Zinc in PDB 4rny: Structure of Helicobacter Pylori CSD3 From the Orthorhombic Crystal

The structure of Structure of Helicobacter Pylori CSD3 From the Orthorhombic Crystal, PDB code: 4rny was solved by D.R.An, H.S.Kim, J.Kim, H.N.Im, H.J.Yoon, J.Y.Yoon, J.Y.Jang, D.Hesek, M.Lee, S.Mobashery, S.-J.Kim, B.I.Lee, S.W.Suh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.618, 112.146, 112.939, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 25.6

The binding sites of Zinc atom in the Structure of Helicobacter Pylori CSD3 From the Orthorhombic Crystal (pdb code 4rny). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Helicobacter Pylori CSD3 From the Orthorhombic Crystal, PDB code: 4rny:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Helicobacter Pylori CSD3 From the Orthorhombic Crystal


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Helicobacter Pylori CSD3 From the Orthorhombic Crystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:26.2 occ:1.00 ND1 A:HIS341 2.0 23.5 1.0 OE2 A:GLU74 2.0 30.8 1.0 OD1 A:ASP263 2.0 24.1 1.0 NE2 A:HIS259 2.1 24.0 1.0 CD A:GLU74 2.7 30.9 1.0 CG A:ASP263 2.8 25.4 1.0 OE1 A:GLU74 2.9 31.1 1.0 CE1 A:HIS341 2.9 24.1 1.0 OD2 A:ASP263 3.0 30.2 1.0 CG A:HIS341 3.1 25.0 1.0 CD2 A:HIS259 3.1 22.7 1.0 CE1 A:HIS259 3.1 24.6 1.0 CB A:HIS341 3.5 24.4 1.0 O A:HOH661 3.8 42.9 1.0 NE2 A:HIS341 4.0 23.9 1.0 CD2 A:HIS341 4.1 24.9 1.0 CG A:GLU74 4.2 31.2 1.0 ND1 A:HIS259 4.2 22.7 1.0 CB A:ASP263 4.2 27.1 1.0 CG A:HIS259 4.2 23.0 1.0 CA A:HIS341 4.3 25.2 1.0 O A:HOH645 4.6 30.2 1.0 N A:ASP263 4.6 27.0 1.0 CB A:GLU74 4.6 28.1 1.0 CA A:ASP263 4.7 26.6 1.0 O A:HOH603 4.8 26.4 1.0 C A:VAL262 4.8 24.9 1.0 O A:VAL262 4.9 25.1 1.0 C A:GLY261 5.0 23.1 1.0

Zinc binding site 2 out of 2 in the Structure of Helicobacter Pylori CSD3 From the Orthorhombic Crystal


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Helicobacter Pylori CSD3 From the Orthorhombic Crystal within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:25.9 occ:1.00 OE2 B:GLU74 2.0 25.2 1.0 OD1 B:ASP263 2.0 25.1 1.0 ND1 B:HIS341 2.0 25.4 1.0 NE2 B:HIS259 2.1 24.0 1.0 CD B:GLU74 2.7 27.0 1.0 CG B:ASP263 2.7 26.6 1.0 OE1 B:GLU74 2.8 25.7 1.0 OD2 B:ASP263 2.8 31.0 1.0 CE1 B:HIS341 2.9 26.7 1.0 CE1 B:HIS259 3.0 27.5 1.0 CD2 B:HIS259 3.1 26.1 1.0 CG B:HIS341 3.1 24.4 1.0 CB B:HIS341 3.5 25.5 1.0 NE2 B:HIS341 4.1 26.3 1.0 CB B:ASP263 4.2 24.9 1.0 CG B:GLU74 4.2 27.3 1.0 ND1 B:HIS259 4.2 25.1 1.0 CD2 B:HIS341 4.2 25.1 1.0 CG B:HIS259 4.2 26.4 1.0 CA B:HIS341 4.4 25.9 1.0 N B:ASP263 4.6 24.5 1.0 CA B:ASP263 4.7 25.9 1.0 CB B:GLU74 4.7 28.6 1.0 C B:VAL262 4.8 24.5 1.0 O B:HOH646 4.8 27.7 1.0 O B:HOH607 4.8 23.8 1.0 O B:VAL262 4.8 24.6 1.0 C B:GLY261 5.0 24.6 1.0

D.R.An, H.S.Kim, J.Kim, H.N.Im, H.J.Yoon, J.Y.Yoon, J.Y.Jang, D.Hesek, M.Lee, S.Mobashery, S.-J.Kim, B.I.Lee, S.W.Suh. Structure of CSD3 From Helicobacter Pylori, A Cell Shape-Determining Metallopeptidase. Acta Crystallogr.,Sect.D V. 71 2015.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004715000152