9 1.0 CE A:LYS349 4.7 34.9 1.0 CB A:LYS349 4.7 30.2 1.0 CB A:MET358 4.7 34.2 1.0 NZ A:LYS349 4.8 38.7 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