Atomistry » Calcium » PDB 3ttb-3ue5 » 3ubf
Atomistry »
  Calcium »
    PDB 3ttb-3ue5 »
      3ubf »

Calcium in PDB 3ubf: Crystal Structure of Drosophila N-Cadherin EC1-3, I

Protein crystallography data

The structure of Crystal Structure of Drosophila N-Cadherin EC1-3, I, PDB code: 3ubf 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) 20.00 / 2.50
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 96.289, 96.289, 148.196, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 27.9

Other elements in 3ubf:

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

Zinc (Zn) 18 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 1 in 3ubf

Go back to Calcium Binding Sites List in 3ubf
Calcium binding site 1 out of 1 in the Crystal Structure of Drosophila N-Cadherin EC1-3, I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Drosophila N-Cadherin EC1-3, I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca754

b:51.4
occ:1.00
OE1 A:GLU498 2.3 45.3 1.0
O A:HOH115 2.3 9.1 1.0
OE2 A:GLU450 2.3 55.2 1.0
O A:HOH165 2.5 2.0 1.0
OD2 A:ASP575 2.8 61.2 1.0
OD1 A:ASP496 3.0 57.6 1.0
CD A:GLU450 3.0 53.5 1.0
OE1 A:GLU450 3.0 53.0 1.0
CD A:GLU498 3.1 48.0 1.0
ZN A:ZN1 3.3 45.2 1.0
OE2 A:GLU498 3.4 46.9 1.0
ZN A:ZN19 3.5 95.0 1.0
CG A:ASP575 3.6 56.9 1.0
CB A:ASP575 3.6 53.1 1.0
CG A:ASP496 4.0 55.4 1.0
N A:TYR497 4.2 46.8 1.0
CG A:GLU498 4.3 52.3 1.0
ZN A:ZN7 4.3 64.6 1.0
CG A:GLU450 4.5 50.9 1.0
N A:GLU498 4.5 50.0 1.0
O A:HOH107 4.5 8.1 1.0
OD1 A:ASP535 4.5 53.7 1.0
CA A:ASP496 4.6 48.9 1.0
OD1 A:ASP573 4.7 51.4 1.0
CB A:GLU498 4.7 54.0 1.0
OD2 A:ASP535 4.7 56.2 1.0
CB A:TYR497 4.7 45.4 1.0
C A:ASP496 4.7 47.9 1.0
OD2 A:ASP496 4.8 58.9 1.0
OD1 A:ASP575 4.8 58.0 1.0
CB A:ASP496 4.9 51.9 1.0
CG A:ASP535 4.9 54.4 1.0
CA A:TYR497 5.0 46.0 1.0
OD2 A:ASP573 5.0 49.5 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: Sat Dec 12 04:32:43 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy