Atomistry » Calcium » PDB 3tz1-3uiq » 3ubg
Atomistry »
  Calcium »
    PDB 3tz1-3uiq »
      3ubg »

Calcium 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:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Drosophila N-Cadherin EC1-3, II, PDB code: 3ubg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3ubg

Go back to Calcium Binding Sites List in 3ubg
Calcium binding site 1 out of 6 in the Crystal Structure of Drosophila N-Cadherin EC1-3, II


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, II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:28.3
occ:1.00
 O A:GLU539 2.4 27.2 1.0
OD2 A:ASP573 2.4 32.7 1.0
OD2 A:ASP622 2.4 27.8 1.0
OD2 A:ASP571 2.5 25.8 1.0
OD1 A:ASN537 2.5 29.6 1.0
OD1 A:ASP571 2.6 24.2 1.0
OE1 A:GLN633 2.6 30.1 1.0
CG A:ASP571 2.8 27.4 1.0
CG A:ASP573 3.4 25.4 1.0
CG A:ASP622 3.5 30.4 1.0
CG A:ASN537 3.5 30.3 1.0
C A:GLU539 3.5 30.7 1.0
CD A:GLN633 3.6 34.9 1.0
CB A:ASP622 3.8 24.1 1.0
NE2 A:GLN633 3.9 35.3 1.0
N A:GLU539 3.9 27.8 1.0
ND2 A:ASN537 4.0 31.1 1.0
CB A:ASP573 4.0 25.8 1.0
CA A:GLU539 4.3 27.1 1.0
CB A:ASP571 4.3 22.3 1.0
OD1 A:ASP573 4.3 26.8 1.0
N A:ASP538 4.5 25.7 1.0
N A:PRO540 4.6 32.1 1.0
OD1 A:ASP622 4.6 31.4 1.0
N A:ASP573 4.6 27.3 1.0
CA A:PRO540 4.7 23.5 1.0
CD A:PRO572 4.7 30.1 1.0
C A:PRO540 4.7 25.3 1.0
CB A:GLU539 4.8 26.4 1.0
C A:ASN537 4.8 26.0 1.0
CB A:ASN537 4.8 24.4 1.0
CG A:GLN633 4.8 38.2 1.0
CD A:PRO541 4.8 22.8 1.0
N A:PRO541 4.9 25.9 1.0
CA A:ASN537 4.9 22.5 1.0
CB A:GLN633 5.0 34.9 1.0
CA A:ASP573 5.0 26.6 1.0
C A:ASP538 5.0 26.5 1.0

Calcium binding site 2 out of 6 in 3ubg

Go back to Calcium Binding Sites List in 3ubg
Calcium binding site 2 out of 6 in the Crystal Structure of Drosophila N-Cadherin EC1-3, II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Drosophila N-Cadherin EC1-3, II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:26.2
occ:1.00
 OD1 A:ASP535 2.4 30.2 1.0
O A:VAL536 2.4 26.2 1.0
OD1 A:ASP573 2.5 26.8 1.0
OD1 A:ASP538 2.5 22.3 1.0
OE1 A:GLU450 2.6 27.5 1.0
OE2 A:GLU498 2.6 26.0 1.0
OE1 A:GLU498 2.7 26.8 1.0
CD A:GLU498 3.0 28.2 1.0
CG A:ASP573 3.5 25.4 1.0
CG A:ASP535 3.5 29.5 1.0
CD A:GLU450 3.5 27.3 1.0
CG A:ASP538 3.6 24.2 1.0
C A:VAL536 3.6 24.2 1.0
OE2 A:GLU450 3.8 25.7 1.0
CA A:CA903 3.8 28.6 1.0
N A:VAL536 3.9 21.7 1.0
N A:ASP538 4.0 25.7 1.0
OD2 A:ASP535 4.1 31.2 1.0
OD2 A:ASP538 4.2 26.1 1.0
CB A:ASP573 4.2 25.8 1.0
CG A:GLU539 4.3 27.8 1.0
OD2 A:ASP573 4.3 32.7 1.0
CA A:VAL536 4.4 21.9 1.0
CG A:GLU498 4.4 18.9 1.0
CA A:ASP573 4.5 26.6 1.0
N A:ASN537 4.5 23.8 1.0
CA A:ASN537 4.5 22.5 1.0
CB A:ASP538 4.5 21.1 1.0
CB A:TYR497 4.6 24.3 1.0
CB A:ASP535 4.6 24.9 1.0
CA A:ASP538 4.7 23.2 1.0
O A:HOH27 4.7 25.4 1.0
CA A:ASP535 4.7 24.6 1.0
C A:ASN537 4.7 26.0 1.0
C A:ASP535 4.8 27.1 1.0
N A:GLU539 4.8 27.8 1.0
CG A:GLU450 4.9 27.5 1.0
CD2 A:TYR497 4.9 24.2 1.0
C A:ASP538 5.0 26.5 1.0

Calcium binding site 3 out of 6 in 3ubg

Go back to Calcium Binding Sites List in 3ubg
Calcium binding site 3 out of 6 in the Crystal Structure of Drosophila N-Cadherin EC1-3, II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Drosophila N-Cadherin EC1-3, II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:28.6
occ:1.00
 OE2 A:GLU539 2.5 26.1 1.0
OE1 A:GLU498 2.5 26.8 1.0
OD1 A:ASP496 2.5 24.5 1.0
OE2 A:GLU450 2.5 25.7 1.0
OD2 A:ASP538 2.6 26.1 1.0
O A:HOH126 2.7 24.5 1.0
OD1 A:ASP538 2.8 22.3 1.0
CG A:ASP538 3.1 24.2 1.0
CD A:GLU450 3.4 27.3 1.0
CD A:GLU539 3.5 26.8 1.0
CG A:ASP496 3.5 26.8 1.0
CD A:GLU498 3.7 28.2 1.0
OE1 A:GLU450 3.7 27.5 1.0
CG A:GLU539 3.8 27.8 1.0
CA A:CA902 3.8 26.2 1.0
CA A:ASP496 4.0 25.6 1.0
N A:TYR497 4.1 22.4 1.0
CB A:ASP496 4.2 25.9 1.0
OD2 A:ASP496 4.4 31.2 1.0
N A:GLU498 4.4 25.3 1.0
C A:ASP496 4.4 25.8 1.0
CG A:GLU450 4.5 27.5 1.0
CB A:ASP538 4.6 21.1 1.0
OE1 A:GLU539 4.6 35.1 1.0
OE2 A:GLU498 4.6 26.0 1.0
CG A:GLU498 4.6 18.9 1.0
O A:HOH29 4.6 27.6 1.0
CB A:GLU498 4.6 23.6 1.0
O A:TRP495 4.9 24.8 1.0
O A:HOH249 4.9 31.0 1.0
O A:ASP538 4.9 22.8 1.0

Calcium binding site 4 out of 6 in 3ubg

Go back to Calcium Binding Sites List in 3ubg
Calcium binding site 4 out of 6 in the Crystal Structure of Drosophila N-Cadherin EC1-3, II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Drosophila N-Cadherin EC1-3, II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca904

b:34.9
occ:1.00
 OE2 B:GLU450 2.3 36.1 1.0
OE2 B:GLU539 2.5 31.3 1.0
OE1 B:GLU498 2.6 29.9 1.0
OD1 B:ASP496 2.6 30.5 1.0
OD1 B:ASP538 2.6 31.3 1.0
OD2 B:ASP538 2.7 33.2 1.0
O B:HOH10 2.7 32.8 1.0
CG B:ASP538 3.0 33.5 1.0
CD B:GLU450 3.0 30.0 1.0
CD B:GLU539 3.4 37.9 1.0
OE1 B:GLU450 3.4 28.8 1.0
CA B:CA905 3.5 31.6 1.0
CG B:GLU539 3.5 35.9 1.0
CG B:ASP496 3.7 35.8 1.0
CD B:GLU498 3.7 32.6 1.0
CG B:GLU450 4.1 29.3 1.0
CA B:ASP496 4.3 33.9 1.0
CB B:ASP496 4.4 32.1 1.0
N B:TYR497 4.4 31.2 1.0
CB B:ASP538 4.5 34.3 1.0
OE2 B:GLU498 4.5 34.8 1.0
CG B:GLU498 4.5 26.7 1.0
OD2 B:ASP496 4.5 36.5 1.0
O B:ASP538 4.6 39.4 1.0
N B:GLU498 4.6 29.5 1.0
OE1 B:GLU539 4.6 47.4 1.0
O B:HOH85 4.6 51.9 1.0
O B:HOH104 4.6 30.9 1.0
C B:ASP496 4.7 27.9 1.0
C B:ASP538 4.8 31.2 1.0
CB B:GLU498 4.8 35.7 1.0
O B:TRP495 4.9 34.8 1.0
CB B:GLU539 5.0 33.4 1.0

Calcium binding site 5 out of 6 in 3ubg

Go back to Calcium Binding Sites List in 3ubg
Calcium binding site 5 out of 6 in the Crystal Structure of Drosophila N-Cadherin EC1-3, II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Drosophila N-Cadherin EC1-3, II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca905

b:31.6
occ:1.00
 OD1 B:ASP535 2.4 34.2 1.0
OD1 B:ASP573 2.6 35.0 1.0
OE2 B:GLU498 2.6 34.8 1.0
OD1 B:ASP538 2.6 31.3 1.0
O B:VAL536 2.6 30.7 1.0
OE1 B:GLU498 2.7 29.9 1.0
OE1 B:GLU450 2.8 28.8 1.0
CD B:GLU498 2.9 32.6 1.0
CA B:CA904 3.5 34.9 1.0
CG B:ASP535 3.5 35.2 1.0
OE2 B:GLU450 3.6 36.1 1.0
CD B:GLU450 3.6 30.0 1.0
CG B:ASP573 3.6 32.7 1.0
CG B:ASP538 3.7 33.5 1.0
C B:VAL536 3.8 30.4 1.0
OD2 B:ASP535 4.1 32.5 1.0
N B:VAL536 4.1 22.3 1.0
CG B:GLU539 4.2 35.9 1.0
N B:ASP538 4.2 28.9 1.0
OD2 B:ASP538 4.3 33.2 1.0
CB B:ASP573 4.4 31.1 1.0
CG B:GLU498 4.4 26.7 1.0
CB B:TYR497 4.4 27.0 1.0
OD2 B:ASP573 4.4 35.5 1.0
CA B:ASP573 4.6 34.6 1.0
CA B:VAL536 4.6 26.9 1.0
CB B:ASP538 4.7 34.3 1.0
CB B:ASP535 4.7 30.1 1.0
N B:ASN537 4.8 26.3 1.0
CA B:ASP538 4.8 27.8 1.0
CA B:ASN537 4.8 27.3 1.0
CA B:ASP535 4.8 30.9 1.0
N B:GLU539 4.8 32.7 1.0
O B:HOH84 4.9 26.2 1.0
CD2 B:TYR497 4.9 27.7 1.0
N B:GLU498 4.9 29.5 1.0
C B:ASP535 4.9 30.6 1.0
C B:ASN537 5.0 34.9 1.0
C B:ASP538 5.0 31.2 1.0

Calcium binding site 6 out of 6 in 3ubg

Go back to Calcium Binding Sites List in 3ubg
Calcium binding site 6 out of 6 in the Crystal Structure of Drosophila N-Cadherin EC1-3, II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Drosophila N-Cadherin EC1-3, II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca906

b:34.2
occ:1.00
 OD2 B:ASP622 2.4 31.9 1.0
O B:GLU539 2.4 32.9 1.0
OE1 B:GLN633 2.5 39.8 1.0
OD1 B:ASN537 2.5 32.9 1.0
OD2 B:ASP571 2.5 33.1 1.0
OD2 B:ASP573 2.5 35.5 1.0
OD1 B:ASP571 2.6 33.8 1.0
CG B:ASP571 2.8 35.2 1.0
CG B:ASP622 3.4 35.9 1.0
CD B:GLN633 3.4 42.0 1.0
CG B:ASN537 3.5 34.8 1.0
CG B:ASP573 3.5 32.7 1.0
C B:GLU539 3.6 33.5 1.0
CB B:ASP622 3.7 35.1 1.0
NE2 B:GLN633 3.8 41.0 1.0
ND2 B:ASN537 3.9 33.2 1.0
CB B:ASP573 4.0 31.1 1.0
N B:GLU539 4.0 32.7 1.0
CB B:ASP571 4.3 28.2 1.0
CA B:GLU539 4.4 32.0 1.0
OD1 B:ASP622 4.5 39.5 1.0
OD1 B:ASP573 4.5 35.0 1.0
N B:PRO540 4.6 31.4 1.0
N B:ASP538 4.6 28.9 1.0
CA B:PRO540 4.7 32.2 1.0
CG B:GLN633 4.7 47.8 1.0
N B:ASP573 4.7 28.9 1.0
C B:PRO540 4.7 32.6 1.0
CB B:ASN537 4.8 31.8 1.0
CB B:GLN633 4.8 40.7 1.0
CD B:PRO541 4.8 28.2 1.0
N B:PRO541 4.9 31.0 1.0
C B:ASN537 4.9 34.9 1.0
CB B:GLU539 4.9 33.4 1.0
CD B:PRO572 4.9 29.7 1.0
CA B:ASN537 5.0 27.3 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 Jul 13 20:06:16 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy