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Zinc in PDB 5j1l: Crystal Structure of CSD1-CSD2 Dimer I

Protein crystallography data

The structure of Crystal Structure of CSD1-CSD2 Dimer I, PDB code: 5j1l 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 / 2.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.359, 82.375, 76.290, 90.00, 106.03, 90.00
R / Rfree (%) 17.4 / 23.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of CSD1-CSD2 Dimer I (pdb code 5j1l). 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 I, PDB code: 5j1l:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5j1l

Go back to Zinc Binding Sites List in 5j1l
Zinc binding site 1 out of 2 in the Crystal Structure of CSD1-CSD2 Dimer I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:82.4
occ:1.00
OD1 A:ASP173 2.6 32.1 1.0
NE2 A:HIS250 2.9 24.6 1.0
OD2 A:ASP173 3.0 35.6 1.0
CG A:ASP173 3.2 31.7 1.0
ND1 A:HIS252 3.3 27.4 1.0
O A:HOH517 3.3 34.1 1.0
NE2 A:HIS219 3.3 27.1 1.0
OD1 A:ASN168 3.7 81.0 1.0
CB A:HIS252 3.7 22.1 1.0
CG A:HIS252 3.7 24.0 1.0
CD2 A:HIS250 3.8 24.2 1.0
CE1 A:HIS250 3.9 24.6 1.0
CD2 A:HIS219 3.9 25.8 1.0
CE1 A:HIS252 4.2 26.6 1.0
ND2 A:ASN168 4.3 83.0 1.0
CG A:ASN168 4.4 85.0 1.0
CE1 A:HIS219 4.4 25.6 1.0
CB A:ASP173 4.6 29.3 1.0
O A:HOH508 4.7 38.1 1.0
CA A:HIS252 4.8 22.0 1.0
CD2 A:HIS252 4.8 26.3 1.0

Zinc binding site 2 out of 2 in 5j1l

Go back to Zinc Binding Sites List in 5j1l
Zinc binding site 2 out of 2 in the Crystal Structure of CSD1-CSD2 Dimer I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:43.6
occ:1.00
OD1 C:ASP173 2.0 41.4 1.0
ND1 C:HIS252 2.3 38.2 1.0
O C:HOH514 2.3 31.4 1.0
NE2 C:HIS169 2.3 44.6 1.0
CG C:ASP173 2.8 42.7 1.0
OD2 C:ASP173 2.9 44.0 1.0
CE1 C:HIS252 3.0 38.0 1.0
CE1 C:HIS169 3.2 47.1 1.0
CG C:HIS252 3.3 36.5 1.0
CD2 C:HIS169 3.4 46.2 1.0
CB C:HIS252 3.7 35.5 1.0
NE2 C:HIS252 4.1 37.8 1.0
CB C:ASP173 4.2 42.9 1.0
NE2 C:HIS250 4.2 50.6 1.0
CD2 C:HIS252 4.2 38.4 1.0
ND1 C:HIS169 4.3 48.9 1.0
CA C:HIS252 4.4 33.9 1.0
CG C:HIS169 4.5 47.6 1.0
N C:ASP173 4.5 39.2 1.0
CA C:ASP173 4.6 40.7 1.0
C C:LEU172 4.7 38.7 1.0
N C:LEU172 4.8 38.4 1.0
O C:LEU172 4.8 38.7 1.0
CD2 C:HIS250 5.0 52.4 1.0
C C:GLY171 5.0 41.3 1.0

Reference:

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
Page generated: Wed Dec 16 06:24:15 2020

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