Calcium in PDB 3t3m: A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas
Protein crystallography data
The structure of A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas, PDB code: 3t3m
was solved by
J.Zhu,
J.Zhu,
T.A.Springer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
59.69 /
2.60
|
|
Space group
|
P 21 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
261.150,
145.330,
104.680,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
17.9 /
22.2
|
Other elements in 3t3m:
The structure of A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas 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 A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas
(pdb code 3t3m). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the
A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas, PDB code: 3t3m:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 3t3m
Go back to
Calcium Binding Sites List in 3t3m
Calcium binding site 1 out
of 12 in the A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2004
b:33.8
occ:1.00
|
O
|
A:THR250
|
2.3
|
35.1
|
1.0
|
|
OD2
|
A:ASP245
|
2.3
|
41.6
|
1.0
|
|
OE2
|
A:GLU243
|
2.4
|
26.8
|
1.0
|
|
O
|
A:ASP247
|
2.4
|
57.0
|
1.0
|
|
OG1
|
A:THR250
|
2.4
|
45.6
|
1.0
|
|
OE1
|
A:GLU243
|
2.5
|
28.4
|
1.0
|
|
OE2
|
A:GLU252
|
2.5
|
40.8
|
1.0
|
|
OE1
|
A:GLU252
|
2.5
|
31.3
|
1.0
|
|
CD
|
A:GLU243
|
2.7
|
30.6
|
1.0
|
|
CD
|
A:GLU252
|
2.8
|
35.2
|
1.0
|
|
CG
|
A:ASP245
|
3.0
|
45.8
|
1.0
|
|
C
|
A:THR250
|
3.2
|
42.4
|
1.0
|
|
OD1
|
A:ASP245
|
3.2
|
50.7
|
1.0
|
|
C
|
A:ASP247
|
3.5
|
47.9
|
1.0
|
|
CB
|
A:THR250
|
3.6
|
47.5
|
1.0
|
|
CA
|
A:THR250
|
3.8
|
48.5
|
1.0
|
|
N
|
A:ASP247
|
4.0
|
54.5
|
1.0
|
|
N
|
A:THR250
|
4.0
|
54.0
|
1.0
|
|
N
|
A:THR251
|
4.1
|
48.5
|
1.0
|
|
CA
|
A:ASP247
|
4.2
|
50.1
|
1.0
|
|
CG
|
A:GLU243
|
4.2
|
23.6
|
1.0
|
|
CB
|
A:ASP245
|
4.3
|
44.4
|
1.0
|
|
N
|
A:ASP245
|
4.3
|
44.3
|
1.0
|
|
CB
|
A:ASP247
|
4.4
|
53.5
|
1.0
|
|
CG
|
A:GLU252
|
4.4
|
29.1
|
1.0
|
|
CA
|
A:THR251
|
4.4
|
47.2
|
1.0
|
|
N
|
A:LEU248
|
4.5
|
51.1
|
1.0
|
|
N
|
A:PHE244
|
4.6
|
31.0
|
1.0
|
|
N
|
A:GLY246
|
4.6
|
49.6
|
1.0
|
|
CA
|
A:GLU243
|
4.7
|
29.1
|
1.0
|
|
CA
|
A:ASP245
|
4.7
|
45.0
|
1.0
|
|
CA
|
A:LEU248
|
4.8
|
55.8
|
1.0
|
|
N
|
A:GLU252
|
4.8
|
29.1
|
1.0
|
|
C
|
A:ASP245
|
4.8
|
44.4
|
1.0
|
|
C
|
A:THR251
|
4.8
|
42.4
|
1.0
|
|
CG2
|
A:THR250
|
4.8
|
43.7
|
1.0
|
|
CB
|
A:GLU243
|
4.9
|
26.9
|
1.0
|
|
C
|
A:LEU248
|
4.9
|
55.8
|
1.0
|
|
C
|
A:GLY246
|
5.0
|
53.5
|
1.0
|
|
Calcium binding site 2 out
of 12 in 3t3m
Go back to
Calcium Binding Sites List in 3t3m
Calcium binding site 2 out
of 12 in the A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2005
b:33.1
occ:1.00
|
O
|
A:HOH535
|
2.3
|
29.1
|
1.0
|
|
O
|
A:ARG303
|
2.3
|
29.3
|
1.0
|
|
OD1
|
A:ASN299
|
2.3
|
29.9
|
1.0
|
|
OD1
|
A:ASP297
|
2.3
|
34.9
|
1.0
|
|
OD1
|
A:ASP305
|
2.4
|
30.4
|
1.0
|
|
OD2
|
A:ASP305
|
2.5
|
40.4
|
1.0
|
|
OD1
|
A:ASP301
|
2.5
|
42.5
|
1.0
|
|
CG
|
A:ASP305
|
2.8
|
35.8
|
1.0
|
|
CG
|
A:ASP301
|
3.4
|
33.8
|
1.0
|
|
C
|
A:ARG303
|
3.4
|
33.5
|
1.0
|
|
CG
|
A:ASP297
|
3.5
|
34.9
|
1.0
|
|
CG
|
A:ASN299
|
3.5
|
31.1
|
1.0
|
|
OD2
|
A:ASP301
|
3.7
|
36.4
|
1.0
|
|
ND2
|
A:ASN299
|
4.1
|
30.2
|
1.0
|
|
CA
|
A:ARG303
|
4.1
|
34.3
|
1.0
|
|
N
|
A:ARG303
|
4.1
|
35.4
|
1.0
|
|
CB
|
A:ARG303
|
4.1
|
34.5
|
1.0
|
|
CB
|
A:ASP297
|
4.2
|
23.6
|
1.0
|
|
CB
|
A:ASP305
|
4.2
|
27.3
|
1.0
|
|
CA
|
A:ASP297
|
4.2
|
33.5
|
1.0
|
|
N
|
A:ASN299
|
4.3
|
24.8
|
1.0
|
|
OD2
|
A:ASP297
|
4.3
|
29.7
|
1.0
|
|
N
|
A:VAL298
|
4.3
|
22.8
|
1.0
|
|
C
|
A:HIS304
|
4.4
|
29.9
|
1.0
|
|
N
|
A:ASP305
|
4.5
|
26.5
|
1.0
|
|
N
|
A:HIS304
|
4.5
|
21.6
|
1.0
|
|
O
|
A:HIS304
|
4.6
|
29.2
|
1.0
|
|
C
|
A:ASP297
|
4.7
|
30.4
|
1.0
|
|
CD2
|
A:LEU332
|
4.7
|
27.5
|
1.0
|
|
CB
|
A:ASN299
|
4.7
|
24.7
|
1.0
|
|
N
|
A:ASP301
|
4.7
|
34.1
|
1.0
|
|
CB
|
A:ASP301
|
4.7
|
31.1
|
1.0
|
|
N
|
A:GLN333
|
4.8
|
32.0
|
1.0
|
|
CA
|
A:ASP305
|
4.8
|
26.7
|
1.0
|
|
CA
|
A:HIS304
|
4.8
|
24.6
|
1.0
|
|
CA
|
A:ASN299
|
4.9
|
28.0
|
1.0
|
|
O
|
A:GLN333
|
4.9
|
34.8
|
1.0
|
|
C
|
A:ASN299
|
5.0
|
33.6
|
1.0
|
|
Calcium binding site 3 out
of 12 in 3t3m
Go back to
Calcium Binding Sites List in 3t3m
Calcium binding site 3 out
of 12 in the A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2006
b:24.3
occ:1.00
|
O
|
A:TYR371
|
2.3
|
37.4
|
1.0
|
|
O
|
A:HOH478
|
2.3
|
25.4
|
1.0
|
|
OD2
|
A:ASP365
|
2.4
|
22.1
|
1.0
|
|
OD1
|
A:ASP367
|
2.4
|
19.8
|
1.0
|
|
OD2
|
A:ASP373
|
2.5
|
31.1
|
1.0
|
|
OD1
|
A:ASP373
|
2.5
|
23.9
|
1.0
|
|
OD1
|
A:ASP369
|
2.5
|
30.2
|
1.0
|
|
CG
|
A:ASP373
|
2.8
|
25.2
|
1.0
|
|
CG
|
A:ASP369
|
3.5
|
25.7
|
1.0
|
|
C
|
A:TYR371
|
3.5
|
30.2
|
1.0
|
|
CG
|
A:ASP365
|
3.5
|
28.9
|
1.0
|
|
CG
|
A:ASP367
|
3.5
|
26.8
|
1.0
|
|
OD2
|
A:ASP369
|
3.9
|
26.4
|
1.0
|
|
OD2
|
A:ASP367
|
4.0
|
32.7
|
1.0
|
|
N
|
A:TYR371
|
4.1
|
35.7
|
1.0
|
|
N
|
A:LEU366
|
4.1
|
27.6
|
1.0
|
|
CA
|
A:TYR371
|
4.2
|
31.4
|
1.0
|
|
N
|
A:ASP367
|
4.2
|
24.3
|
1.0
|
|
CA
|
A:ASP365
|
4.2
|
23.5
|
1.0
|
|
CB
|
A:TYR371
|
4.3
|
29.3
|
1.0
|
|
OD1
|
A:ASP365
|
4.3
|
28.2
|
1.0
|
|
CB
|
A:ASP373
|
4.4
|
23.5
|
1.0
|
|
CB
|
A:ASP365
|
4.4
|
20.0
|
1.0
|
|
C
|
A:ASP365
|
4.5
|
19.0
|
1.0
|
|
CD2
|
A:LEU393
|
4.5
|
20.5
|
1.0
|
|
N
|
A:GLY394
|
4.5
|
25.4
|
1.0
|
|
N
|
A:ASP369
|
4.5
|
24.8
|
1.0
|
|
N
|
A:ASN372
|
4.5
|
20.9
|
1.0
|
|
C
|
A:ASN372
|
4.6
|
25.9
|
1.0
|
|
CB
|
A:ASP369
|
4.6
|
31.0
|
1.0
|
|
N
|
A:ARG368
|
4.7
|
30.2
|
1.0
|
|
CA
|
A:ASN372
|
4.8
|
19.1
|
1.0
|
|
CB
|
A:ASP367
|
4.8
|
19.7
|
1.0
|
|
N
|
A:ASP373
|
4.8
|
22.5
|
1.0
|
|
O
|
A:ASN372
|
4.8
|
23.9
|
1.0
|
|
CA
|
A:ASP367
|
4.9
|
19.7
|
1.0
|
|
CB
|
A:LEU393
|
4.9
|
23.3
|
1.0
|
|
O
|
A:GLY394
|
4.9
|
30.1
|
1.0
|
|
C
|
A:ASP367
|
5.0
|
24.4
|
1.0
|
|
Calcium binding site 4 out
of 12 in 3t3m
Go back to
Calcium Binding Sites List in 3t3m
Calcium binding site 4 out
of 12 in the A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2007
b:27.5
occ:1.00
|
O
|
A:TYR432
|
2.3
|
19.2
|
1.0
|
|
OD1
|
A:ASP428
|
2.3
|
23.6
|
1.0
|
|
OD1
|
A:ASP426
|
2.3
|
31.9
|
1.0
|
|
O
|
A:HOH621
|
2.4
|
18.3
|
1.0
|
|
OD1
|
A:ASN430
|
2.4
|
26.3
|
1.0
|
|
OD1
|
A:ASP434
|
2.4
|
34.9
|
1.0
|
|
OD2
|
A:ASP434
|
2.5
|
30.3
|
1.0
|
|
CG
|
A:ASP434
|
2.8
|
27.0
|
1.0
|
|
CG
|
A:ASP428
|
3.3
|
26.3
|
1.0
|
|
CG
|
A:ASN430
|
3.3
|
26.3
|
1.0
|
|
C
|
A:TYR432
|
3.4
|
26.2
|
1.0
|
|
CG
|
A:ASP426
|
3.5
|
25.8
|
1.0
|
|
OD2
|
A:ASP428
|
3.7
|
27.1
|
1.0
|
|
ND2
|
A:ASN430
|
3.9
|
24.4
|
1.0
|
|
N
|
A:TYR432
|
4.1
|
21.0
|
1.0
|
|
CA
|
A:ASP426
|
4.1
|
25.5
|
1.0
|
|
CA
|
A:TYR432
|
4.1
|
20.4
|
1.0
|
|
O
|
A:ALA450
|
4.2
|
19.0
|
1.0
|
|
CB
|
A:TYR432
|
4.3
|
26.8
|
1.0
|
|
CB
|
A:ASP434
|
4.3
|
24.9
|
1.0
|
|
N
|
A:ILE427
|
4.3
|
29.8
|
1.0
|
|
N
|
A:ASP428
|
4.3
|
27.8
|
1.0
|
|
N
|
A:ASN430
|
4.3
|
30.1
|
1.0
|
|
CB
|
A:ASP426
|
4.3
|
18.5
|
1.0
|
|
OD2
|
A:ASP426
|
4.3
|
27.2
|
1.0
|
|
N
|
A:ALA450
|
4.4
|
16.6
|
1.0
|
|
CB
|
A:ASN430
|
4.5
|
23.7
|
1.0
|
|
N
|
A:PRO433
|
4.5
|
27.9
|
1.0
|
|
C
|
A:ASP426
|
4.5
|
26.5
|
1.0
|
|
CB
|
A:ASP428
|
4.6
|
18.8
|
1.0
|
|
C
|
A:PRO433
|
4.6
|
28.2
|
1.0
|
|
N
|
A:ASP429
|
4.6
|
36.7
|
1.0
|
|
N
|
A:ASP434
|
4.7
|
22.4
|
1.0
|
|
CA
|
A:PRO433
|
4.7
|
25.9
|
1.0
|
|
CA
|
A:ASP428
|
4.8
|
24.1
|
1.0
|
|
CA
|
A:ASN430
|
4.8
|
21.4
|
1.0
|
|
O
|
A:PRO433
|
4.9
|
23.9
|
1.0
|
|
CB
|
A:ALA450
|
4.9
|
16.9
|
1.0
|
|
CA
|
A:ASP434
|
4.9
|
24.0
|
1.0
|
|
N
|
A:GLY431
|
4.9
|
31.7
|
1.0
|
|
C
|
A:ASP428
|
4.9
|
27.2
|
1.0
|
|
Calcium binding site 5 out
of 12 in 3t3m
Go back to
Calcium Binding Sites List in 3t3m
Calcium binding site 5 out
of 12 in the A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2002
b:30.9
occ:1.00
|
OD1
|
B:ASP127
|
2.3
|
35.1
|
1.0
|
|
O
|
B:SER123
|
2.4
|
25.6
|
1.0
|
|
O
|
B:HOH503
|
2.4
|
26.0
|
1.0
|
|
O
|
B:HOH517
|
2.4
|
23.6
|
1.0
|
|
OD1
|
B:ASP126
|
2.5
|
37.4
|
1.0
|
|
OD2
|
B:ASP126
|
2.5
|
37.1
|
1.0
|
|
O
|
B:MET335
|
2.5
|
27.4
|
1.0
|
|
CG
|
B:ASP126
|
2.8
|
37.3
|
1.0
|
|
CG
|
B:ASP127
|
3.4
|
35.6
|
1.0
|
|
C
|
B:SER123
|
3.6
|
26.3
|
1.0
|
|
C
|
B:MET335
|
3.7
|
38.8
|
1.0
|
|
OD2
|
B:ASP127
|
3.8
|
31.5
|
1.0
|
|
O
|
B:HOH488
|
4.0
|
31.4
|
1.0
|
|
CA
|
B:MET124
|
4.1
|
25.2
|
1.0
|
|
O
|
B:HOH588
|
4.3
|
63.8
|
1.0
|
|
CB
|
B:ASP126
|
4.3
|
26.8
|
1.0
|
|
N
|
B:MET124
|
4.3
|
26.9
|
1.0
|
|
N
|
B:ASP127
|
4.4
|
28.6
|
1.0
|
|
CA
|
B:ASP336
|
4.4
|
30.4
|
1.0
|
|
OD2
|
B:ASP251
|
4.5
|
31.8
|
1.0
|
|
N
|
B:ASP336
|
4.5
|
31.4
|
1.0
|
|
CB
|
B:ASP127
|
4.6
|
27.7
|
1.0
|
|
C
|
B:MET124
|
4.7
|
25.7
|
1.0
|
|
CA
|
B:MET335
|
4.7
|
35.6
|
1.0
|
|
CA
|
B:SER123
|
4.7
|
18.7
|
1.0
|
|
SD
|
B:MET124
|
4.8
|
29.8
|
1.0
|
|
N
|
B:ASP126
|
4.8
|
31.8
|
1.0
|
|
CA
|
B:ASP126
|
5.0
|
32.5
|
1.0
|
|
Calcium binding site 6 out
of 12 in 3t3m
Go back to
Calcium Binding Sites List in 3t3m
Calcium binding site 6 out
of 12 in the A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2003
b:24.1
occ:1.00
|
OD1
|
B:ASP217
|
2.3
|
21.6
|
1.0
|
|
OE1
|
B:GLU220
|
2.3
|
26.4
|
1.0
|
|
OD2
|
B:ASP158
|
2.4
|
22.1
|
1.0
|
|
O
|
B:PRO219
|
2.4
|
17.7
|
1.0
|
|
O
|
B:ASP217
|
2.4
|
31.4
|
1.0
|
|
OD1
|
B:ASN215
|
2.4
|
21.5
|
1.0
|
|
CG
|
B:ASP217
|
3.2
|
25.8
|
1.0
|
|
C
|
B:ASP217
|
3.4
|
21.6
|
1.0
|
|
CD
|
B:GLU220
|
3.4
|
30.8
|
1.0
|
|
CG
|
B:ASP158
|
3.5
|
22.6
|
1.0
|
|
C
|
B:PRO219
|
3.5
|
22.3
|
1.0
|
|
CG
|
B:ASN215
|
3.5
|
21.2
|
1.0
|
|
OD2
|
B:ASP217
|
3.7
|
26.4
|
1.0
|
|
CB
|
B:ASP158
|
3.9
|
13.5
|
1.0
|
|
ND2
|
B:ASN215
|
4.0
|
15.1
|
1.0
|
|
CA
|
B:GLU220
|
4.0
|
24.7
|
1.0
|
|
CA
|
B:ASP217
|
4.0
|
18.8
|
1.0
|
|
N
|
B:ASP217
|
4.1
|
21.8
|
1.0
|
|
OE2
|
B:GLU220
|
4.1
|
27.3
|
1.0
|
|
NE2
|
B:HIS255
|
4.1
|
27.1
|
1.0
|
|
N
|
B:GLU220
|
4.1
|
22.8
|
1.0
|
|
CB
|
B:ASP217
|
4.2
|
25.9
|
1.0
|
|
C
|
B:ALA218
|
4.2
|
29.6
|
1.0
|
|
O
|
B:ALA218
|
4.3
|
27.9
|
1.0
|
|
N
|
B:PRO219
|
4.4
|
22.9
|
1.0
|
|
N
|
B:ALA218
|
4.4
|
20.2
|
1.0
|
|
CD2
|
B:HIS255
|
4.4
|
18.4
|
1.0
|
|
CG
|
B:GLU220
|
4.5
|
30.5
|
1.0
|
|
CA
|
B:PRO219
|
4.5
|
18.7
|
1.0
|
|
OD1
|
B:ASP158
|
4.5
|
19.8
|
1.0
|
|
CB
|
B:GLU220
|
4.7
|
26.5
|
1.0
|
|
CB
|
B:ASN215
|
4.8
|
22.9
|
1.0
|
|
CA
|
B:ALA218
|
4.8
|
20.4
|
1.0
|
|
C12
|
A:RC25000
|
4.9
|
22.2
|
1.0
|
|
CD1
|
B:TYR164
|
4.9
|
25.1
|
1.0
|
|
CB
|
B:TYR164
|
4.9
|
23.0
|
1.0
|
|
C
|
B:GLU220
|
5.0
|
27.0
|
1.0
|
|
Calcium binding site 7 out
of 12 in 3t3m
Go back to
Calcium Binding Sites List in 3t3m
Calcium binding site 7 out
of 12 in the A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2004
b:67.1
occ:1.00
|
OD2
|
C:ASP245
|
2.3
|
58.3
|
1.0
|
|
O
|
C:ASP247
|
2.3
|
78.3
|
1.0
|
|
O
|
C:THR250
|
2.4
|
53.9
|
1.0
|
|
OE2
|
C:GLU243
|
2.4
|
66.0
|
1.0
|
|
OE2
|
C:GLU252
|
2.4
|
64.7
|
1.0
|
|
OG1
|
C:THR250
|
2.4
|
64.0
|
1.0
|
|
OE1
|
C:GLU243
|
2.5
|
59.4
|
1.0
|
|
OE1
|
C:GLU252
|
2.5
|
61.3
|
1.0
|
|
CD
|
C:GLU243
|
2.7
|
60.4
|
1.0
|
|
CD
|
C:GLU252
|
2.8
|
64.3
|
1.0
|
|
C
|
C:THR250
|
3.0
|
56.9
|
1.0
|
|
CG
|
C:ASP245
|
3.1
|
64.8
|
1.0
|
|
OD1
|
C:ASP245
|
3.3
|
66.7
|
1.0
|
|
C
|
C:ASP247
|
3.4
|
77.5
|
1.0
|
|
CB
|
C:THR250
|
3.5
|
60.6
|
1.0
|
|
CA
|
C:THR250
|
3.6
|
58.9
|
1.0
|
|
N
|
C:THR250
|
3.8
|
66.0
|
1.0
|
|
N
|
C:THR251
|
3.9
|
68.5
|
1.0
|
|
CA
|
C:ASP247
|
4.2
|
78.5
|
1.0
|
|
N
|
C:ASP247
|
4.2
|
80.8
|
1.0
|
|
CG
|
C:GLU243
|
4.2
|
56.2
|
1.0
|
|
CA
|
C:THR251
|
4.2
|
67.8
|
1.0
|
|
CG
|
C:GLU252
|
4.3
|
57.8
|
1.0
|
|
CB
|
C:ASP247
|
4.3
|
80.3
|
1.0
|
|
O
|
C:HOH659
|
4.4
|
67.3
|
1.0
|
|
N
|
C:LEU248
|
4.4
|
73.2
|
1.0
|
|
CB
|
C:ASP245
|
4.4
|
63.5
|
1.0
|
|
N
|
C:ASP245
|
4.5
|
64.7
|
1.0
|
|
N
|
C:GLU252
|
4.6
|
55.2
|
1.0
|
|
CA
|
C:LEU248
|
4.6
|
70.7
|
1.0
|
|
O
|
C:HOH556
|
4.7
|
54.8
|
1.0
|
|
C
|
C:THR251
|
4.7
|
63.5
|
1.0
|
|
CA
|
C:GLU243
|
4.7
|
57.5
|
1.0
|
|
C
|
C:LEU248
|
4.7
|
70.7
|
1.0
|
|
N
|
C:PHE244
|
4.7
|
68.6
|
1.0
|
|
N
|
C:GLY246
|
4.7
|
96.1
|
1.0
|
|
CG2
|
C:THR250
|
4.8
|
63.7
|
1.0
|
|
CA
|
C:ASP245
|
4.8
|
65.5
|
1.0
|
|
C
|
C:GLY246
|
4.9
|
0.4
|
1.0
|
|
CB
|
C:GLU243
|
4.9
|
55.8
|
1.0
|
|
C
|
C:ASP245
|
4.9
|
68.8
|
1.0
|
|
N
|
C:ASN249
|
5.0
|
90.0
|
1.0
|
|
Calcium binding site 8 out
of 12 in 3t3m
Go back to
Calcium Binding Sites List in 3t3m
Calcium binding site 8 out
of 12 in the A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2005
b:48.3
occ:1.00
|
O
|
C:ARG303
|
2.3
|
63.1
|
1.0
|
|
O
|
C:HOH768
|
2.3
|
48.5
|
1.0
|
|
OD1
|
C:ASN299
|
2.3
|
54.3
|
1.0
|
|
OD1
|
C:ASP297
|
2.4
|
54.6
|
1.0
|
|
OD2
|
C:ASP305
|
2.5
|
55.2
|
1.0
|
|
OD1
|
C:ASP305
|
2.5
|
48.3
|
1.0
|
|
OD1
|
C:ASP301
|
2.5
|
60.7
|
1.0
|
|
CG
|
C:ASP305
|
2.8
|
51.7
|
1.0
|
|
CG
|
C:ASP301
|
3.2
|
61.7
|
1.0
|
|
OD2
|
C:ASP301
|
3.3
|
66.5
|
1.0
|
|
C
|
C:ARG303
|
3.4
|
66.8
|
1.0
|
|
CG
|
C:ASN299
|
3.4
|
51.0
|
1.0
|
|
CG
|
C:ASP297
|
3.5
|
58.0
|
1.0
|
|
ND2
|
C:ASN299
|
3.9
|
52.7
|
1.0
|
|
N
|
C:ARG303
|
4.0
|
64.2
|
1.0
|
|
CA
|
C:ARG303
|
4.0
|
67.0
|
1.0
|
|
CB
|
C:ARG303
|
4.1
|
68.0
|
1.0
|
|
CA
|
C:ASP297
|
4.2
|
55.6
|
1.0
|
|
CB
|
C:ASP297
|
4.2
|
56.7
|
1.0
|
|
CB
|
C:ASP305
|
4.3
|
43.6
|
1.0
|
|
N
|
C:ASN299
|
4.4
|
47.7
|
1.0
|
|
OD2
|
C:ASP297
|
4.4
|
60.4
|
1.0
|
|
N
|
C:ASP305
|
4.4
|
51.4
|
1.0
|
|
C
|
C:HIS304
|
4.4
|
50.8
|
1.0
|
|
N
|
C:VAL298
|
4.5
|
59.9
|
1.0
|
|
N
|
C:HIS304
|
4.5
|
61.1
|
1.0
|
|
N
|
C:ASP301
|
4.5
|
61.0
|
1.0
|
|
CB
|
C:ASP301
|
4.5
|
59.5
|
1.0
|
|
CD2
|
C:LEU332
|
4.6
|
63.2
|
1.0
|
|
C
|
C:ASP297
|
4.6
|
55.5
|
1.0
|
|
CB
|
C:ASN299
|
4.7
|
47.1
|
1.0
|
|
O
|
C:HIS304
|
4.7
|
51.9
|
1.0
|
|
N
|
C:GLY302
|
4.8
|
58.6
|
1.0
|
|
CA
|
C:HIS304
|
4.8
|
51.0
|
1.0
|
|
CA
|
C:ASP305
|
4.8
|
49.2
|
1.0
|
|
CA
|
C:ASN299
|
4.9
|
50.1
|
1.0
|
|
N
|
C:GLY300
|
4.9
|
65.0
|
1.0
|
|
CA
|
C:ASP301
|
4.9
|
60.2
|
1.0
|
|
C
|
C:ASN299
|
5.0
|
52.0
|
1.0
|
|
N
|
C:GLN333
|
5.0
|
45.4
|
1.0
|
|
Calcium binding site 9 out
of 12 in 3t3m
Go back to
Calcium Binding Sites List in 3t3m
Calcium binding site 9 out
of 12 in the A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2006
b:45.2
occ:1.00
|
O
|
C:TYR371
|
2.3
|
56.1
|
1.0
|
|
O
|
C:HOH654
|
2.3
|
38.0
|
1.0
|
|
OD1
|
C:ASP367
|
2.3
|
55.2
|
1.0
|
|
OD2
|
C:ASP365
|
2.4
|
49.8
|
1.0
|
|
OD1
|
C:ASP369
|
2.5
|
58.7
|
1.0
|
|
OD1
|
C:ASP373
|
2.5
|
50.4
|
1.0
|
|
OD2
|
C:ASP373
|
2.6
|
47.8
|
1.0
|
|
CG
|
C:ASP373
|
2.9
|
48.3
|
1.0
|
|
CG
|
C:ASP369
|
3.3
|
58.6
|
1.0
|
|
C
|
C:TYR371
|
3.4
|
59.4
|
1.0
|
|
CG
|
C:ASP367
|
3.5
|
51.8
|
1.0
|
|
CG
|
C:ASP365
|
3.5
|
49.1
|
1.0
|
|
OD2
|
C:ASP369
|
3.6
|
57.8
|
1.0
|
|
OD2
|
C:ASP367
|
4.0
|
50.8
|
1.0
|
|
N
|
C:TYR371
|
4.1
|
62.8
|
1.0
|
|
N
|
C:ASP367
|
4.2
|
51.6
|
1.0
|
|
CA
|
C:TYR371
|
4.2
|
55.3
|
1.0
|
|
N
|
C:LEU366
|
4.2
|
50.8
|
1.0
|
|
CA
|
C:ASP365
|
4.2
|
43.0
|
1.0
|
|
OD1
|
C:ASP365
|
4.2
|
52.9
|
1.0
|
|
CB
|
C:TYR371
|
4.3
|
56.3
|
1.0
|
|
CB
|
C:ASP373
|
4.4
|
42.9
|
1.0
|
|
CB
|
C:ASP365
|
4.4
|
41.4
|
1.0
|
|
C
|
C:ASP365
|
4.4
|
47.1
|
1.0
|
|
N
|
C:ASP369
|
4.4
|
59.2
|
1.0
|
|
N
|
C:ASN372
|
4.5
|
54.9
|
1.0
|
|
C
|
C:ASN372
|
4.6
|
51.4
|
1.0
|
|
N
|
C:ARG368
|
4.6
|
65.2
|
1.0
|
|
CB
|
C:ASP369
|
4.6
|
54.3
|
1.0
|
|
N
|
C:GLY394
|
4.6
|
47.5
|
1.0
|
|
CD2
|
C:LEU393
|
4.7
|
41.5
|
1.0
|
|
CB
|
C:ASP367
|
4.7
|
50.2
|
1.0
|
|
CA
|
C:ASN372
|
4.7
|
50.2
|
1.0
|
|
N
|
C:ASP373
|
4.7
|
47.0
|
1.0
|
|
CA
|
C:ASP367
|
4.8
|
53.1
|
1.0
|
|
O
|
C:ASN372
|
4.8
|
53.1
|
1.0
|
|
C
|
C:ASP367
|
4.9
|
57.5
|
1.0
|
|
O
|
C:GLY394
|
4.9
|
46.6
|
1.0
|
|
N
|
C:GLY370
|
5.0
|
58.7
|
1.0
|
|
Calcium binding site 10 out
of 12 in 3t3m
Go back to
Calcium Binding Sites List in 3t3m
Calcium binding site 10 out
of 12 in the A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of A Novel High Affinity Integrin ALPHAIIBBETA3 Receptor Antagonist That Unexpectedly Displaces MG2+ From the BETA3 Midas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2007
b:44.9
occ:1.00
|
OD1
|
C:ASP428
|
2.3
|
43.8
|
1.0
|
|
O
|
C:TYR432
|
2.3
|
44.9
|
1.0
|
|
OD1
|
C:ASP426
|
2.3
|
51.1
|
1.0
|
|
OD1
|
C:ASN430
|
2.4
|
50.4
|
1.0
|
|
O
|
C:HOH475
|
2.4
|
45.4
|
1.0
|
|
OD2
|
C:ASP434
|
2.4
|
43.7
|
1.0
|
|
OD1
|
C:ASP434
|
2.5
|
44.2
|
1.0
|
|
CG
|
C:ASP434
|
2.8
|
41.8
|
1.0
|
|
CG
|
C:ASN430
|
3.3
|
45.1
|
1.0
|
|
CG
|
C:ASP428
|
3.4
|
49.6
|
1.0
|
|
CG
|
C:ASP426
|
3.4
|
47.6
|
1.0
|
|
C
|
C:TYR432
|
3.5
|
47.0
|
1.0
|
|
OD2
|
C:ASP428
|
3.8
|
44.9
|
1.0
|
|
ND2
|
C:ASN430
|
4.0
|
40.4
|
1.0
|
|
CA
|
C:ASP426
|
4.1
|
43.9
|
1.0
|
|
CB
|
C:ASP426
|
4.2
|
45.3
|
1.0
|
|
O
|
C:ALA450
|
4.2
|
50.4
|
1.0
|
|
CA
|
C:TYR432
|
4.2
|
44.3
|
1.0
|
|
N
|
C:TYR432
|
4.2
|
50.7
|
1.0
|
|
CB
|
C:ASP434
|
4.2
|
32.3
|
1.0
|
|
OD2
|
C:ASP426
|
4.2
|
51.8
|
1.0
|
|
N
|
C:ASN430
|
4.3
|
50.5
|
1.0
|
|
CB
|
C:ASN430
|
4.3
|
46.2
|
1.0
|
|
CB
|
C:TYR432
|
4.3
|
45.9
|
1.0
|
|
N
|
C:ASP428
|
4.3
|
47.6
|
1.0
|
|
N
|
C:ALA450
|
4.4
|
41.8
|
1.0
|
|
N
|
C:ILE427
|
4.4
|
56.7
|
1.0
|
|
C
|
C:ASP426
|
4.4
|
46.0
|
1.0
|
|
N
|
C:PRO433
|
4.5
|
47.7
|
1.0
|
|
C
|
C:PRO433
|
4.5
|
43.3
|
1.0
|
|
N
|
C:ASP434
|
4.5
|
35.7
|
1.0
|
|
CB
|
C:ASP428
|
4.6
|
45.2
|
1.0
|
|
N
|
C:ASP429
|
4.7
|
72.8
|
1.0
|
|
CA
|
C:PRO433
|
4.7
|
45.6
|
1.0
|
|
CA
|
C:ASN430
|
4.8
|
46.9
|
1.0
|
|
CB
|
C:ALA450
|
4.8
|
42.9
|
1.0
|
|
O
|
C:PRO433
|
4.8
|
37.5
|
1.0
|
|
CA
|
C:ASP434
|
4.9
|
31.0
|
1.0
|
|
CA
|
C:ASP428
|
4.9
|
44.5
|
1.0
|
|
C
|
C:ASP428
|
4.9
|
51.0
|
1.0
|
|
CA
|
C:ALA450
|
5.0
|
41.5
|
1.0
|
|
Reference:
J.Zhu,
W.S.Choi,
J.G.Mccoy,
A.Negri,
J.Zhu,
S.Naini,
J.Li,
M.Shen,
W.Huang,
D.Bougie,
M.Rasmussen,
R.Aster,
C.J.Thomas,
M.Filizola,
T.A.Springer,
B.S.Coller.
Structure-Guided Design of A High-Affinity Platelet Integrin ALPHAIIBBETA3 Receptor Antagonist That Disrupts MG2+ Binding to the Midas Sci Transl Med V. 4 5RA32 2012.
ISSN: ISSN 1946-6234
PubMed: 22422993
DOI: 10.1126/SCITRANSLMED.3003576
Page generated: Sat Dec 12 04:31:03 2020
|
