Calcium in PDB 3zdx: Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex
Protein crystallography data
The structure of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex, PDB code: 3zdx
was solved by
J.H.Zhu,
J.Q.Zhu,
T.A.Springer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.361 /
2.45
|
|
Space group
|
P 21 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
259.710,
144.960,
104.770,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
16.28 /
19.71
|
Other elements in 3zdx:
The structure of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex
(pdb code 3zdx). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex, PDB code: 3zdx:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 3zdx
Go back to
Calcium Binding Sites List in 3zdx
Calcium binding site 1 out
of 8 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2004
b:28.7
occ:1.00
|
OD1
|
A:ASP245
|
2.3
|
34.9
|
1.0
|
|
O
|
A:ASP247
|
2.3
|
45.0
|
1.0
|
|
OE2
|
A:GLU243
|
2.4
|
27.6
|
1.0
|
|
O
|
A:THR250
|
2.4
|
35.6
|
1.0
|
|
OG1
|
A:THR250
|
2.4
|
33.2
|
1.0
|
|
OE1
|
A:GLU243
|
2.4
|
27.1
|
1.0
|
|
OE2
|
A:GLU252
|
2.4
|
30.2
|
1.0
|
|
OE1
|
A:GLU252
|
2.5
|
29.0
|
1.0
|
|
CD
|
A:GLU243
|
2.7
|
34.3
|
1.0
|
|
CD
|
A:GLU252
|
2.8
|
28.2
|
1.0
|
|
CG
|
A:ASP245
|
3.1
|
43.2
|
1.0
|
|
C
|
A:THR250
|
3.2
|
44.5
|
1.0
|
|
C
|
A:ASP247
|
3.5
|
34.7
|
1.0
|
|
H
|
A:THR250
|
3.5
|
80.5
|
1.0
|
|
OD2
|
A:ASP245
|
3.5
|
51.1
|
1.0
|
|
CB
|
A:THR250
|
3.5
|
33.0
|
1.0
|
|
H
|
A:ASP247
|
3.5
|
54.5
|
1.0
|
|
HB3
|
A:ASP247
|
3.6
|
42.4
|
1.0
|
|
H
|
A:ASP245
|
3.6
|
35.1
|
1.0
|
|
CA
|
A:THR250
|
3.8
|
48.7
|
1.0
|
|
HA
|
A:GLU243
|
3.8
|
22.9
|
1.0
|
|
HB
|
A:THR250
|
3.9
|
39.5
|
1.0
|
|
N
|
A:THR250
|
4.0
|
67.2
|
1.0
|
|
HA
|
A:THR251
|
4.0
|
47.7
|
1.0
|
|
N
|
A:ASP247
|
4.0
|
45.5
|
1.0
|
|
H
|
A:PHE244
|
4.1
|
21.7
|
1.0
|
|
CA
|
A:ASP247
|
4.1
|
33.3
|
1.0
|
|
N
|
A:THR251
|
4.1
|
43.3
|
1.0
|
|
CG
|
A:GLU243
|
4.2
|
28.2
|
1.0
|
|
HA
|
A:LEU248
|
4.2
|
43.4
|
1.0
|
|
CG
|
A:GLU252
|
4.3
|
23.7
|
1.0
|
|
CB
|
A:ASP247
|
4.3
|
35.4
|
1.0
|
|
CB
|
A:ASP245
|
4.4
|
32.1
|
1.0
|
|
N
|
A:ASP245
|
4.4
|
29.3
|
1.0
|
|
CA
|
A:THR251
|
4.5
|
39.9
|
1.0
|
|
N
|
A:LEU248
|
4.5
|
34.2
|
1.0
|
|
H
|
A:GLU252
|
4.5
|
33.0
|
1.0
|
|
HG3
|
A:GLU243
|
4.5
|
33.7
|
1.0
|
|
HB3
|
A:ASP245
|
4.5
|
38.4
|
1.0
|
|
H
|
A:GLY246
|
4.6
|
49.2
|
1.0
|
|
O
|
A:HOH4329
|
4.6
|
49.8
|
1.0
|
|
HG2
|
A:GLU252
|
4.6
|
28.3
|
1.0
|
|
HG3
|
A:GLU252
|
4.7
|
28.3
|
1.0
|
|
CA
|
A:GLU243
|
4.7
|
19.1
|
1.0
|
|
HG2
|
A:GLU243
|
4.7
|
33.7
|
1.0
|
|
HA
|
A:THR250
|
4.7
|
58.3
|
1.0
|
|
N
|
A:PHE244
|
4.7
|
18.2
|
1.0
|
|
CA
|
A:ASP245
|
4.7
|
38.4
|
1.0
|
|
CG2
|
A:THR250
|
4.7
|
34.8
|
1.0
|
|
CA
|
A:LEU248
|
4.7
|
36.2
|
1.0
|
|
N
|
A:GLY246
|
4.7
|
41.1
|
1.0
|
|
N
|
A:GLU252
|
4.7
|
27.6
|
1.0
|
|
O
|
A:HOH4326
|
4.8
|
50.8
|
1.0
|
|
HG21
|
A:THR250
|
4.8
|
41.6
|
1.0
|
|
C
|
A:ASP245
|
4.8
|
42.3
|
1.0
|
|
C
|
A:THR251
|
4.8
|
32.5
|
1.0
|
|
CB
|
A:GLU243
|
4.8
|
28.3
|
1.0
|
|
HB2
|
A:GLU243
|
4.8
|
33.8
|
1.0
|
|
H
|
A:THR251
|
4.9
|
51.9
|
1.0
|
|
C
|
A:LEU248
|
4.9
|
39.4
|
1.0
|
|
HG22
|
A:THR250
|
5.0
|
41.6
|
1.0
|
|
Calcium binding site 2 out
of 8 in 3zdx
Go back to
Calcium Binding Sites List in 3zdx
Calcium binding site 2 out
of 8 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2005
b:15.3
occ:1.00
|
OD1
|
A:ASN299
|
2.3
|
15.8
|
1.0
|
|
O
|
A:ARG303
|
2.3
|
13.7
|
1.0
|
|
O
|
A:HOH4377
|
2.4
|
23.2
|
1.0
|
|
OD1
|
A:ASP297
|
2.4
|
18.1
|
1.0
|
|
OD1
|
A:ASP305
|
2.5
|
22.1
|
1.0
|
|
OD2
|
A:ASP305
|
2.5
|
22.2
|
1.0
|
|
OD1
|
A:ASP301
|
2.5
|
33.1
|
1.0
|
|
CG
|
A:ASP305
|
2.8
|
17.0
|
1.0
|
|
CG
|
A:ASP301
|
3.3
|
29.6
|
1.0
|
|
HB2
|
A:ARG303
|
3.4
|
30.6
|
1.0
|
|
CG
|
A:ASN299
|
3.4
|
20.5
|
1.0
|
|
OD2
|
A:ASP301
|
3.4
|
26.7
|
1.0
|
|
C
|
A:ARG303
|
3.5
|
24.5
|
1.0
|
|
H
|
A:ASN299
|
3.5
|
28.9
|
1.0
|
|
CG
|
A:ASP297
|
3.5
|
27.6
|
1.0
|
|
HA
|
A:ASP297
|
3.5
|
19.4
|
1.0
|
|
H
|
A:ARG303
|
3.6
|
24.4
|
1.0
|
|
HD22
|
A:ASN299
|
3.8
|
30.1
|
1.0
|
|
H
|
A:ASP301
|
3.8
|
31.9
|
1.0
|
|
H
|
A:VAL298
|
3.8
|
14.5
|
1.0
|
|
HD23
|
A:LEU332
|
3.9
|
23.6
|
1.0
|
|
ND2
|
A:ASN299
|
4.0
|
25.2
|
1.0
|
|
CA
|
A:ARG303
|
4.1
|
20.2
|
1.0
|
|
CB
|
A:ARG303
|
4.1
|
25.6
|
1.0
|
|
N
|
A:ARG303
|
4.1
|
20.4
|
1.0
|
|
H
|
A:GLN333
|
4.2
|
20.2
|
1.0
|
|
HB2
|
A:ASP297
|
4.2
|
17.8
|
1.0
|
|
CB
|
A:ASP297
|
4.2
|
14.9
|
1.0
|
|
CA
|
A:ASP297
|
4.2
|
16.3
|
1.0
|
|
CB
|
A:ASP305
|
4.2
|
19.7
|
1.0
|
|
N
|
A:ASN299
|
4.3
|
24.2
|
1.0
|
|
N
|
A:VAL298
|
4.4
|
12.1
|
1.0
|
|
OD2
|
A:ASP297
|
4.4
|
24.9
|
1.0
|
|
HB3
|
A:ARG303
|
4.5
|
30.6
|
1.0
|
|
N
|
A:ASP305
|
4.5
|
12.3
|
1.0
|
|
C
|
A:HIS304
|
4.5
|
16.5
|
1.0
|
|
N
|
A:HIS304
|
4.6
|
20.2
|
1.0
|
|
HB3
|
A:GLN333
|
4.6
|
16.8
|
1.0
|
|
N
|
A:ASP301
|
4.6
|
26.7
|
1.0
|
|
HB2
|
A:ASP305
|
4.6
|
23.5
|
1.0
|
|
H
|
A:ASP305
|
4.6
|
14.6
|
1.0
|
|
CB
|
A:ASN299
|
4.6
|
15.6
|
1.0
|
|
HD21
|
A:LEU332
|
4.6
|
23.6
|
1.0
|
|
HB3
|
A:LEU332
|
4.7
|
26.6
|
1.0
|
|
H
|
A:GLY300
|
4.7
|
31.0
|
1.0
|
|
CB
|
A:ASP301
|
4.7
|
23.8
|
1.0
|
|
C
|
A:ASP297
|
4.7
|
14.5
|
1.0
|
|
HG23
|
A:VAL298
|
4.7
|
22.5
|
1.0
|
|
CD2
|
A:LEU332
|
4.7
|
19.8
|
1.0
|
|
HA
|
A:HIS304
|
4.7
|
16.9
|
1.0
|
|
HA
|
A:LEU332
|
4.8
|
29.5
|
1.0
|
|
HB3
|
A:ASP305
|
4.8
|
23.5
|
1.0
|
|
O
|
A:HIS304
|
4.8
|
19.7
|
1.0
|
|
CA
|
A:ASP305
|
4.8
|
16.7
|
1.0
|
|
CA
|
A:ASN299
|
4.8
|
17.1
|
1.0
|
|
H
|
A:GLY302
|
4.9
|
25.2
|
1.0
|
|
HD21
|
A:ASN299
|
4.9
|
30.1
|
1.0
|
|
HB3
|
A:ASN299
|
4.9
|
18.6
|
1.0
|
|
CA
|
A:HIS304
|
4.9
|
14.2
|
1.0
|
|
HA
|
A:ASP305
|
4.9
|
20.0
|
1.0
|
|
N
|
A:GLN333
|
4.9
|
16.9
|
1.0
|
|
N
|
A:GLY300
|
4.9
|
25.9
|
1.0
|
|
O
|
A:GLN333
|
5.0
|
25.1
|
1.0
|
|
C
|
A:ASN299
|
5.0
|
27.1
|
1.0
|
|
Calcium binding site 3 out
of 8 in 3zdx
Go back to
Calcium Binding Sites List in 3zdx
Calcium binding site 3 out
of 8 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2006
b:14.6
occ:1.00
|
O
|
A:TYR371
|
2.2
|
18.2
|
1.0
|
|
OD1
|
A:ASP367
|
2.3
|
20.0
|
1.0
|
|
O
|
A:HOH4437
|
2.4
|
13.7
|
1.0
|
|
OD1
|
A:ASP365
|
2.4
|
13.6
|
1.0
|
|
OD1
|
A:ASP369
|
2.5
|
21.9
|
1.0
|
|
OD1
|
A:ASP373
|
2.5
|
18.0
|
1.0
|
|
OD2
|
A:ASP373
|
2.5
|
10.9
|
1.0
|
|
CG
|
A:ASP373
|
2.8
|
16.3
|
1.0
|
|
CG
|
A:ASP369
|
3.3
|
23.4
|
1.0
|
|
C
|
A:TYR371
|
3.4
|
17.0
|
1.0
|
|
H
|
A:TYR371
|
3.4
|
27.3
|
1.0
|
|
HB2
|
A:TYR371
|
3.5
|
32.1
|
1.0
|
|
CG
|
A:ASP367
|
3.5
|
24.1
|
1.0
|
|
H
|
A:ASP367
|
3.5
|
22.3
|
1.0
|
|
H
|
A:ASP369
|
3.6
|
18.5
|
1.0
|
|
CG
|
A:ASP365
|
3.6
|
30.1
|
1.0
|
|
HA
|
A:ASP365
|
3.6
|
25.7
|
1.0
|
|
HD23
|
A:LEU393
|
3.7
|
15.4
|
1.0
|
|
OD2
|
A:ASP369
|
3.8
|
36.0
|
1.0
|
|
H
|
A:GLY394
|
3.9
|
16.8
|
1.0
|
|
H
|
A:LEU366
|
3.9
|
24.2
|
1.0
|
|
OD2
|
A:ASP367
|
4.0
|
25.6
|
1.0
|
|
N
|
A:TYR371
|
4.1
|
22.9
|
1.0
|
|
CA
|
A:TYR371
|
4.1
|
22.4
|
1.0
|
|
HB3
|
A:LEU393
|
4.1
|
13.0
|
1.0
|
|
CB
|
A:TYR371
|
4.2
|
26.8
|
1.0
|
|
H
|
A:ARG368
|
4.2
|
25.1
|
1.0
|
|
N
|
A:ASP367
|
4.3
|
18.7
|
1.0
|
|
OD2
|
A:ASP365
|
4.3
|
24.3
|
1.0
|
|
CA
|
A:ASP365
|
4.3
|
21.5
|
1.0
|
|
N
|
A:LEU366
|
4.3
|
20.3
|
1.0
|
|
CB
|
A:ASP373
|
4.4
|
14.0
|
1.0
|
|
N
|
A:ASP369
|
4.4
|
15.5
|
1.0
|
|
HA
|
A:ASN372
|
4.4
|
16.4
|
1.0
|
|
N
|
A:ASN372
|
4.4
|
13.1
|
1.0
|
|
CB
|
A:ASP369
|
4.5
|
19.1
|
1.0
|
|
CB
|
A:ASP365
|
4.5
|
14.9
|
1.0
|
|
HB3
|
A:ASP369
|
4.5
|
22.8
|
1.0
|
|
C
|
A:ASN372
|
4.5
|
12.5
|
1.0
|
|
HB3
|
A:TYR371
|
4.5
|
32.1
|
1.0
|
|
N
|
A:GLY394
|
4.6
|
14.1
|
1.0
|
|
C
|
A:ASP365
|
4.6
|
16.9
|
1.0
|
|
HA
|
A:LEU393
|
4.6
|
15.3
|
1.0
|
|
CD2
|
A:LEU393
|
4.6
|
12.9
|
1.0
|
|
N
|
A:ARG368
|
4.6
|
21.0
|
1.0
|
|
H
|
A:GLY370
|
4.7
|
29.5
|
1.0
|
|
CA
|
A:ASN372
|
4.7
|
13.8
|
1.0
|
|
CB
|
A:ASP367
|
4.7
|
14.5
|
1.0
|
|
O
|
A:ASN372
|
4.7
|
15.0
|
1.0
|
|
HD21
|
A:LEU393
|
4.7
|
15.4
|
1.0
|
|
N
|
A:ASP373
|
4.8
|
17.2
|
1.0
|
|
HB2
|
A:ASP373
|
4.8
|
16.7
|
1.0
|
|
HB3
|
A:LEU366
|
4.8
|
17.0
|
1.0
|
|
HB3
|
A:ASP373
|
4.8
|
16.7
|
1.0
|
|
HB2
|
A:ASP365
|
4.8
|
17.8
|
1.0
|
|
CA
|
A:ASP367
|
4.9
|
18.7
|
1.0
|
|
O
|
A:GLY394
|
4.9
|
15.1
|
1.0
|
|
CB
|
A:LEU393
|
4.9
|
10.9
|
1.0
|
|
CA
|
A:ASP369
|
4.9
|
16.6
|
1.0
|
|
C
|
A:ASP367
|
5.0
|
15.7
|
1.0
|
|
Calcium binding site 4 out
of 8 in 3zdx
Go back to
Calcium Binding Sites List in 3zdx
Calcium binding site 4 out
of 8 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2007
b:14.7
occ:1.00
|
OD1
|
A:ASP426
|
2.3
|
21.8
|
1.0
|
|
O
|
A:TYR432
|
2.3
|
12.5
|
1.0
|
|
OD1
|
A:ASP428
|
2.3
|
16.7
|
1.0
|
|
O
|
A:HOH4504
|
2.4
|
13.1
|
1.0
|
|
OD1
|
A:ASN430
|
2.4
|
18.1
|
1.0
|
|
OD1
|
A:ASP434
|
2.4
|
20.6
|
1.0
|
|
OD2
|
A:ASP434
|
2.4
|
18.1
|
1.0
|
|
CG
|
A:ASP434
|
2.8
|
20.7
|
1.0
|
|
CG
|
A:ASN430
|
3.3
|
17.6
|
1.0
|
|
CG
|
A:ASP428
|
3.4
|
20.9
|
1.0
|
|
H
|
A:ASN430
|
3.4
|
29.1
|
1.0
|
|
H
|
A:TYR432
|
3.4
|
22.2
|
1.0
|
|
CG
|
A:ASP426
|
3.4
|
22.4
|
1.0
|
|
HA
|
A:ASP426
|
3.4
|
15.5
|
1.0
|
|
C
|
A:TYR432
|
3.5
|
22.3
|
1.0
|
|
H
|
A:ASP428
|
3.5
|
24.4
|
1.0
|
|
HB2
|
A:TYR432
|
3.6
|
15.8
|
1.0
|
|
OD2
|
A:ASP428
|
3.8
|
16.2
|
1.0
|
|
H
|
A:ILE427
|
3.9
|
16.0
|
1.0
|
|
HD22
|
A:ASN430
|
3.9
|
21.2
|
1.0
|
|
H
|
A:ALA450
|
3.9
|
14.0
|
1.0
|
|
ND2
|
A:ASN430
|
4.0
|
17.7
|
1.0
|
|
N
|
A:TYR432
|
4.1
|
18.6
|
1.0
|
|
CA
|
A:TYR432
|
4.1
|
11.5
|
1.0
|
|
CA
|
A:ASP426
|
4.2
|
13.0
|
1.0
|
|
O
|
A:ALA450
|
4.2
|
15.6
|
1.0
|
|
OD2
|
A:ASP426
|
4.2
|
19.2
|
1.0
|
|
HB1
|
A:ALA450
|
4.2
|
12.2
|
1.0
|
|
N
|
A:ASN430
|
4.2
|
24.3
|
1.0
|
|
H
|
A:ASP429
|
4.2
|
33.5
|
1.0
|
|
HG2
|
A:ARG449
|
4.3
|
17.7
|
1.0
|
|
CB
|
A:ASP434
|
4.3
|
12.5
|
1.0
|
|
CB
|
A:ASP426
|
4.3
|
15.6
|
1.0
|
|
CB
|
A:TYR432
|
4.3
|
13.3
|
1.0
|
|
HB3
|
A:ASN430
|
4.3
|
14.4
|
1.0
|
|
N
|
A:ASP428
|
4.3
|
20.4
|
1.0
|
|
N
|
A:ILE427
|
4.3
|
13.4
|
1.0
|
|
CB
|
A:ASN430
|
4.4
|
12.1
|
1.0
|
|
HB2
|
A:ASP426
|
4.5
|
18.6
|
1.0
|
|
HG23
|
A:ILE427
|
4.5
|
26.5
|
1.0
|
|
N
|
A:PRO433
|
4.5
|
14.2
|
1.0
|
|
C
|
A:ASP426
|
4.6
|
22.3
|
1.0
|
|
HA
|
A:PRO433
|
4.6
|
17.3
|
1.0
|
|
N
|
A:ALA450
|
4.6
|
11.8
|
1.0
|
|
N
|
A:ASP429
|
4.6
|
28.1
|
1.0
|
|
H
|
A:GLY431
|
4.6
|
21.6
|
1.0
|
|
HA
|
A:ARG449
|
4.6
|
15.1
|
1.0
|
|
CB
|
A:ASP428
|
4.6
|
11.0
|
1.0
|
|
N
|
A:ASP434
|
4.6
|
15.8
|
1.0
|
|
HB3
|
A:ARG449
|
4.6
|
12.7
|
1.0
|
|
C
|
A:PRO433
|
4.6
|
15.8
|
1.0
|
|
HB2
|
A:ASP434
|
4.7
|
14.9
|
1.0
|
|
HB3
|
A:TYR432
|
4.7
|
15.8
|
1.0
|
|
HB3
|
A:ASP434
|
4.7
|
14.9
|
1.0
|
|
CA
|
A:ASN430
|
4.7
|
18.2
|
1.0
|
|
HD21
|
A:ASN430
|
4.8
|
21.2
|
1.0
|
|
H
|
A:ASP434
|
4.8
|
18.9
|
1.0
|
|
CA
|
A:PRO433
|
4.8
|
14.5
|
1.0
|
|
N
|
A:GLY431
|
4.9
|
18.1
|
1.0
|
|
CA
|
A:ASP428
|
4.9
|
17.0
|
1.0
|
|
HA
|
A:ASP434
|
4.9
|
16.8
|
1.0
|
|
CA
|
A:ASP434
|
4.9
|
14.1
|
1.0
|
|
HB3
|
A:ASP428
|
4.9
|
13.1
|
1.0
|
|
C
|
A:ASP428
|
5.0
|
24.0
|
1.0
|
|
C
|
A:ASN430
|
5.0
|
14.8
|
1.0
|
|
Calcium binding site 5 out
of 8 in 3zdx
Go back to
Calcium Binding Sites List in 3zdx
Calcium binding site 5 out
of 8 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2004
b:47.8
occ:1.00
|
OD1
|
C:ASP245
|
2.3
|
39.9
|
1.0
|
|
O
|
C:THR250
|
2.3
|
46.9
|
1.0
|
|
O
|
C:ASP247
|
2.3
|
74.8
|
1.0
|
|
OE2
|
C:GLU243
|
2.4
|
62.8
|
1.0
|
|
OG1
|
C:THR250
|
2.4
|
49.2
|
1.0
|
|
OE2
|
C:GLU252
|
2.4
|
51.4
|
1.0
|
|
OE1
|
C:GLU243
|
2.4
|
48.7
|
1.0
|
|
OE1
|
C:GLU252
|
2.5
|
44.2
|
1.0
|
|
CD
|
C:GLU243
|
2.7
|
39.8
|
1.0
|
|
CD
|
C:GLU252
|
2.8
|
55.2
|
1.0
|
|
C
|
C:THR250
|
3.0
|
55.7
|
1.0
|
|
CG
|
C:ASP245
|
3.2
|
52.0
|
1.0
|
|
H
|
C:THR250
|
3.3
|
84.0
|
1.0
|
|
CB
|
C:THR250
|
3.5
|
46.0
|
1.0
|
|
C
|
C:ASP247
|
3.5
|
68.3
|
1.0
|
|
OD2
|
C:ASP245
|
3.5
|
62.6
|
1.0
|
|
CA
|
C:THR250
|
3.6
|
46.2
|
1.0
|
|
HB3
|
C:ASP247
|
3.7
|
80.5
|
1.0
|
|
H
|
C:ASP245
|
3.7
|
59.6
|
1.0
|
|
HB
|
C:THR250
|
3.8
|
55.1
|
1.0
|
|
N
|
C:THR250
|
3.8
|
70.1
|
1.0
|
|
HA
|
C:THR251
|
3.8
|
61.2
|
1.0
|
|
HA
|
C:GLU243
|
3.9
|
46.2
|
1.0
|
|
N
|
C:THR251
|
4.0
|
63.7
|
1.0
|
|
H
|
C:PHE244
|
4.1
|
50.4
|
1.0
|
|
HA
|
C:LEU248
|
4.1
|
71.3
|
1.0
|
|
CG
|
C:GLU243
|
4.2
|
38.4
|
1.0
|
|
CA
|
C:ASP247
|
4.3
|
62.6
|
1.0
|
|
CG
|
C:GLU252
|
4.3
|
57.5
|
1.0
|
|
CA
|
C:THR251
|
4.3
|
51.0
|
1.0
|
|
H
|
C:GLU252
|
4.4
|
47.6
|
1.0
|
|
N
|
C:ASP247
|
4.4
|
67.2
|
1.0
|
|
CB
|
C:ASP247
|
4.4
|
67.2
|
1.0
|
|
H
|
C:ASP247
|
4.4
|
80.5
|
1.0
|
|
CB
|
C:ASP245
|
4.4
|
45.5
|
1.0
|
|
N
|
C:ASP245
|
4.5
|
49.8
|
1.0
|
|
N
|
C:LEU248
|
4.5
|
59.6
|
1.0
|
|
HA
|
C:THR250
|
4.6
|
55.4
|
1.0
|
|
HG3
|
C:GLU243
|
4.6
|
46.0
|
1.0
|
|
HB3
|
C:ASP245
|
4.6
|
54.5
|
1.0
|
|
N
|
C:GLU252
|
4.6
|
39.8
|
1.0
|
|
H
|
C:THR251
|
4.6
|
76.4
|
1.0
|
|
HG2
|
C:GLU252
|
4.7
|
68.9
|
1.0
|
|
CA
|
C:LEU248
|
4.7
|
59.5
|
1.0
|
|
HG3
|
C:GLU252
|
4.7
|
68.9
|
1.0
|
|
CA
|
C:GLU243
|
4.7
|
38.6
|
1.0
|
|
C
|
C:THR251
|
4.7
|
52.4
|
1.0
|
|
HG2
|
C:GLU243
|
4.7
|
46.0
|
1.0
|
|
CG2
|
C:THR250
|
4.7
|
64.3
|
1.0
|
|
N
|
C:PHE244
|
4.8
|
42.1
|
1.0
|
|
C
|
C:LEU248
|
4.8
|
56.1
|
1.0
|
|
H
|
C:GLY246
|
4.8
|
78.2
|
1.0
|
|
CA
|
C:ASP245
|
4.8
|
62.1
|
1.0
|
|
HG21
|
C:THR250
|
4.8
|
77.1
|
1.0
|
|
CB
|
C:GLU243
|
4.9
|
34.4
|
1.0
|
|
HB2
|
C:GLU243
|
4.9
|
41.2
|
1.0
|
|
C
|
C:ASP245
|
4.9
|
60.1
|
1.0
|
|
C
|
C:GLY246
|
4.9
|
88.7
|
1.0
|
|
N
|
C:GLY246
|
4.9
|
65.2
|
1.0
|
|
Calcium binding site 6 out
of 8 in 3zdx
Go back to
Calcium Binding Sites List in 3zdx
Calcium binding site 6 out
of 8 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2005
b:38.0
occ:1.00
|
OD1
|
C:ASN299
|
2.3
|
39.2
|
1.0
|
|
O
|
C:ARG303
|
2.3
|
38.8
|
1.0
|
|
O
|
C:HOH4201
|
2.4
|
47.3
|
1.0
|
|
OD1
|
C:ASP297
|
2.4
|
34.9
|
1.0
|
|
OD2
|
C:ASP305
|
2.4
|
45.0
|
1.0
|
|
OD1
|
C:ASP301
|
2.5
|
50.8
|
1.0
|
|
OD1
|
C:ASP305
|
2.5
|
37.5
|
1.0
|
|
CG
|
C:ASP305
|
2.8
|
45.9
|
1.0
|
|
CG
|
C:ASP301
|
3.3
|
40.6
|
1.0
|
|
CG
|
C:ASN299
|
3.4
|
42.4
|
1.0
|
|
HB2
|
C:ARG303
|
3.4
|
60.7
|
1.0
|
|
C
|
C:ARG303
|
3.4
|
51.2
|
1.0
|
|
HD22
|
C:ASN299
|
3.5
|
45.5
|
1.0
|
|
OD2
|
C:ASP301
|
3.5
|
57.9
|
1.0
|
|
HA
|
C:ASP297
|
3.5
|
50.6
|
1.0
|
|
CG
|
C:ASP297
|
3.5
|
51.2
|
1.0
|
|
H
|
C:ASN299
|
3.6
|
43.5
|
1.0
|
|
H
|
C:ARG303
|
3.6
|
47.1
|
1.0
|
|
HD23
|
C:LEU332
|
3.7
|
47.0
|
1.0
|
|
ND2
|
C:ASN299
|
3.8
|
38.0
|
1.0
|
|
H
|
C:VAL298
|
3.9
|
39.7
|
1.0
|
|
H
|
C:ASP301
|
3.9
|
56.4
|
1.0
|
|
CA
|
C:ARG303
|
4.1
|
50.0
|
1.0
|
|
N
|
C:ARG303
|
4.1
|
39.3
|
1.0
|
|
CB
|
C:ARG303
|
4.2
|
50.7
|
1.0
|
|
H
|
C:GLN333
|
4.2
|
35.7
|
1.0
|
|
CB
|
C:ASP305
|
4.2
|
34.4
|
1.0
|
|
CA
|
C:ASP297
|
4.3
|
42.3
|
1.0
|
|
CB
|
C:ASP297
|
4.3
|
34.6
|
1.0
|
|
HB2
|
C:ASP297
|
4.3
|
41.5
|
1.0
|
|
N
|
C:ASN299
|
4.4
|
36.3
|
1.0
|
|
OD2
|
C:ASP297
|
4.4
|
50.4
|
1.0
|
|
HD21
|
C:LEU332
|
4.4
|
47.0
|
1.0
|
|
N
|
C:VAL298
|
4.4
|
33.2
|
1.0
|
|
N
|
C:ASP305
|
4.4
|
34.6
|
1.0
|
|
C
|
C:HIS304
|
4.4
|
38.0
|
1.0
|
|
CD2
|
C:LEU332
|
4.5
|
39.2
|
1.0
|
|
N
|
C:HIS304
|
4.5
|
43.8
|
1.0
|
|
H
|
C:ASP305
|
4.6
|
41.5
|
1.0
|
|
CB
|
C:ASP301
|
4.6
|
50.6
|
1.0
|
|
HB3
|
C:ARG303
|
4.6
|
60.7
|
1.0
|
|
HB3
|
C:LEU332
|
4.6
|
46.5
|
1.0
|
|
HB2
|
C:ASP305
|
4.6
|
41.2
|
1.0
|
|
CB
|
C:ASN299
|
4.7
|
35.1
|
1.0
|
|
HB3
|
C:GLN333
|
4.7
|
39.5
|
1.0
|
|
O
|
C:HIS304
|
4.7
|
40.0
|
1.0
|
|
N
|
C:ASP301
|
4.7
|
47.1
|
1.0
|
|
HD21
|
C:ASN299
|
4.7
|
45.5
|
1.0
|
|
HA
|
C:HIS304
|
4.7
|
34.8
|
1.0
|
|
C
|
C:ASP297
|
4.7
|
31.1
|
1.0
|
|
HG23
|
C:VAL298
|
4.7
|
47.3
|
1.0
|
|
HB3
|
C:ASP301
|
4.7
|
60.7
|
1.0
|
|
HB3
|
C:ASP305
|
4.8
|
41.2
|
1.0
|
|
HA
|
C:LEU332
|
4.8
|
51.1
|
1.0
|
|
H
|
C:GLY302
|
4.8
|
60.9
|
1.0
|
|
CA
|
C:ASP305
|
4.8
|
38.0
|
1.0
|
|
CA
|
C:HIS304
|
4.8
|
29.1
|
1.0
|
|
HA
|
C:ASP305
|
4.9
|
45.5
|
1.0
|
|
CA
|
C:ASN299
|
4.9
|
47.6
|
1.0
|
|
N
|
C:GLN333
|
4.9
|
29.9
|
1.0
|
|
O
|
C:GLN333
|
5.0
|
45.2
|
1.0
|
|
Calcium binding site 7 out
of 8 in 3zdx
Go back to
Calcium Binding Sites List in 3zdx
Calcium binding site 7 out
of 8 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2006
b:33.7
occ:1.00
|
O
|
C:TYR371
|
2.2
|
37.0
|
1.0
|
|
OD1
|
C:ASP367
|
2.3
|
37.0
|
1.0
|
|
O
|
C:HOH4245
|
2.4
|
32.1
|
1.0
|
|
OD1
|
C:ASP369
|
2.4
|
49.7
|
1.0
|
|
OD1
|
C:ASP365
|
2.5
|
36.8
|
1.0
|
|
OD1
|
C:ASP373
|
2.5
|
31.6
|
1.0
|
|
OD2
|
C:ASP373
|
2.5
|
30.9
|
1.0
|
|
CG
|
C:ASP373
|
2.8
|
33.8
|
1.0
|
|
H
|
C:ASP367
|
3.4
|
54.3
|
1.0
|
|
C
|
C:TYR371
|
3.4
|
38.7
|
1.0
|
|
CG
|
C:ASP369
|
3.4
|
51.8
|
1.0
|
|
CG
|
C:ASP367
|
3.4
|
47.2
|
1.0
|
|
CG
|
C:ASP365
|
3.5
|
49.5
|
1.0
|
|
H
|
C:TYR371
|
3.5
|
57.1
|
1.0
|
|
HA
|
C:ASP365
|
3.6
|
53.0
|
1.0
|
|
H
|
C:ASP369
|
3.6
|
67.5
|
1.0
|
|
HB2
|
C:TYR371
|
3.7
|
56.5
|
1.0
|
|
HD23
|
C:LEU393
|
3.7
|
44.9
|
1.0
|
|
H
|
C:LEU366
|
3.8
|
50.2
|
1.0
|
|
OD2
|
C:ASP367
|
3.9
|
44.3
|
1.0
|
|
H
|
C:GLY394
|
3.9
|
34.1
|
1.0
|
|
OD2
|
C:ASP369
|
3.9
|
50.0
|
1.0
|
|
OD2
|
C:ASP365
|
4.1
|
47.6
|
1.0
|
|
N
|
C:TYR371
|
4.2
|
47.7
|
1.0
|
|
CA
|
C:TYR371
|
4.2
|
42.0
|
1.0
|
|
HB3
|
C:LEU393
|
4.2
|
42.0
|
1.0
|
|
HA
|
C:ASN372
|
4.2
|
39.1
|
1.0
|
|
N
|
C:ASP367
|
4.2
|
45.3
|
1.0
|
|
N
|
C:LEU366
|
4.2
|
42.0
|
1.0
|
|
H
|
C:ARG368
|
4.3
|
71.8
|
1.0
|
|
CA
|
C:ASP365
|
4.3
|
44.3
|
1.0
|
|
CB
|
C:ASP373
|
4.3
|
31.2
|
1.0
|
|
CB
|
C:TYR371
|
4.4
|
47.1
|
1.0
|
|
N
|
C:ASN372
|
4.4
|
44.4
|
1.0
|
|
C
|
C:ASN372
|
4.5
|
35.9
|
1.0
|
|
N
|
C:ASP369
|
4.5
|
56.4
|
1.0
|
|
CB
|
C:ASP365
|
4.5
|
28.2
|
1.0
|
|
H
|
C:GLY370
|
4.5
|
53.0
|
1.0
|
|
C
|
C:ASP365
|
4.5
|
39.6
|
1.0
|
|
CB
|
C:ASP369
|
4.6
|
37.7
|
1.0
|
|
HB3
|
C:ASP369
|
4.6
|
45.2
|
1.0
|
|
N
|
C:GLY394
|
4.6
|
28.5
|
1.0
|
|
CA
|
C:ASN372
|
4.6
|
32.7
|
1.0
|
|
HA
|
C:LEU393
|
4.6
|
33.4
|
1.0
|
|
CD2
|
C:LEU393
|
4.6
|
37.5
|
1.0
|
|
N
|
C:ASP373
|
4.7
|
37.4
|
1.0
|
|
N
|
C:ARG368
|
4.7
|
59.9
|
1.0
|
|
O
|
C:ASN372
|
4.7
|
35.8
|
1.0
|
|
CB
|
C:ASP367
|
4.7
|
39.9
|
1.0
|
|
HB3
|
C:LEU366
|
4.7
|
37.0
|
1.0
|
|
HB2
|
C:ASP373
|
4.7
|
37.4
|
1.0
|
|
HB3
|
C:TYR371
|
4.8
|
56.5
|
1.0
|
|
HB3
|
C:ASP373
|
4.8
|
37.4
|
1.0
|
|
HD21
|
C:LEU393
|
4.8
|
44.9
|
1.0
|
|
O
|
C:GLY394
|
4.9
|
35.7
|
1.0
|
|
CA
|
C:ASP367
|
4.9
|
47.7
|
1.0
|
|
HB2
|
C:ASP365
|
4.9
|
33.8
|
1.0
|
|
H
|
C:ASP373
|
4.9
|
44.7
|
1.0
|
|
HA3
|
C:GLY394
|
5.0
|
34.4
|
1.0
|
|
HD11
|
C:LEU393
|
5.0
|
38.0
|
1.0
|
|
CB
|
C:LEU393
|
5.0
|
35.1
|
1.0
|
|
Calcium binding site 8 out
of 8 in 3zdx
Go back to
Calcium Binding Sites List in 3zdx
Calcium binding site 8 out
of 8 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2007
b:38.0
occ:1.00
|
O
|
C:TYR432
|
2.3
|
29.3
|
1.0
|
|
OD1
|
C:ASP428
|
2.3
|
30.4
|
1.0
|
|
OD1
|
C:ASP426
|
2.4
|
35.5
|
1.0
|
|
O
|
C:HOH4295
|
2.4
|
29.5
|
1.0
|
|
OD1
|
C:ASN430
|
2.4
|
59.9
|
1.0
|
|
OD1
|
C:ASP434
|
2.4
|
40.4
|
1.0
|
|
OD2
|
C:ASP434
|
2.5
|
36.1
|
1.0
|
|
CG
|
C:ASP434
|
2.8
|
42.6
|
1.0
|
|
CG
|
C:ASN430
|
3.3
|
45.2
|
1.0
|
|
CG
|
C:ASP428
|
3.4
|
53.6
|
1.0
|
|
CG
|
C:ASP426
|
3.4
|
43.4
|
1.0
|
|
C
|
C:TYR432
|
3.4
|
45.4
|
1.0
|
|
H
|
C:TYR432
|
3.4
|
52.2
|
1.0
|
|
HA
|
C:ASP426
|
3.5
|
44.6
|
1.0
|
|
H
|
C:ASN430
|
3.5
|
57.3
|
1.0
|
|
H
|
C:ASP428
|
3.5
|
54.6
|
1.0
|
|
HB2
|
C:TYR432
|
3.6
|
48.5
|
1.0
|
|
H
|
C:ALA450
|
3.8
|
32.2
|
1.0
|
|
OD2
|
C:ASP428
|
3.8
|
46.2
|
1.0
|
|
HD22
|
C:ASN430
|
3.8
|
41.0
|
1.0
|
|
ND2
|
C:ASN430
|
3.9
|
34.2
|
1.0
|
|
H
|
C:ILE427
|
4.0
|
43.6
|
1.0
|
|
HB1
|
C:ALA450
|
4.0
|
36.3
|
1.0
|
|
N
|
C:TYR432
|
4.1
|
43.6
|
1.0
|
|
CA
|
C:TYR432
|
4.1
|
36.6
|
1.0
|
|
CA
|
C:ASP426
|
4.2
|
37.3
|
1.0
|
|
O
|
C:ALA450
|
4.2
|
38.1
|
1.0
|
|
HB3
|
C:ASN430
|
4.2
|
45.4
|
1.0
|
|
OD2
|
C:ASP426
|
4.2
|
64.0
|
1.0
|
|
CB
|
C:ASP434
|
4.2
|
27.6
|
1.0
|
|
CB
|
C:ASP426
|
4.3
|
41.1
|
1.0
|
|
N
|
C:ASN430
|
4.3
|
47.9
|
1.0
|
|
CB
|
C:ASN430
|
4.3
|
38.0
|
1.0
|
|
CB
|
C:TYR432
|
4.3
|
40.5
|
1.0
|
|
HG2
|
C:ARG449
|
4.4
|
47.8
|
1.0
|
|
N
|
C:ASP428
|
4.4
|
45.6
|
1.0
|
|
H
|
C:ASP429
|
4.4
|
66.9
|
1.0
|
|
N
|
C:ILE427
|
4.4
|
36.4
|
1.0
|
|
HB2
|
C:ASP426
|
4.4
|
49.3
|
1.0
|
|
N
|
C:PRO433
|
4.5
|
40.9
|
1.0
|
|
N
|
C:ALA450
|
4.5
|
26.9
|
1.0
|
|
HA
|
C:PRO433
|
4.5
|
45.3
|
1.0
|
|
N
|
C:ASP434
|
4.6
|
28.7
|
1.0
|
|
C
|
C:PRO433
|
4.6
|
39.9
|
1.0
|
|
C
|
C:ASP426
|
4.6
|
37.3
|
1.0
|
|
HG23
|
C:ILE427
|
4.6
|
31.1
|
1.0
|
|
HB3
|
C:TYR432
|
4.6
|
48.5
|
1.0
|
|
HB2
|
C:ASP434
|
4.6
|
33.0
|
1.0
|
|
HA
|
C:ARG449
|
4.6
|
28.3
|
1.0
|
|
CB
|
C:ASP428
|
4.6
|
32.8
|
1.0
|
|
N
|
C:ASP429
|
4.7
|
55.9
|
1.0
|
|
HD21
|
C:ASN430
|
4.7
|
41.0
|
1.0
|
|
H
|
C:ASP434
|
4.7
|
34.4
|
1.0
|
|
H
|
C:GLY431
|
4.7
|
48.0
|
1.0
|
|
CA
|
C:ASN430
|
4.7
|
44.6
|
1.0
|
|
CA
|
C:PRO433
|
4.7
|
37.9
|
1.0
|
|
HB3
|
C:ASP434
|
4.8
|
33.0
|
1.0
|
|
HB3
|
C:ARG449
|
4.8
|
27.6
|
1.0
|
|
HA
|
C:ASP434
|
4.9
|
22.3
|
1.0
|
|
CA
|
C:ASP434
|
4.9
|
18.6
|
1.0
|
|
CA
|
C:ASP428
|
4.9
|
44.4
|
1.0
|
|
CB
|
C:ALA450
|
4.9
|
30.4
|
1.0
|
|
HB3
|
C:ASP428
|
4.9
|
39.3
|
1.0
|
|
C
|
C:ASP428
|
5.0
|
50.7
|
1.0
|
|
N
|
C:GLY431
|
5.0
|
40.0
|
1.0
|
|
O
|
C:PRO433
|
5.0
|
31.9
|
1.0
|
|
Reference:
J.Zhu,
J.Zhu,
T.A.Springer.
Complete Integrin Headpiece Opening in Eight Steps. J.Cell Biol. V. 201 1053 2013.
ISSN: ISSN 0021-9525
PubMed: 23798730
DOI: 10.1083/JCB.201212037
Page generated: Sat Jul 13 21:30:21 2024
|
