Calcium in PDB 4xl1: Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1)
Protein crystallography data
The structure of Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1), PDB code: 4xl1
was solved by
V.C.Luca,
K.M.Jude,
K.C.Garcia,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
49.56 /
2.30
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.809,
93.700,
99.126,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
21.8 /
25.9
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1)
(pdb code 4xl1). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1), PDB code: 4xl1:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 4xl1
Go back to
Calcium Binding Sites List in 4xl1
Calcium binding site 1 out
of 6 in the Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca605
b:26.0
occ:0.69
|
O
|
A:VAL453
|
2.3
|
34.0
|
1.0
|
|
OD1
|
A:ASP469
|
2.3
|
53.5
|
1.0
|
|
OE1
|
A:GLU455
|
2.4
|
38.5
|
1.0
|
|
O
|
A:HOH740
|
2.4
|
36.5
|
1.0
|
|
O
|
A:HOH729
|
2.4
|
48.9
|
1.0
|
|
O
|
A:GLN470
|
2.4
|
30.5
|
1.0
|
|
OD1
|
A:ASP452
|
2.5
|
47.6
|
1.0
|
|
OD2
|
A:ASP469
|
2.6
|
47.4
|
1.0
|
|
CG
|
A:ASP469
|
2.7
|
48.1
|
1.0
|
|
C
|
A:GLN470
|
3.3
|
37.4
|
1.0
|
|
CG
|
A:ASP452
|
3.4
|
46.4
|
1.0
|
|
CD
|
A:GLU455
|
3.4
|
43.9
|
1.0
|
|
C
|
A:VAL453
|
3.5
|
43.5
|
1.0
|
|
OD2
|
A:ASP452
|
3.7
|
44.2
|
1.0
|
|
OE2
|
A:GLU455
|
3.8
|
46.4
|
1.0
|
|
N
|
A:GLN470
|
3.9
|
38.0
|
1.0
|
|
C
|
A:ASP469
|
4.1
|
37.5
|
1.0
|
|
O
|
A:HOH730
|
4.1
|
40.8
|
1.0
|
|
CA
|
A:GLN470
|
4.1
|
40.4
|
1.0
|
|
CB
|
A:ASP469
|
4.1
|
47.4
|
1.0
|
|
N
|
A:ILE471
|
4.2
|
37.8
|
1.0
|
|
CA
|
A:ILE471
|
4.3
|
45.0
|
1.0
|
|
N
|
A:VAL453
|
4.3
|
33.0
|
1.0
|
|
N
|
A:GLU455
|
4.4
|
40.6
|
1.0
|
|
CA
|
A:ASN454
|
4.4
|
41.4
|
1.0
|
|
N
|
A:ASN454
|
4.4
|
41.5
|
1.0
|
|
O
|
A:ASP469
|
4.4
|
33.8
|
1.0
|
|
CA
|
A:VAL453
|
4.4
|
46.0
|
1.0
|
|
C
|
A:ASP452
|
4.5
|
36.1
|
1.0
|
|
N
|
A:GLY472
|
4.5
|
47.6
|
1.0
|
|
CA
|
A:ASP469
|
4.6
|
42.8
|
1.0
|
|
CB
|
A:ASP452
|
4.7
|
37.2
|
1.0
|
|
O
|
A:GLY443
|
4.8
|
44.2
|
1.0
|
|
CG
|
A:GLU455
|
4.8
|
43.0
|
1.0
|
|
O
|
A:ASP452
|
4.9
|
31.9
|
1.0
|
|
CB
|
A:VAL453
|
4.9
|
48.0
|
1.0
|
|
OG1
|
B:THR110
|
4.9
|
47.8
|
1.0
|
|
C
|
A:ASN454
|
5.0
|
43.4
|
1.0
|
|
C
|
A:ILE471
|
5.0
|
47.4
|
1.0
|
|
Calcium binding site 2 out
of 6 in 4xl1
Go back to
Calcium Binding Sites List in 4xl1
Calcium binding site 2 out
of 6 in the Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca606
b:35.9
occ:0.81
|
O
|
A:THR491
|
2.4
|
35.0
|
1.0
|
|
OD1
|
A:ASN490
|
2.4
|
43.7
|
1.0
|
|
OE1
|
A:GLU493
|
2.4
|
42.1
|
1.0
|
|
O
|
A:LYS508
|
2.4
|
37.6
|
1.0
|
|
O
|
A:HOH702
|
2.4
|
43.2
|
1.0
|
|
OD1
|
A:ASP507
|
2.4
|
43.3
|
1.0
|
|
O
|
A:HOH727
|
2.4
|
36.4
|
1.0
|
|
OD2
|
A:ASP507
|
2.4
|
48.0
|
1.0
|
|
CG
|
A:ASP507
|
2.7
|
44.3
|
1.0
|
|
CD
|
A:GLU493
|
3.4
|
47.3
|
1.0
|
|
CG
|
A:ASN490
|
3.5
|
40.6
|
1.0
|
|
C
|
A:LYS508
|
3.5
|
45.2
|
1.0
|
|
C
|
A:THR491
|
3.5
|
42.1
|
1.0
|
|
OE2
|
A:GLU493
|
3.8
|
47.0
|
1.0
|
|
ND2
|
A:ASN490
|
4.0
|
35.9
|
1.0
|
|
N
|
A:LYS508
|
4.0
|
43.4
|
1.0
|
|
CB
|
A:ASP507
|
4.1
|
41.3
|
1.0
|
|
C
|
A:ASP507
|
4.3
|
44.5
|
1.0
|
|
N
|
A:GLU493
|
4.3
|
43.2
|
1.0
|
|
CA
|
A:LYS508
|
4.3
|
46.9
|
1.0
|
|
N
|
A:THR491
|
4.3
|
39.2
|
1.0
|
|
N
|
A:ASP492
|
4.4
|
45.8
|
1.0
|
|
CA
|
A:ASP492
|
4.4
|
48.3
|
1.0
|
|
C
|
A:ASN490
|
4.5
|
34.5
|
1.0
|
|
CA
|
A:THR491
|
4.5
|
43.4
|
1.0
|
|
N
|
A:ILE509
|
4.5
|
39.8
|
1.0
|
|
O
|
A:GLU511
|
4.6
|
45.1
|
1.0
|
|
CA
|
A:ILE509
|
4.6
|
42.9
|
1.0
|
|
CA
|
A:ASP507
|
4.6
|
43.9
|
1.0
|
|
N
|
A:ASN510
|
4.6
|
39.8
|
1.0
|
|
O
|
A:ASN490
|
4.7
|
35.6
|
1.0
|
|
CB
|
A:ASN490
|
4.7
|
38.7
|
1.0
|
|
O
|
A:ASP507
|
4.7
|
47.3
|
1.0
|
|
CG
|
A:GLU493
|
4.7
|
49.3
|
1.0
|
|
O
|
A:GLY481
|
4.9
|
43.9
|
1.0
|
|
C
|
A:ASP492
|
4.9
|
45.8
|
1.0
|
|
CB
|
A:GLU493
|
4.9
|
50.5
|
1.0
|
|
Calcium binding site 3 out
of 6 in 4xl1
Go back to
Calcium Binding Sites List in 4xl1
Calcium binding site 3 out
of 6 in the Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca607
b:90.1
occ:0.77
|
N
|
A:GLY434
|
2.3
|
85.6
|
1.0
|
|
N
|
A:SER435
|
2.3
|
91.7
|
1.0
|
|
O
|
A:THR432
|
2.3
|
52.1
|
1.0
|
|
O
|
A:HOH773
|
2.6
|
52.7
|
1.0
|
|
O
|
A:SER435
|
2.7
|
79.6
|
1.0
|
|
OD1
|
A:ASN431
|
2.8
|
47.7
|
0.6
|
|
CA
|
A:GLY434
|
2.8
|
92.8
|
1.0
|
|
C
|
A:GLY434
|
2.8
|
93.9
|
1.0
|
|
OE1
|
A:GLU415
|
3.0
|
97.7
|
1.0
|
|
C
|
A:LEU433
|
3.1
|
77.2
|
1.0
|
|
CA
|
A:SER435
|
3.2
|
89.9
|
1.0
|
|
C
|
A:SER435
|
3.3
|
77.7
|
1.0
|
|
C
|
A:THR432
|
3.5
|
55.3
|
1.0
|
|
CA
|
A:LEU433
|
3.7
|
71.1
|
1.0
|
|
CG
|
A:ASN431
|
3.8
|
49.9
|
0.6
|
|
O
|
A:GLY434
|
3.9
|
94.7
|
1.0
|
|
O
|
A:LEU433
|
3.9
|
75.9
|
1.0
|
|
N
|
A:LEU433
|
4.1
|
62.6
|
1.0
|
|
ND2
|
A:ASN431
|
4.1
|
44.4
|
0.6
|
|
OD2
|
A:ASP414
|
4.2
|
0.5
|
1.0
|
|
CD
|
A:GLU415
|
4.2
|
91.6
|
1.0
|
|
N
|
A:THR432
|
4.4
|
53.9
|
1.0
|
|
CB
|
A:SER435
|
4.6
|
96.8
|
1.0
|
|
CA
|
A:THR432
|
4.6
|
53.0
|
1.0
|
|
N
|
A:PHE436
|
4.7
|
68.4
|
1.0
|
|
CB
|
A:GLU415
|
4.7
|
80.5
|
1.0
|
|
OG1
|
A:THR432
|
4.9
|
59.6
|
1.0
|
|
Calcium binding site 4 out
of 6 in 4xl1
Go back to
Calcium Binding Sites List in 4xl1
Calcium binding site 4 out
of 6 in the Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca605
b:38.4
occ:0.78
|
O
|
D:LYS508
|
2.3
|
41.6
|
1.0
|
|
OE1
|
D:GLU493
|
2.3
|
45.9
|
1.0
|
|
O
|
D:THR491
|
2.4
|
40.1
|
1.0
|
|
OD1
|
D:ASP507
|
2.4
|
53.0
|
1.0
|
|
OD1
|
D:ASN490
|
2.4
|
44.6
|
1.0
|
|
O
|
D:HOH717
|
2.4
|
45.8
|
1.0
|
|
OD2
|
D:ASP507
|
2.4
|
54.7
|
1.0
|
|
CG
|
D:ASP507
|
2.7
|
53.5
|
1.0
|
|
CD
|
D:GLU493
|
3.5
|
46.9
|
1.0
|
|
C
|
D:LYS508
|
3.5
|
47.4
|
1.0
|
|
CG
|
D:ASN490
|
3.5
|
45.7
|
1.0
|
|
C
|
D:THR491
|
3.5
|
46.3
|
1.0
|
|
OE2
|
D:GLU493
|
3.9
|
48.6
|
1.0
|
|
N
|
D:LYS508
|
4.0
|
51.2
|
1.0
|
|
ND2
|
D:ASN490
|
4.1
|
39.7
|
1.0
|
|
CB
|
D:ASP507
|
4.1
|
51.7
|
1.0
|
|
N
|
D:THR491
|
4.3
|
45.6
|
1.0
|
|
N
|
D:GLU493
|
4.3
|
39.5
|
1.0
|
|
C
|
D:ASP507
|
4.3
|
53.1
|
1.0
|
|
CA
|
D:LYS508
|
4.3
|
51.5
|
1.0
|
|
C
|
D:ASN490
|
4.4
|
45.5
|
1.0
|
|
O
|
D:GLU511
|
4.4
|
51.4
|
1.0
|
|
N
|
D:ASP492
|
4.4
|
46.0
|
1.0
|
|
CA
|
D:THR491
|
4.4
|
47.5
|
1.0
|
|
N
|
D:ILE509
|
4.4
|
51.6
|
1.0
|
|
CA
|
D:ASP492
|
4.5
|
48.1
|
1.0
|
|
N
|
D:ASN510
|
4.5
|
41.8
|
1.0
|
|
CA
|
D:ILE509
|
4.5
|
46.9
|
1.0
|
|
CA
|
D:ASP507
|
4.6
|
51.7
|
1.0
|
|
O
|
D:ASN490
|
4.6
|
47.5
|
1.0
|
|
CB
|
D:ASN490
|
4.7
|
46.8
|
1.0
|
|
CG
|
D:GLU493
|
4.7
|
48.0
|
1.0
|
|
O
|
D:GLY481
|
4.8
|
50.5
|
1.0
|
|
CB
|
D:GLU493
|
4.9
|
44.8
|
1.0
|
|
O
|
D:ASP507
|
4.9
|
55.3
|
1.0
|
|
C
|
D:ASP492
|
4.9
|
46.0
|
1.0
|
|
CB
|
D:THR491
|
5.0
|
49.3
|
1.0
|
|
CA
|
D:ASN490
|
5.0
|
44.1
|
1.0
|
|
Calcium binding site 5 out
of 6 in 4xl1
Go back to
Calcium Binding Sites List in 4xl1
Calcium binding site 5 out
of 6 in the Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca606
b:40.6
occ:1.00
|
O
|
D:GLN470
|
2.3
|
37.8
|
1.0
|
|
O
|
D:VAL453
|
2.4
|
29.0
|
1.0
|
|
OD1
|
D:ASP469
|
2.4
|
42.1
|
1.0
|
|
O
|
D:HOH715
|
2.4
|
28.0
|
1.0
|
|
OD1
|
D:ASP452
|
2.4
|
43.3
|
1.0
|
|
O
|
D:HOH718
|
2.4
|
33.4
|
1.0
|
|
OE1
|
D:GLU455
|
2.4
|
40.1
|
1.0
|
|
CG
|
D:ASP469
|
3.2
|
41.9
|
1.0
|
|
C
|
D:GLN470
|
3.2
|
38.8
|
1.0
|
|
CG
|
D:ASP452
|
3.3
|
43.8
|
1.0
|
|
OD2
|
D:ASP469
|
3.4
|
45.3
|
1.0
|
|
CD
|
D:GLU455
|
3.5
|
41.2
|
1.0
|
|
OD2
|
D:ASP452
|
3.6
|
46.0
|
1.0
|
|
C
|
D:VAL453
|
3.6
|
35.1
|
1.0
|
|
OE2
|
D:GLU455
|
3.8
|
40.8
|
1.0
|
|
N
|
D:GLN470
|
3.8
|
32.6
|
1.0
|
|
CA
|
D:GLN470
|
4.1
|
34.5
|
1.0
|
|
N
|
D:ILE471
|
4.1
|
38.2
|
1.0
|
|
CA
|
D:ILE471
|
4.2
|
39.6
|
1.0
|
|
C
|
D:ASP469
|
4.2
|
39.0
|
1.0
|
|
O
|
D:HOH721
|
4.2
|
58.3
|
1.0
|
|
N
|
D:GLY472
|
4.3
|
45.5
|
1.0
|
|
N
|
D:VAL453
|
4.4
|
37.0
|
1.0
|
|
N
|
D:GLU455
|
4.4
|
35.9
|
1.0
|
|
CA
|
D:ASN454
|
4.4
|
32.5
|
1.0
|
|
N
|
D:ASN454
|
4.5
|
35.3
|
1.0
|
|
O
|
D:ASP469
|
4.5
|
40.9
|
1.0
|
|
CB
|
D:ASP469
|
4.5
|
36.4
|
1.0
|
|
CA
|
D:VAL453
|
4.5
|
37.5
|
1.0
|
|
C
|
D:ASP452
|
4.6
|
34.1
|
1.0
|
|
CB
|
D:ASP452
|
4.7
|
37.8
|
1.0
|
|
CA
|
D:ASP469
|
4.7
|
38.6
|
1.0
|
|
C
|
D:ILE471
|
4.8
|
42.5
|
1.0
|
|
CG
|
D:GLU455
|
4.8
|
42.2
|
1.0
|
|
O
|
D:GLU473
|
4.8
|
42.6
|
1.0
|
|
O
|
D:GLY443
|
4.9
|
46.1
|
1.0
|
|
O
|
D:ASP452
|
4.9
|
33.6
|
1.0
|
|
C
|
D:ASN454
|
5.0
|
34.8
|
1.0
|
|
Calcium binding site 6 out
of 6 in 4xl1
Go back to
Calcium Binding Sites List in 4xl1
Calcium binding site 6 out
of 6 in the Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Complex of NOTCH1 (EGF11-13) Bound to Delta-Like 4 (N-EGF1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca607
b:45.6
occ:0.60
|
OD1
|
D:ASP412
|
2.2
|
51.1
|
0.7
|
|
O
|
D:THR432
|
2.2
|
47.7
|
1.0
|
|
N
|
D:SER435
|
2.2
|
66.7
|
1.0
|
|
N
|
D:GLY434
|
2.3
|
64.4
|
1.0
|
|
OD2
|
D:ASP412
|
2.5
|
50.2
|
0.7
|
|
OE2
|
D:GLU415
|
2.5
|
55.6
|
0.6
|
|
OD1
|
D:ASN431
|
2.6
|
46.8
|
0.5
|
|
O
|
D:SER435
|
2.6
|
55.5
|
1.0
|
|
OE1
|
D:GLU415
|
2.6
|
52.2
|
0.6
|
|
CG
|
D:ASP412
|
2.6
|
54.2
|
0.7
|
|
O
|
D:VAL413
|
2.8
|
64.5
|
1.0
|
|
CA
|
D:GLY434
|
2.9
|
64.8
|
1.0
|
|
C
|
D:GLY434
|
2.9
|
66.0
|
1.0
|
|
CD
|
D:GLU415
|
2.9
|
54.7
|
0.6
|
|
C
|
D:LEU433
|
3.1
|
62.1
|
1.0
|
|
CA
|
D:SER435
|
3.2
|
64.7
|
1.0
|
|
C
|
D:SER435
|
3.3
|
55.3
|
1.0
|
|
C
|
D:THR432
|
3.3
|
52.6
|
1.0
|
|
CG
|
D:ASN431
|
3.7
|
42.9
|
0.5
|
|
CA
|
D:LEU433
|
3.7
|
63.7
|
1.0
|
|
C
|
D:VAL413
|
3.9
|
66.3
|
1.0
|
|
O
|
D:LEU433
|
4.0
|
59.7
|
1.0
|
|
N
|
D:LEU433
|
4.0
|
54.5
|
1.0
|
|
O
|
D:GLY434
|
4.0
|
68.5
|
1.0
|
|
CB
|
D:ASP412
|
4.1
|
62.4
|
0.7
|
|
ND2
|
D:ASN431
|
4.1
|
40.9
|
0.5
|
|
N
|
D:THR432
|
4.2
|
42.2
|
1.0
|
|
N
|
D:VAL413
|
4.2
|
61.9
|
1.0
|
|
CG
|
D:GLU415
|
4.3
|
55.1
|
0.5
|
|
CG
|
D:GLU415
|
4.4
|
55.0
|
0.6
|
|
CA
|
D:THR432
|
4.4
|
44.0
|
1.0
|
|
OE2
|
D:GLU415
|
4.4
|
59.7
|
0.5
|
|
CB
|
D:ASP412
|
4.5
|
62.2
|
0.3
|
|
OG1
|
D:THR432
|
4.5
|
41.0
|
1.0
|
|
CB
|
D:SER435
|
4.5
|
71.4
|
1.0
|
|
N
|
D:PHE436
|
4.6
|
52.8
|
1.0
|
|
CA
|
D:VAL413
|
4.6
|
67.9
|
1.0
|
|
CA
|
D:ASP412
|
4.9
|
65.8
|
0.3
|
|
CA
|
D:ASP412
|
4.9
|
65.9
|
0.7
|
|
N
|
D:ASP414
|
4.9
|
66.9
|
1.0
|
|
CD
|
D:GLU415
|
4.9
|
56.2
|
0.5
|
|
C
|
D:ASP412
|
4.9
|
65.0
|
1.0
|
|
CB
|
D:ASN431
|
5.0
|
42.0
|
0.5
|
|
Reference:
V.C.Luca,
K.M.Jude,
N.W.Pierce,
M.V.Nachury,
S.Fischer,
K.C.Garcia.
Structural Basis For NOTCH1 Engagement of Delta-Like 4. Science V. 347 2015.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.1261093
Page generated: Sun Jul 14 14:36:37 2024
|
