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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

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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

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