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Zinc in PDB 3ubg: Crystal Structure of Drosophila N-Cadherin EC1-3, II

Protein crystallography data

The structure of Crystal Structure of Drosophila N-Cadherin EC1-3, II, PDB code: 3ubg was solved by X.Jin, M.A.Walker, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.218, 113.769, 87.872, 90.00, 123.57, 90.00
R / Rfree (%) 19.6 / 26.7

Other elements in 3ubg:

The structure of Crystal Structure of Drosophila N-Cadherin EC1-3, II also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Drosophila N-Cadherin EC1-3, II (pdb code 3ubg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Drosophila N-Cadherin EC1-3, II, PDB code: 3ubg:

Zinc binding site 1 out of 1 in 3ubg

Go back to Zinc Binding Sites List in 3ubg
Zinc binding site 1 out of 1 in the Crystal Structure of Drosophila N-Cadherin EC1-3, 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 Drosophila N-Cadherin EC1-3, II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:39.3
occ:1.00
NE2 B:HIS576 2.1 36.2 1.0
NE2 A:HIS576 2.2 36.2 1.0
O B:HOH115 2.4 35.4 1.0
O B:HOH145 2.6 37.9 1.0
CE1 B:HIS576 3.0 39.1 1.0
CE1 A:HIS576 3.1 34.9 1.0
CD2 B:HIS576 3.1 33.4 1.0
CD2 A:HIS576 3.2 30.1 1.0
O B:HOH275 3.3 34.2 1.0
O B:HOH318 3.3 53.2 1.0
O A:HOH394 3.6 36.9 1.0
O A:HOH166 3.9 29.9 1.0
O B:HOH62 4.0 31.4 1.0
ND1 B:HIS576 4.2 33.4 1.0
CG B:HIS576 4.2 31.9 1.0
ND1 A:HIS576 4.3 34.1 1.0
CG A:HIS576 4.3 29.1 1.0
O B:HOH393 4.4 36.7 1.0
O B:HOH392 4.4 37.7 1.0
O B:ASP573 4.7 33.9 1.0
O A:ASP573 4.8 32.0 1.0

Reference:

X.Jin, M.A.Walker, K.Felsovalyi, J.Vendome, F.Bahna, S.Mannepalli, F.Cosmanescu, G.Ahlsen, B.Honig, L.Shapiro. Crystal Structures of Drosophila N-Cadherin Ectodomain Regions Reveal A Widely Used Class of CA2+-Free Interdomain Linkers. Proc.Natl.Acad.Sci.Usa V. 109 E127 2012.
ISSN: ISSN 0027-8424
PubMed: 22171007
DOI: 10.1073/PNAS.1117538108
Page generated: Wed Dec 16 04:53:58 2020

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