Calcium in PDB 3nid: The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening
Protein crystallography data
The structure of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening, PDB code: 3nid
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)
|
48.21 /
2.30
|
|
Space group
|
P 21 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
258.970,
144.490,
104.200,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
17.9 /
21.5
|
Other elements in 3nid:
The structure of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening also contains other interesting chemical elements:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Calcium atom in the The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening
(pdb code 3nid). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the
The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening, PDB code: 3nid:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 3nid
Go back to
Calcium Binding Sites List in 3nid
Calcium binding site 1 out
of 12 in the The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2004
b:29.2
occ:1.00
|
O
|
A:THR250
|
2.2
|
30.6
|
1.0
|
|
OD2
|
A:ASP245
|
2.2
|
32.6
|
1.0
|
|
OE1
|
A:GLU243
|
2.4
|
27.0
|
1.0
|
|
OG1
|
A:THR250
|
2.4
|
38.4
|
1.0
|
|
O
|
A:ASP247
|
2.4
|
47.5
|
1.0
|
|
OE2
|
A:GLU243
|
2.5
|
31.5
|
1.0
|
|
OE2
|
A:GLU252
|
2.5
|
27.4
|
1.0
|
|
OE1
|
A:GLU252
|
2.6
|
27.0
|
1.0
|
|
CD
|
A:GLU243
|
2.8
|
30.0
|
1.0
|
|
CD
|
A:GLU252
|
2.9
|
24.5
|
1.0
|
|
C
|
A:THR250
|
3.2
|
36.2
|
1.0
|
|
CG
|
A:ASP245
|
3.2
|
39.6
|
1.0
|
|
C
|
A:ASP247
|
3.5
|
44.9
|
1.0
|
|
CB
|
A:THR250
|
3.5
|
40.5
|
1.0
|
|
OD1
|
A:ASP245
|
3.6
|
50.0
|
1.0
|
|
CA
|
A:THR250
|
3.8
|
38.9
|
1.0
|
|
N
|
A:THR250
|
4.0
|
44.6
|
1.0
|
|
N
|
A:ASP247
|
4.0
|
47.6
|
1.0
|
|
CA
|
A:ASP247
|
4.1
|
48.2
|
1.0
|
|
N
|
A:THR251
|
4.2
|
35.8
|
1.0
|
|
CB
|
A:ASP247
|
4.3
|
49.4
|
1.0
|
|
CG
|
A:GLU243
|
4.3
|
24.5
|
1.0
|
|
N
|
A:ASP245
|
4.3
|
31.4
|
1.0
|
|
CG
|
A:GLU252
|
4.4
|
22.9
|
1.0
|
|
CB
|
A:ASP245
|
4.4
|
35.5
|
1.0
|
|
O
|
A:HOH709
|
4.5
|
24.7
|
1.0
|
|
N
|
A:LEU248
|
4.5
|
47.8
|
1.0
|
|
CA
|
A:THR251
|
4.5
|
32.8
|
1.0
|
|
N
|
A:PHE244
|
4.6
|
21.5
|
1.0
|
|
CA
|
A:GLU243
|
4.6
|
21.1
|
1.0
|
|
N
|
A:GLY246
|
4.7
|
43.7
|
1.0
|
|
CA
|
A:ASP245
|
4.7
|
36.1
|
1.0
|
|
CA
|
A:LEU248
|
4.8
|
49.0
|
1.0
|
|
N
|
A:GLU252
|
4.8
|
24.0
|
1.0
|
|
CG2
|
A:THR250
|
4.8
|
35.9
|
1.0
|
|
C
|
A:ASP245
|
4.8
|
41.1
|
1.0
|
|
C
|
A:THR251
|
4.8
|
27.2
|
1.0
|
|
CB
|
A:GLU243
|
4.9
|
21.0
|
1.0
|
|
C
|
A:LEU248
|
5.0
|
49.2
|
1.0
|
|
Calcium binding site 2 out
of 12 in 3nid
Go back to
Calcium Binding Sites List in 3nid
Calcium binding site 2 out
of 12 in the The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2005
b:19.8
occ:1.00
|
OD1
|
A:ASN299
|
2.2
|
17.4
|
1.0
|
|
O
|
A:ARG303
|
2.3
|
16.1
|
1.0
|
|
OD1
|
A:ASP297
|
2.3
|
17.7
|
1.0
|
|
O
|
A:HOH471
|
2.4
|
3.9
|
1.0
|
|
OD1
|
A:ASP305
|
2.5
|
17.4
|
1.0
|
|
OD1
|
A:ASP301
|
2.6
|
22.6
|
1.0
|
|
OD2
|
A:ASP305
|
2.6
|
21.7
|
1.0
|
|
CG
|
A:ASP305
|
2.9
|
13.8
|
1.0
|
|
CG
|
A:ASP301
|
3.3
|
21.7
|
1.0
|
|
CG
|
A:ASN299
|
3.4
|
22.1
|
1.0
|
|
OD2
|
A:ASP301
|
3.4
|
31.6
|
1.0
|
|
C
|
A:ARG303
|
3.4
|
22.2
|
1.0
|
|
CG
|
A:ASP297
|
3.5
|
27.7
|
1.0
|
|
ND2
|
A:ASN299
|
4.0
|
29.5
|
1.0
|
|
CB
|
A:ARG303
|
4.1
|
27.0
|
1.0
|
|
CA
|
A:ARG303
|
4.1
|
24.2
|
1.0
|
|
N
|
A:ARG303
|
4.2
|
27.0
|
1.0
|
|
CB
|
A:ASP297
|
4.3
|
19.4
|
1.0
|
|
CA
|
A:ASP297
|
4.3
|
19.0
|
1.0
|
|
N
|
A:ASN299
|
4.3
|
21.7
|
1.0
|
|
CB
|
A:ASP305
|
4.4
|
13.8
|
1.0
|
|
OD2
|
A:ASP297
|
4.4
|
27.3
|
1.0
|
|
N
|
A:ASP305
|
4.4
|
16.3
|
1.0
|
|
N
|
A:VAL298
|
4.5
|
18.4
|
1.0
|
|
C
|
A:HIS304
|
4.5
|
15.8
|
1.0
|
|
N
|
A:HIS304
|
4.5
|
23.4
|
1.0
|
|
CB
|
A:ASN299
|
4.6
|
22.5
|
1.0
|
|
N
|
A:ASP301
|
4.7
|
22.2
|
1.0
|
|
CB
|
A:ASP301
|
4.7
|
27.2
|
1.0
|
|
C
|
A:ASP297
|
4.7
|
17.3
|
1.0
|
|
CD2
|
A:LEU332
|
4.7
|
15.1
|
1.0
|
|
N
|
A:GLN333
|
4.8
|
21.3
|
1.0
|
|
CA
|
A:ASN299
|
4.8
|
22.2
|
1.0
|
|
O
|
A:HIS304
|
4.8
|
18.3
|
1.0
|
|
O
|
A:GLN333
|
4.9
|
22.7
|
1.0
|
|
CA
|
A:HIS304
|
4.9
|
17.6
|
1.0
|
|
CA
|
A:ASP305
|
4.9
|
16.6
|
1.0
|
|
C
|
A:ASN299
|
5.0
|
23.4
|
1.0
|
|
Calcium binding site 3 out
of 12 in 3nid
Go back to
Calcium Binding Sites List in 3nid
Calcium binding site 3 out
of 12 in the The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2006
b:16.9
occ:1.00
|
O
|
A:HOH470
|
2.2
|
9.5
|
1.0
|
|
O
|
A:TYR371
|
2.3
|
19.7
|
1.0
|
|
OD1
|
A:ASP367
|
2.3
|
17.7
|
1.0
|
|
OD2
|
A:ASP365
|
2.3
|
16.1
|
1.0
|
|
OD2
|
A:ASP373
|
2.5
|
15.8
|
1.0
|
|
OD1
|
A:ASP369
|
2.5
|
17.6
|
1.0
|
|
OD1
|
A:ASP373
|
2.6
|
14.0
|
1.0
|
|
CG
|
A:ASP373
|
2.9
|
21.4
|
1.0
|
|
CG
|
A:ASP369
|
3.4
|
22.4
|
1.0
|
|
C
|
A:TYR371
|
3.4
|
16.5
|
1.0
|
|
CG
|
A:ASP367
|
3.5
|
18.7
|
1.0
|
|
CG
|
A:ASP365
|
3.5
|
20.4
|
1.0
|
|
OD2
|
A:ASP369
|
3.8
|
32.0
|
1.0
|
|
OD2
|
A:ASP367
|
4.0
|
32.8
|
1.0
|
|
N
|
A:TYR371
|
4.0
|
21.1
|
1.0
|
|
CA
|
A:TYR371
|
4.1
|
18.6
|
1.0
|
|
N
|
A:ASP367
|
4.2
|
15.9
|
1.0
|
|
CB
|
A:TYR371
|
4.2
|
20.3
|
1.0
|
|
CA
|
A:ASP365
|
4.3
|
18.2
|
1.0
|
|
OD1
|
A:ASP365
|
4.3
|
19.1
|
1.0
|
|
N
|
A:LEU366
|
4.3
|
17.6
|
1.0
|
|
CB
|
A:ASP373
|
4.4
|
14.2
|
1.0
|
|
CB
|
A:ASP365
|
4.4
|
18.5
|
1.0
|
|
N
|
A:ASP369
|
4.5
|
17.6
|
1.0
|
|
N
|
A:ASN372
|
4.5
|
16.5
|
1.0
|
|
C
|
A:ASP365
|
4.5
|
17.2
|
1.0
|
|
CB
|
A:ASP369
|
4.6
|
18.6
|
1.0
|
|
N
|
A:ARG368
|
4.6
|
21.2
|
1.0
|
|
C
|
A:ASN372
|
4.6
|
18.8
|
1.0
|
|
CB
|
A:ASP367
|
4.7
|
18.0
|
1.0
|
|
CA
|
A:ASN372
|
4.7
|
13.9
|
1.0
|
|
N
|
A:GLY394
|
4.7
|
14.0
|
1.0
|
|
CD2
|
A:LEU393
|
4.8
|
12.1
|
1.0
|
|
N
|
A:ASP373
|
4.8
|
14.6
|
1.0
|
|
CA
|
A:ASP367
|
4.8
|
19.6
|
1.0
|
|
O
|
A:GLY394
|
4.8
|
19.8
|
1.0
|
|
O
|
A:ASN372
|
4.9
|
18.9
|
1.0
|
|
CB
|
A:LEU393
|
4.9
|
15.5
|
1.0
|
|
C
|
A:ASP367
|
5.0
|
19.6
|
1.0
|
|
CA
|
A:ASP369
|
5.0
|
18.9
|
1.0
|
|
N
|
A:GLY370
|
5.0
|
21.0
|
1.0
|
|
Calcium binding site 4 out
of 12 in 3nid
Go back to
Calcium Binding Sites List in 3nid
Calcium binding site 4 out
of 12 in the The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2007
b:16.3
occ:1.00
|
OD1
|
A:ASP428
|
2.3
|
14.1
|
1.0
|
|
OD1
|
A:ASP426
|
2.3
|
19.1
|
1.0
|
|
O
|
A:TYR432
|
2.3
|
17.9
|
1.0
|
|
OD1
|
A:ASN430
|
2.4
|
22.5
|
1.0
|
|
O
|
A:HOH472
|
2.5
|
2.0
|
1.0
|
|
OD2
|
A:ASP434
|
2.5
|
15.3
|
1.0
|
|
OD1
|
A:ASP434
|
2.5
|
16.0
|
1.0
|
|
CG
|
A:ASP434
|
2.8
|
20.0
|
1.0
|
|
CG
|
A:ASN430
|
3.3
|
15.1
|
1.0
|
|
CG
|
A:ASP428
|
3.4
|
25.2
|
1.0
|
|
CG
|
A:ASP426
|
3.4
|
16.0
|
1.0
|
|
C
|
A:TYR432
|
3.5
|
18.9
|
1.0
|
|
OD2
|
A:ASP428
|
3.8
|
17.1
|
1.0
|
|
ND2
|
A:ASN430
|
4.0
|
20.6
|
1.0
|
|
CA
|
A:ASP426
|
4.1
|
15.6
|
1.0
|
|
N
|
A:TYR432
|
4.2
|
18.6
|
1.0
|
|
O
|
A:ALA450
|
4.2
|
18.0
|
1.0
|
|
OD2
|
A:ASP426
|
4.2
|
20.0
|
1.0
|
|
N
|
A:ASN430
|
4.2
|
21.4
|
1.0
|
|
CB
|
A:ASP426
|
4.2
|
15.6
|
1.0
|
|
N
|
A:ILE427
|
4.2
|
16.8
|
1.0
|
|
CA
|
A:TYR432
|
4.3
|
18.8
|
1.0
|
|
N
|
A:ASP428
|
4.3
|
19.6
|
1.0
|
|
CB
|
A:ASP434
|
4.3
|
15.7
|
1.0
|
|
CB
|
A:ASN430
|
4.3
|
18.8
|
1.0
|
|
CB
|
A:TYR432
|
4.4
|
18.5
|
1.0
|
|
C
|
A:ASP426
|
4.4
|
14.3
|
1.0
|
|
N
|
A:PRO433
|
4.5
|
16.7
|
1.0
|
|
N
|
A:ASP434
|
4.6
|
17.0
|
1.0
|
|
C
|
A:PRO433
|
4.6
|
16.9
|
1.0
|
|
N
|
A:ALA450
|
4.6
|
16.4
|
1.0
|
|
CB
|
A:ASP428
|
4.6
|
15.1
|
1.0
|
|
N
|
A:ASP429
|
4.7
|
23.9
|
1.0
|
|
CA
|
A:PRO433
|
4.7
|
18.0
|
1.0
|
|
CA
|
A:ASN430
|
4.7
|
21.6
|
1.0
|
|
CA
|
A:ASP428
|
4.9
|
19.8
|
1.0
|
|
N
|
A:GLY431
|
4.9
|
21.7
|
1.0
|
|
C
|
A:ASN430
|
5.0
|
21.1
|
1.0
|
|
CA
|
A:ASP434
|
5.0
|
16.6
|
1.0
|
|
C
|
A:ASP428
|
5.0
|
23.4
|
1.0
|
|
CB
|
A:ALA450
|
5.0
|
11.3
|
1.0
|
|
Calcium binding site 5 out
of 12 in 3nid
Go back to
Calcium Binding Sites List in 3nid
Calcium binding site 5 out
of 12 in the The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2002
b:36.0
occ:1.00
|
OD1
|
B:ASP127
|
2.4
|
26.7
|
1.0
|
|
O
|
B:MET335
|
2.4
|
25.9
|
1.0
|
|
O
|
B:HOH474
|
2.4
|
5.5
|
1.0
|
|
O
|
B:HOH475
|
2.4
|
6.9
|
1.0
|
|
O
|
B:SER123
|
2.4
|
18.8
|
1.0
|
|
OD1
|
B:ASP126
|
2.6
|
39.4
|
1.0
|
|
OD2
|
B:ASP126
|
2.7
|
35.8
|
1.0
|
|
CG
|
B:ASP126
|
3.0
|
40.5
|
1.0
|
|
CG
|
B:ASP127
|
3.5
|
32.7
|
1.0
|
|
C
|
B:MET335
|
3.6
|
27.5
|
1.0
|
|
C
|
B:SER123
|
3.6
|
17.5
|
1.0
|
|
O
|
B:HOH476
|
3.9
|
11.6
|
1.0
|
|
OD2
|
B:ASP127
|
3.9
|
27.2
|
1.0
|
|
CA
|
B:MET124
|
4.1
|
20.0
|
1.0
|
|
O
|
B:HOH1009
|
4.1
|
17.1
|
1.0
|
|
N
|
B:MET124
|
4.3
|
16.2
|
1.0
|
|
CA
|
B:ASP336
|
4.4
|
26.6
|
1.0
|
|
N
|
B:ASP336
|
4.4
|
25.9
|
1.0
|
|
OD2
|
B:ASP251
|
4.5
|
21.4
|
1.0
|
|
N
|
B:ASP127
|
4.5
|
21.8
|
1.0
|
|
CB
|
B:ASP126
|
4.5
|
26.4
|
1.0
|
|
CA
|
B:MET335
|
4.6
|
29.4
|
1.0
|
|
O
|
B:HOH929
|
4.6
|
11.7
|
1.0
|
|
C
|
B:MET124
|
4.7
|
20.5
|
1.0
|
|
SD
|
B:MET124
|
4.7
|
24.2
|
1.0
|
|
CB
|
B:ASP127
|
4.7
|
20.6
|
1.0
|
|
CA
|
B:SER123
|
4.8
|
17.6
|
1.0
|
|
CB
|
B:MET335
|
4.9
|
31.1
|
1.0
|
|
N
|
B:ASP126
|
5.0
|
24.5
|
1.0
|
|
Calcium binding site 6 out
of 12 in 3nid
Go back to
Calcium Binding Sites List in 3nid
Calcium binding site 6 out
of 12 in the The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2003
b:14.0
occ:1.00
|
OD1
|
B:ASP217
|
2.2
|
14.3
|
1.0
|
|
OE1
|
B:GLU220
|
2.2
|
18.9
|
1.0
|
|
OD1
|
B:ASN215
|
2.3
|
20.7
|
1.0
|
|
O
|
B:PRO219
|
2.3
|
11.4
|
1.0
|
|
OD2
|
B:ASP158
|
2.3
|
12.4
|
1.0
|
|
O
|
B:ASP217
|
2.4
|
20.4
|
1.0
|
|
CG
|
B:ASP217
|
3.2
|
12.6
|
1.0
|
|
CD
|
B:GLU220
|
3.3
|
22.2
|
1.0
|
|
CG
|
B:ASN215
|
3.3
|
21.8
|
1.0
|
|
C
|
B:ASP217
|
3.4
|
15.0
|
1.0
|
|
CG
|
B:ASP158
|
3.5
|
20.2
|
1.0
|
|
C
|
B:PRO219
|
3.5
|
14.3
|
1.0
|
|
ND2
|
B:ASN215
|
3.7
|
16.1
|
1.0
|
|
OE2
|
B:GLU220
|
3.9
|
20.8
|
1.0
|
|
OD2
|
B:ASP217
|
3.9
|
21.3
|
1.0
|
|
CB
|
B:ASP158
|
3.9
|
10.5
|
1.0
|
|
N
|
B:ASP217
|
3.9
|
14.5
|
1.0
|
|
CA
|
B:ASP217
|
4.0
|
15.6
|
1.0
|
|
CA
|
B:GLU220
|
4.0
|
14.0
|
1.0
|
|
NE2
|
B:HIS255
|
4.1
|
13.6
|
1.0
|
|
N
|
B:GLU220
|
4.2
|
14.9
|
1.0
|
|
CB
|
B:ASP217
|
4.2
|
15.1
|
1.0
|
|
C
|
B:ALA218
|
4.3
|
15.3
|
1.0
|
|
O
|
B:ALA218
|
4.3
|
19.7
|
1.0
|
|
N
|
B:PRO219
|
4.3
|
13.9
|
1.0
|
|
N
|
B:ALA218
|
4.4
|
19.5
|
1.0
|
|
CG
|
B:GLU220
|
4.4
|
16.6
|
1.0
|
|
CD2
|
B:HIS255
|
4.5
|
7.6
|
1.0
|
|
CA
|
B:PRO219
|
4.5
|
14.9
|
1.0
|
|
OD1
|
B:ASP158
|
4.5
|
9.6
|
1.0
|
|
CB
|
B:ASN215
|
4.7
|
17.7
|
1.0
|
|
CB
|
B:GLU220
|
4.7
|
17.2
|
1.0
|
|
CA
|
B:ALA218
|
4.8
|
15.7
|
1.0
|
|
CD
|
B:PRO219
|
4.8
|
14.7
|
1.0
|
|
CD1
|
B:TYR164
|
4.9
|
24.6
|
1.0
|
|
CB
|
B:TYR164
|
4.9
|
14.2
|
1.0
|
|
C
|
B:GLU220
|
5.0
|
15.6
|
1.0
|
|
Calcium binding site 7 out
of 12 in 3nid
Go back to
Calcium Binding Sites List in 3nid
Calcium binding site 7 out
of 12 in the The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2004
b:45.7
occ:1.00
|
O
|
C:THR250
|
2.1
|
43.9
|
1.0
|
|
OD2
|
C:ASP245
|
2.3
|
51.9
|
1.0
|
|
O
|
C:ASP247
|
2.4
|
62.0
|
1.0
|
|
OG1
|
C:THR250
|
2.5
|
56.0
|
1.0
|
|
OE1
|
C:GLU243
|
2.5
|
40.2
|
1.0
|
|
OE2
|
C:GLU252
|
2.5
|
44.1
|
1.0
|
|
OE1
|
C:GLU252
|
2.7
|
43.6
|
1.0
|
|
OE2
|
C:GLU243
|
2.7
|
56.5
|
1.0
|
|
CD
|
C:GLU243
|
2.9
|
46.6
|
1.0
|
|
CD
|
C:GLU252
|
3.0
|
44.1
|
1.0
|
|
C
|
C:THR250
|
3.1
|
52.3
|
1.0
|
|
CG
|
C:ASP245
|
3.3
|
56.3
|
1.0
|
|
C
|
C:ASP247
|
3.5
|
64.4
|
1.0
|
|
CB
|
C:THR250
|
3.6
|
55.7
|
1.0
|
|
OD1
|
C:ASP245
|
3.7
|
54.7
|
1.0
|
|
CA
|
C:THR250
|
3.7
|
54.9
|
1.0
|
|
N
|
C:THR250
|
4.0
|
61.5
|
1.0
|
|
N
|
C:ASP247
|
4.0
|
64.0
|
1.0
|
|
N
|
C:THR251
|
4.1
|
51.4
|
1.0
|
|
CA
|
C:ASP247
|
4.1
|
65.8
|
1.0
|
|
CB
|
C:ASP247
|
4.2
|
66.9
|
1.0
|
|
N
|
C:ASP245
|
4.4
|
47.5
|
1.0
|
|
CG
|
C:GLU243
|
4.4
|
45.5
|
1.0
|
|
CA
|
C:THR251
|
4.5
|
49.9
|
1.0
|
|
CG
|
C:GLU252
|
4.5
|
40.8
|
1.0
|
|
CB
|
C:ASP245
|
4.5
|
52.6
|
1.0
|
|
N
|
C:LEU248
|
4.6
|
66.2
|
1.0
|
|
C
|
C:THR251
|
4.7
|
46.2
|
1.0
|
|
N
|
C:GLU252
|
4.8
|
40.1
|
1.0
|
|
N
|
C:PHE244
|
4.8
|
37.1
|
1.0
|
|
CA
|
C:ASP245
|
4.8
|
53.4
|
1.0
|
|
CA
|
C:GLU243
|
4.8
|
37.5
|
1.0
|
|
CG2
|
C:THR250
|
4.8
|
54.3
|
1.0
|
|
CA
|
C:LEU248
|
4.8
|
66.2
|
1.0
|
|
N
|
C:GLY246
|
4.9
|
58.5
|
1.0
|
|
C
|
C:ASP245
|
4.9
|
56.5
|
1.0
|
|
O
|
C:HOH923
|
4.9
|
29.6
|
1.0
|
|
Calcium binding site 8 out
of 12 in 3nid
Go back to
Calcium Binding Sites List in 3nid
Calcium binding site 8 out
of 12 in the The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2005
b:39.0
occ:1.00
|
OD1
|
C:ASN299
|
2.2
|
38.1
|
1.0
|
|
OD1
|
C:ASP297
|
2.2
|
32.9
|
1.0
|
|
O
|
C:ARG303
|
2.4
|
36.4
|
1.0
|
|
O
|
C:HOH466
|
2.5
|
6.5
|
1.0
|
|
OD1
|
C:ASP305
|
2.5
|
49.0
|
1.0
|
|
OD2
|
C:ASP305
|
2.6
|
37.9
|
1.0
|
|
OD1
|
C:ASP301
|
2.6
|
45.8
|
1.0
|
|
CG
|
C:ASP305
|
2.9
|
34.7
|
1.0
|
|
CG
|
C:ASN299
|
3.4
|
49.1
|
1.0
|
|
CG
|
C:ASP297
|
3.4
|
48.2
|
1.0
|
|
CG
|
C:ASP301
|
3.4
|
47.9
|
1.0
|
|
OD2
|
C:ASP301
|
3.5
|
56.5
|
1.0
|
|
C
|
C:ARG303
|
3.5
|
40.4
|
1.0
|
|
ND2
|
C:ASN299
|
4.0
|
40.1
|
1.0
|
|
CA
|
C:ASP297
|
4.1
|
36.3
|
1.0
|
|
CB
|
C:ASP297
|
4.2
|
35.8
|
1.0
|
|
N
|
C:ASN299
|
4.2
|
44.0
|
1.0
|
|
CA
|
C:ARG303
|
4.2
|
43.2
|
1.0
|
|
N
|
C:ARG303
|
4.2
|
46.0
|
1.0
|
|
CB
|
C:ARG303
|
4.3
|
43.8
|
1.0
|
|
OD2
|
C:ASP297
|
4.3
|
53.5
|
1.0
|
|
N
|
C:VAL298
|
4.3
|
36.0
|
1.0
|
|
CB
|
C:ASP305
|
4.3
|
32.5
|
1.0
|
|
N
|
C:ASP305
|
4.4
|
32.7
|
1.0
|
|
C
|
C:HIS304
|
4.5
|
32.9
|
1.0
|
|
C
|
C:ASP297
|
4.6
|
37.2
|
1.0
|
|
CB
|
C:ASN299
|
4.6
|
46.4
|
1.0
|
|
N
|
C:HIS304
|
4.6
|
37.8
|
1.0
|
|
N
|
C:ASP301
|
4.7
|
47.6
|
1.0
|
|
CA
|
C:ASN299
|
4.7
|
46.2
|
1.0
|
|
CB
|
C:ASP301
|
4.8
|
49.5
|
1.0
|
|
O
|
C:HIS304
|
4.8
|
35.9
|
1.0
|
|
CA
|
C:HIS304
|
4.9
|
34.1
|
1.0
|
|
N
|
C:GLY300
|
4.9
|
48.5
|
1.0
|
|
CD2
|
C:LEU332
|
4.9
|
28.4
|
1.0
|
|
CA
|
C:ASP305
|
4.9
|
31.4
|
1.0
|
|
C
|
C:ASN299
|
4.9
|
49.5
|
1.0
|
|
N
|
C:GLN333
|
4.9
|
40.3
|
1.0
|
|
Calcium binding site 9 out
of 12 in 3nid
Go back to
Calcium Binding Sites List in 3nid
Calcium binding site 9 out
of 12 in the The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2006
b:34.7
occ:1.00
|
O
|
C:HOH464
|
2.1
|
3.4
|
1.0
|
|
OD1
|
C:ASP367
|
2.3
|
38.8
|
1.0
|
|
O
|
C:TYR371
|
2.3
|
37.9
|
1.0
|
|
OD2
|
C:ASP365
|
2.4
|
32.5
|
1.0
|
|
OD1
|
C:ASP373
|
2.5
|
40.5
|
1.0
|
|
OD2
|
C:ASP373
|
2.5
|
34.9
|
1.0
|
|
OD1
|
C:ASP369
|
2.6
|
42.4
|
1.0
|
|
CG
|
C:ASP373
|
2.9
|
36.7
|
1.0
|
|
CG
|
C:ASP367
|
3.4
|
43.8
|
1.0
|
|
CG
|
C:ASP365
|
3.5
|
43.1
|
1.0
|
|
C
|
C:TYR371
|
3.5
|
36.7
|
1.0
|
|
CG
|
C:ASP369
|
3.6
|
47.3
|
1.0
|
|
OD2
|
C:ASP367
|
3.8
|
57.5
|
1.0
|
|
OD2
|
C:ASP369
|
4.2
|
56.0
|
1.0
|
|
N
|
C:LEU366
|
4.2
|
38.0
|
1.0
|
|
CA
|
C:ASP365
|
4.2
|
37.8
|
1.0
|
|
OD1
|
C:ASP365
|
4.2
|
38.4
|
1.0
|
|
N
|
C:ASP367
|
4.2
|
44.0
|
1.0
|
|
N
|
C:TYR371
|
4.2
|
42.9
|
1.0
|
|
CA
|
C:TYR371
|
4.3
|
38.8
|
1.0
|
|
CB
|
C:ASP373
|
4.4
|
29.2
|
1.0
|
|
CB
|
C:ASP365
|
4.4
|
38.3
|
1.0
|
|
CB
|
C:TYR371
|
4.4
|
38.5
|
1.0
|
|
C
|
C:ASP365
|
4.5
|
36.7
|
1.0
|
|
N
|
C:ASN372
|
4.5
|
36.6
|
1.0
|
|
N
|
C:ASP369
|
4.5
|
48.1
|
1.0
|
|
C
|
C:ASN372
|
4.5
|
33.4
|
1.0
|
|
N
|
C:GLY394
|
4.6
|
36.3
|
1.0
|
|
CA
|
C:ASN372
|
4.6
|
33.2
|
1.0
|
|
N
|
C:ARG368
|
4.6
|
48.8
|
1.0
|
|
CB
|
C:ASP367
|
4.7
|
44.7
|
1.0
|
|
N
|
C:ASP373
|
4.7
|
31.0
|
1.0
|
|
CD2
|
C:LEU393
|
4.8
|
25.9
|
1.0
|
|
CB
|
C:ASP369
|
4.8
|
45.6
|
1.0
|
|
O
|
C:ASN372
|
4.8
|
33.1
|
1.0
|
|
CA
|
C:ASP367
|
4.8
|
44.9
|
1.0
|
|
O
|
C:GLY394
|
4.9
|
39.5
|
1.0
|
|
CB
|
C:LEU393
|
5.0
|
38.0
|
1.0
|
|
Calcium binding site 10 out
of 12 in 3nid
Go back to
Calcium Binding Sites List in 3nid
Calcium binding site 10 out
of 12 in the The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of The Closed Headpiece of Integrin Alphaiib BETA3 and Its Complex with An Alpahiib BETA3 -Specific Antagonist That Does Not Induce Opening within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2007
b:36.1
occ:1.00
|
O
|
C:HOH465
|
2.3
|
8.4
|
1.0
|
|
OD1
|
C:ASP428
|
2.3
|
33.5
|
1.0
|
|
O
|
C:TYR432
|
2.3
|
33.3
|
1.0
|
|
OD1
|
C:ASN430
|
2.4
|
44.7
|
1.0
|
|
OD1
|
C:ASP426
|
2.4
|
41.5
|
1.0
|
|
OD1
|
C:ASP434
|
2.5
|
40.7
|
1.0
|
|
OD2
|
C:ASP434
|
2.6
|
36.0
|
1.0
|
|
CG
|
C:ASP434
|
2.9
|
34.5
|
1.0
|
|
CG
|
C:ASN430
|
3.4
|
43.5
|
1.0
|
|
CG
|
C:ASP428
|
3.4
|
51.8
|
1.0
|
|
CG
|
C:ASP426
|
3.5
|
43.6
|
1.0
|
|
C
|
C:TYR432
|
3.5
|
36.7
|
1.0
|
|
OD2
|
C:ASP428
|
3.9
|
48.9
|
1.0
|
|
ND2
|
C:ASN430
|
4.0
|
34.6
|
1.0
|
|
CA
|
C:ASP426
|
4.2
|
38.6
|
1.0
|
|
N
|
C:ASN430
|
4.2
|
48.3
|
1.0
|
|
N
|
C:TYR432
|
4.2
|
40.6
|
1.0
|
|
O
|
C:ALA450
|
4.3
|
35.4
|
1.0
|
|
CB
|
C:ASP426
|
4.3
|
41.2
|
1.0
|
|
CA
|
C:TYR432
|
4.3
|
39.7
|
1.0
|
|
N
|
C:ASP428
|
4.3
|
43.7
|
1.0
|
|
CB
|
C:ASN430
|
4.4
|
47.0
|
1.0
|
|
N
|
C:ILE427
|
4.4
|
39.4
|
1.0
|
|
CB
|
C:ASP434
|
4.4
|
31.4
|
1.0
|
|
OD2
|
C:ASP426
|
4.4
|
57.8
|
1.0
|
|
CB
|
C:TYR432
|
4.5
|
38.9
|
1.0
|
|
C
|
C:ASP426
|
4.5
|
41.4
|
1.0
|
|
N
|
C:PRO433
|
4.5
|
35.2
|
1.0
|
|
N
|
C:ALA450
|
4.6
|
30.2
|
1.0
|
|
C
|
C:PRO433
|
4.6
|
33.4
|
1.0
|
|
N
|
C:ASP434
|
4.6
|
30.0
|
1.0
|
|
N
|
C:ASP429
|
4.7
|
49.2
|
1.0
|
|
CB
|
C:ASP428
|
4.7
|
42.4
|
1.0
|
|
CA
|
C:PRO433
|
4.7
|
34.7
|
1.0
|
|
CA
|
C:ASN430
|
4.7
|
49.0
|
1.0
|
|
CA
|
C:ASP428
|
4.9
|
43.6
|
1.0
|
|
N
|
C:GLY431
|
4.9
|
49.9
|
1.0
|
|
CB
|
C:ALA450
|
4.9
|
26.6
|
1.0
|
|
C
|
C:ASP428
|
5.0
|
46.9
|
1.0
|
|
CA
|
C:ASP434
|
5.0
|
28.5
|
1.0
|
|
Reference:
J.H.Zhu,
J.Q.Zhu,
A.Negri,
D.Provasi,
M.Filizola,
B.S.Coller,
T.A.Springer.
Closed Headpiece of Integrin {Alpha}Iib{Beta}3 and Its Complex with An {Alpha}Iib{Beta}3-Specific Antagonist That Does Not Induce Opening. Blood V. 116 5050 2010.
ISSN: ISSN 0006-4971
PubMed: 20679525
DOI: 10.1182/BLOOD-2010-04-281154
Page generated: Sat Dec 12 04:22:10 2020
|
