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:
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
![](/pictures/CA/pdb/ub/3ubg-CA-sphere_01.jpg) Mono view
![](/pictures/CA/pdb/ub/3ubg-CA-sphere_01_stereo.jpg) 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
![](/pictures/CA/pdb/ub/3ubg-CA-sphere_02.jpg) Mono view
![](/pictures/CA/pdb/ub/3ubg-CA-sphere_02_stereo.jpg) 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
![](/pictures/CA/pdb/ub/3ubg-CA-sphere_03.jpg) Mono view
![](/pictures/CA/pdb/ub/3ubg-CA-sphere_03_stereo.jpg) 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
![](/pictures/CA/pdb/ub/3ubg-CA-sphere_04.jpg) Mono view
![](/pictures/CA/pdb/ub/3ubg-CA-sphere_04_stereo.jpg) 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
![](/pictures/CA/pdb/ub/3ubg-CA-sphere_05.jpg) Mono view
![](/pictures/CA/pdb/ub/3ubg-CA-sphere_05_stereo.jpg) 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
![](/pictures/CA/pdb/ub/3ubg-CA-sphere_06.jpg) Mono view
![](/pictures/CA/pdb/ub/3ubg-CA-sphere_06_stereo.jpg) 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
|