Zinc in PDB 5j1m: Crystal Structure of CSD1-CSD2 Dimer II

The structure of Crystal Structure of CSD1-CSD2 Dimer II, PDB code: 5j1m was solved by D.R.An, S.W.Suh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.149, 80.013, 74.594, 90.00, 104.43, 90.00
R / Rfree (%)	16.8 / 23.3

The binding sites of Zinc atom in the Crystal Structure of CSD1-CSD2 Dimer II (pdb code 5j1m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of CSD1-CSD2 Dimer II, PDB code: 5j1m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of CSD1-CSD2 Dimer II


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 CSD1-CSD2 Dimer II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:43.8 occ:1.00 OD1 A:ASP173 1.9 35.0 1.0 O A:HOH502 2.1 32.9 1.0 ND1 A:HIS252 2.2 39.1 1.0 ND1 A:HIS164 2.4 53.0 1.0 CG A:ASP173 2.7 36.0 1.0 OD2 A:ASP173 2.9 36.5 1.0 CE1 A:HIS252 3.1 38.7 1.0 CG A:HIS252 3.2 37.0 1.0 CE1 A:HIS164 3.3 55.3 1.0 CG A:HIS164 3.3 54.7 1.0 CB A:HIS252 3.5 34.5 1.0 NE2 A:HIS250 3.6 32.4 1.0 CB A:HIS164 3.6 54.6 1.0 CB A:ASP173 4.1 34.9 1.0 CD2 A:HIS250 4.2 34.4 1.0 NE2 A:HIS219 4.2 35.8 1.0 NE2 A:HIS252 4.2 39.9 1.0 CD2 A:HIS252 4.3 39.8 1.0 CA A:HIS252 4.3 33.1 1.0 NE2 A:HIS164 4.4 62.1 1.0 CD2 A:HIS164 4.4 58.6 1.0 CD2 A:LEU166 4.4 70.4 1.0 CA A:ASP173 4.6 36.6 1.0 CB A:LEU166 4.6 68.8 1.0 O A:HIS164 4.7 48.4 1.0 CE1 A:HIS250 4.7 31.9 1.0 N A:ASP173 4.8 38.1 1.0 CD2 A:HIS219 4.8 34.8 1.0 CA A:HIS164 4.9 54.1 1.0 O A:LEU172 4.9 40.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of CSD1-CSD2 Dimer II


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 CSD1-CSD2 Dimer II within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:74.7 occ:1.00 OD1 C:ASP173 1.8 63.0 1.0 O C:HOH501 2.0 32.1 1.0 ND1 C:HIS252 2.4 52.0 1.0 CG C:ASP173 2.5 67.4 1.0 OD2 C:ASP173 2.6 74.4 1.0 CE1 C:HIS169 2.6 99.6 1.0 NE2 C:HIS169 2.8 98.1 1.0 CE1 C:HIS252 3.2 51.0 1.0 CG C:HIS252 3.3 48.3 1.0 CB C:HIS252 3.7 42.5 1.0 ND1 C:HIS169 3.9 0.5 1.0 CB C:ASP173 4.0 61.3 1.0 NE2 C:HIS250 4.1 73.5 1.0 CD2 C:HIS169 4.1 98.0 1.0 NE2 C:HIS219 4.2 47.6 1.0 NE2 C:HIS252 4.3 52.7 1.0 CD2 C:HIS252 4.3 51.5 1.0 CA C:HIS252 4.5 41.2 1.0 CA C:ASP173 4.6 59.4 1.0 CG C:HIS169 4.6 0.1 1.0 CD2 C:HIS250 4.7 68.5 1.0 N C:ASP173 4.7 59.1 1.0 CD2 C:HIS219 4.8 46.0 1.0 C C:LEU172 4.9 55.9 1.0

D.R.An, H.N.Im, J.Y.Jang, H.S.Kim, J.Kim, H.J.Yoon, D.Hesek, M.Lee, S.Mobashery, S.J.Kim, S.W.Suh. Structural Basis of the Heterodimer Formation Between Cell Shape-Determining Proteins CSD1 and CSD2 From Helicobacter Pylori Plos One V. 11 64243 2016.
ISSN: ESSN 1932-6203
PubMed: 27711177
DOI: 10.1371/JOURNAL.PONE.0164243