Calcium in PDB 3vi4: Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide
Protein crystallography data
The structure of Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide, PDB code: 3vi4
was solved by
M.Nagae,
T.Nogi,
J.Takagi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
100.00 /
2.90
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.805,
103.869,
125.262,
75.72,
70.16,
70.90
|
|
R / Rfree (%)
|
21.5 /
27.5
|
Other elements in 3vi4:
The structure of Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide
(pdb code 3vi4). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the
Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide, PDB code: 3vi4:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 3vi4
Go back to
Calcium Binding Sites List in 3vi4
Calcium binding site 1 out
of 10 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2001
b:69.6
occ:1.00
|
O
|
A:THR245
|
2.3
|
68.4
|
1.0
|
|
OG
|
A:SER241
|
2.3
|
68.2
|
1.0
|
|
OD1
|
A:ASP243
|
2.3
|
79.0
|
1.0
|
|
OE2
|
A:GLU239
|
2.3
|
64.7
|
1.0
|
|
OD2
|
A:ASP247
|
2.3
|
66.9
|
1.0
|
|
OD1
|
A:ASP247
|
2.9
|
69.5
|
1.0
|
|
CG
|
A:ASP247
|
2.9
|
64.5
|
1.0
|
|
OE1
|
A:GLU239
|
3.0
|
67.4
|
1.0
|
|
CD
|
A:GLU239
|
3.0
|
64.0
|
1.0
|
|
CG
|
A:ASP243
|
3.1
|
78.5
|
1.0
|
|
OD2
|
A:ASP243
|
3.4
|
81.4
|
1.0
|
|
C
|
A:THR245
|
3.5
|
67.3
|
1.0
|
|
CB
|
A:SER241
|
3.7
|
67.4
|
1.0
|
|
OG1
|
A:THR245
|
3.9
|
85.0
|
1.0
|
|
N
|
A:THR245
|
4.0
|
69.8
|
1.0
|
|
OD1
|
A:ASN266
|
4.2
|
67.2
|
1.0
|
|
CA
|
A:THR245
|
4.2
|
70.7
|
1.0
|
|
CB
|
A:ASP247
|
4.3
|
60.3
|
1.0
|
|
N
|
A:ASP247
|
4.4
|
67.3
|
1.0
|
|
CB
|
A:ASP243
|
4.4
|
71.0
|
1.0
|
|
C
|
A:ASP243
|
4.4
|
68.6
|
1.0
|
|
C
|
A:GLU246
|
4.5
|
66.9
|
1.0
|
|
N
|
A:ASP244
|
4.5
|
69.5
|
1.0
|
|
CG
|
A:GLU239
|
4.5
|
59.6
|
1.0
|
|
N
|
A:GLU246
|
4.5
|
65.3
|
1.0
|
|
N
|
A:SER241
|
4.5
|
64.1
|
1.0
|
|
N
|
A:ASP243
|
4.5
|
70.9
|
1.0
|
|
CA
|
A:SER241
|
4.6
|
65.9
|
1.0
|
|
CA
|
A:ASP243
|
4.6
|
68.7
|
1.0
|
|
CB
|
A:THR245
|
4.7
|
75.0
|
1.0
|
|
N
|
A:GLY267
|
4.7
|
57.2
|
1.0
|
|
CA
|
A:GLU246
|
4.7
|
65.0
|
1.0
|
|
O
|
A:ASP243
|
4.7
|
68.2
|
1.0
|
|
C
|
A:SER241
|
4.8
|
69.9
|
1.0
|
|
CA
|
A:ASP247
|
4.8
|
62.2
|
1.0
|
|
O
|
A:GLU246
|
4.9
|
65.6
|
1.0
|
|
O
|
A:SER241
|
4.9
|
72.8
|
1.0
|
|
C
|
A:ASP244
|
4.9
|
69.8
|
1.0
|
|
Calcium binding site 2 out
of 10 in 3vi4
Go back to
Calcium Binding Sites List in 3vi4
Calcium binding site 2 out
of 10 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2002
b:81.7
occ:1.00
|
OD1
|
A:ASN295
|
2.3
|
72.1
|
1.0
|
|
OD2
|
A:ASP293
|
2.3
|
72.3
|
1.0
|
|
O
|
A:LEU299
|
2.3
|
79.0
|
1.0
|
|
OD1
|
A:ASP301
|
2.3
|
73.9
|
1.0
|
|
OD1
|
A:ASP297
|
2.7
|
71.8
|
1.0
|
|
OD2
|
A:ASP301
|
2.7
|
74.8
|
1.0
|
|
CG
|
A:ASP301
|
2.8
|
74.3
|
1.0
|
|
CG
|
A:ASN295
|
3.1
|
67.1
|
1.0
|
|
ND2
|
A:ASN295
|
3.2
|
66.7
|
1.0
|
|
C
|
A:LEU299
|
3.4
|
78.3
|
1.0
|
|
CG
|
A:ASP293
|
3.5
|
75.8
|
1.0
|
|
O
|
A:ASP297
|
3.6
|
82.7
|
1.0
|
|
CG
|
A:ASP297
|
3.8
|
74.8
|
1.0
|
|
O
|
A:GLN329
|
3.8
|
71.5
|
1.0
|
|
CB
|
A:LEU299
|
3.9
|
71.2
|
1.0
|
|
CA
|
A:LEU299
|
4.1
|
78.9
|
1.0
|
|
N
|
A:LEU299
|
4.2
|
86.3
|
1.0
|
|
OD2
|
A:ASP297
|
4.3
|
77.1
|
1.0
|
|
CB
|
A:ASP301
|
4.3
|
69.9
|
1.0
|
|
CB
|
A:ASP293
|
4.4
|
74.2
|
1.0
|
|
OD1
|
A:ASP293
|
4.4
|
82.2
|
1.0
|
|
C
|
A:ASP300
|
4.4
|
75.1
|
1.0
|
|
CA
|
A:ASP293
|
4.5
|
72.3
|
1.0
|
|
N
|
A:ASP300
|
4.5
|
77.3
|
1.0
|
|
N
|
A:ASP301
|
4.5
|
70.5
|
1.0
|
|
CB
|
A:ASN295
|
4.6
|
68.8
|
1.0
|
|
CD2
|
A:LEU328
|
4.6
|
55.4
|
1.0
|
|
O
|
A:ASP300
|
4.6
|
73.2
|
1.0
|
|
N
|
A:GLN329
|
4.6
|
64.3
|
1.0
|
|
C
|
A:ASP297
|
4.7
|
80.4
|
1.0
|
|
N
|
A:ASN295
|
4.7
|
67.7
|
1.0
|
|
N
|
A:VAL294
|
4.7
|
72.4
|
1.0
|
|
CA
|
A:ASP300
|
4.8
|
75.9
|
1.0
|
|
CA
|
A:ASP301
|
4.9
|
67.1
|
1.0
|
|
C
|
A:GLN329
|
4.9
|
69.0
|
1.0
|
|
Calcium binding site 3 out
of 10 in 3vi4
Go back to
Calcium Binding Sites List in 3vi4
Calcium binding site 3 out
of 10 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2003
b:73.5
occ:1.00
|
O
|
A:TYR366
|
2.3
|
66.0
|
1.0
|
|
OD1
|
A:ASP362
|
2.3
|
77.4
|
1.0
|
|
OD2
|
A:ASP364
|
2.3
|
65.9
|
1.0
|
|
OD2
|
A:ASP368
|
2.3
|
75.9
|
1.0
|
|
OD2
|
A:ASP360
|
2.3
|
77.4
|
1.0
|
|
OD1
|
A:ASP368
|
2.9
|
73.8
|
1.0
|
|
CG
|
A:ASP368
|
2.9
|
73.5
|
1.0
|
|
C
|
A:TYR366
|
3.3
|
69.3
|
1.0
|
|
CG
|
A:ASP362
|
3.4
|
78.5
|
1.0
|
|
CG
|
A:ASP364
|
3.4
|
66.2
|
1.0
|
|
CG
|
A:ASP360
|
3.4
|
79.6
|
1.0
|
|
CB
|
A:TYR366
|
3.8
|
71.8
|
1.0
|
|
OD2
|
A:ASP362
|
3.8
|
79.9
|
1.0
|
|
CA
|
A:TYR366
|
3.8
|
71.5
|
1.0
|
|
OD1
|
A:ASP364
|
3.9
|
64.0
|
1.0
|
|
N
|
A:TYR366
|
3.9
|
74.8
|
1.0
|
|
OD1
|
A:ASP360
|
4.2
|
77.9
|
1.0
|
|
N
|
A:ASP362
|
4.3
|
82.7
|
1.0
|
|
N
|
A:LEU361
|
4.3
|
74.2
|
1.0
|
|
CA
|
A:ASP360
|
4.4
|
77.5
|
1.0
|
|
N
|
A:ASN367
|
4.4
|
70.7
|
1.0
|
|
CB
|
A:ASP360
|
4.4
|
78.5
|
1.0
|
|
CB
|
A:ASP368
|
4.4
|
71.3
|
1.0
|
|
O
|
A:GLY389
|
4.5
|
62.5
|
1.0
|
|
N
|
A:ASP364
|
4.5
|
72.7
|
1.0
|
|
N
|
A:ASP368
|
4.5
|
67.4
|
1.0
|
|
C
|
A:ASP360
|
4.6
|
75.2
|
1.0
|
|
C
|
A:ASN367
|
4.6
|
69.8
|
1.0
|
|
CB
|
A:ASP364
|
4.6
|
69.8
|
1.0
|
|
N
|
A:GLY389
|
4.7
|
65.5
|
1.0
|
|
CA
|
A:ASN367
|
4.7
|
70.2
|
1.0
|
|
CB
|
A:ASP362
|
4.7
|
77.2
|
1.0
|
|
CA
|
A:ASP362
|
4.9
|
80.4
|
1.0
|
|
N
|
A:GLN363
|
4.9
|
79.3
|
1.0
|
|
CA
|
A:ASP364
|
4.9
|
69.1
|
1.0
|
|
C
|
A:ASP362
|
4.9
|
82.9
|
1.0
|
|
CA
|
A:ASP368
|
5.0
|
67.1
|
1.0
|
|
Calcium binding site 4 out
of 10 in 3vi4
Go back to
Calcium Binding Sites List in 3vi4
Calcium binding site 4 out
of 10 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2004
b:81.1
occ:1.00
|
OD1
|
A:ASP426
|
2.3
|
92.0
|
1.0
|
|
O
|
A:TYR430
|
2.3
|
77.8
|
1.0
|
|
OD1
|
A:ASP424
|
2.3
|
80.9
|
1.0
|
|
OD2
|
A:ASP432
|
2.3
|
76.6
|
1.0
|
|
OD1
|
A:ASN428
|
2.3
|
93.0
|
1.0
|
|
OD1
|
A:ASP432
|
2.8
|
79.8
|
1.0
|
|
CG
|
A:ASP432
|
2.9
|
75.8
|
1.0
|
|
CG
|
A:ASP426
|
2.9
|
92.7
|
1.0
|
|
OD2
|
A:ASP426
|
3.1
|
87.4
|
1.0
|
|
CG
|
A:ASN428
|
3.4
|
94.1
|
1.0
|
|
CG
|
A:ASP424
|
3.4
|
86.1
|
1.0
|
|
C
|
A:TYR430
|
3.5
|
74.7
|
1.0
|
|
O
|
A:ASN428
|
3.7
|
91.0
|
1.0
|
|
ND2
|
A:ASN428
|
3.9
|
90.9
|
1.0
|
|
N
|
A:ASP426
|
4.0
|
96.0
|
1.0
|
|
OD2
|
A:ASP424
|
4.1
|
89.5
|
1.0
|
|
CB
|
A:ASP426
|
4.2
|
92.6
|
1.0
|
|
N
|
A:TYR430
|
4.3
|
75.0
|
1.0
|
|
CA
|
A:TYR430
|
4.3
|
78.0
|
1.0
|
|
O
|
A:GLY448
|
4.3
|
98.6
|
1.0
|
|
N
|
A:LEU425
|
4.3
|
84.8
|
1.0
|
|
CA
|
A:ASP424
|
4.3
|
78.2
|
1.0
|
|
CB
|
A:TYR430
|
4.4
|
84.1
|
1.0
|
|
CB
|
A:ASP432
|
4.4
|
71.1
|
1.0
|
|
C
|
A:PRO431
|
4.4
|
66.9
|
1.0
|
|
N
|
A:GLY448
|
4.4
|
80.2
|
1.0
|
|
CA
|
A:ASP426
|
4.5
|
94.0
|
1.0
|
|
CB
|
A:ASP424
|
4.5
|
80.7
|
1.0
|
|
N
|
A:PRO431
|
4.5
|
71.2
|
1.0
|
|
C
|
A:ASN428
|
4.6
|
85.8
|
1.0
|
|
N
|
A:ASP432
|
4.6
|
67.0
|
1.0
|
|
C
|
A:ASP424
|
4.6
|
79.0
|
1.0
|
|
O
|
A:PRO431
|
4.6
|
69.7
|
1.0
|
|
CA
|
A:PRO431
|
4.6
|
68.8
|
1.0
|
|
C
|
A:ASP426
|
4.7
|
93.4
|
1.0
|
|
CB
|
A:ASN428
|
4.7
|
92.5
|
1.0
|
|
O
|
A:ASP426
|
4.7
|
82.4
|
1.0
|
|
CA
|
A:GLY448
|
4.8
|
84.1
|
1.0
|
|
N
|
A:ASN428
|
4.9
|
92.3
|
1.0
|
|
CA
|
A:ASN428
|
4.9
|
88.7
|
1.0
|
|
CA
|
A:ASP432
|
5.0
|
67.9
|
1.0
|
|
Calcium binding site 5 out
of 10 in 3vi4
Go back to
Calcium Binding Sites List in 3vi4
Calcium binding site 5 out
of 10 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca501
b:59.0
occ:1.00
|
O
|
B:PRO228
|
2.3
|
56.8
|
1.0
|
|
OD1
|
B:ASN224
|
2.3
|
66.3
|
1.0
|
|
OE1
|
B:GLU169
|
2.3
|
52.7
|
1.0
|
|
O
|
B:ASP226
|
2.3
|
53.2
|
1.0
|
|
OE2
|
B:GLU229
|
2.3
|
58.7
|
1.0
|
|
OD1
|
B:ASP226
|
2.6
|
59.2
|
1.0
|
|
CG
|
B:ASN224
|
3.2
|
69.3
|
1.0
|
|
CD
|
B:GLU169
|
3.4
|
55.5
|
1.0
|
|
ND2
|
B:ASN224
|
3.4
|
71.1
|
1.0
|
|
C
|
B:ASP226
|
3.4
|
58.6
|
1.0
|
|
C
|
B:PRO228
|
3.4
|
54.6
|
1.0
|
|
CD
|
B:GLU229
|
3.5
|
55.4
|
1.0
|
|
CG
|
B:GLU169
|
3.7
|
54.1
|
1.0
|
|
CG
|
B:ASP226
|
3.8
|
57.8
|
1.0
|
|
CA
|
B:GLU229
|
3.8
|
50.7
|
1.0
|
|
O
|
B:SER227
|
4.0
|
63.4
|
1.0
|
|
N
|
B:GLU229
|
4.1
|
52.0
|
1.0
|
|
N
|
B:ASP226
|
4.1
|
57.4
|
1.0
|
|
CA
|
B:ASP226
|
4.1
|
57.8
|
1.0
|
|
C
|
B:SER227
|
4.2
|
60.4
|
1.0
|
|
CE1
|
B:HIS263
|
4.2
|
44.2
|
1.0
|
|
CB
|
B:GLU169
|
4.2
|
53.2
|
1.0
|
|
OE1
|
B:GLU229
|
4.3
|
60.1
|
1.0
|
|
N
|
B:PRO228
|
4.4
|
57.2
|
1.0
|
|
CG
|
B:GLU229
|
4.5
|
53.8
|
1.0
|
|
OE2
|
B:GLU169
|
4.5
|
56.8
|
1.0
|
|
N
|
B:SER227
|
4.5
|
59.0
|
1.0
|
|
CB
|
B:GLU229
|
4.5
|
50.2
|
1.0
|
|
CB
|
B:ASP226
|
4.5
|
57.9
|
1.0
|
|
CA
|
B:PRO228
|
4.6
|
56.8
|
1.0
|
|
CB
|
B:ASN224
|
4.6
|
65.6
|
1.0
|
|
OD2
|
B:ASP226
|
4.7
|
56.6
|
1.0
|
|
O
|
B:TYR175
|
4.7
|
50.2
|
1.0
|
|
ND1
|
B:HIS263
|
4.7
|
43.9
|
1.0
|
|
CA
|
B:SER227
|
4.8
|
60.7
|
1.0
|
|
C
|
B:GLU229
|
4.9
|
49.5
|
1.0
|
|
CD
|
B:PRO228
|
4.9
|
56.8
|
1.0
|
|
N
|
B:LEU225
|
4.9
|
63.8
|
1.0
|
|
C
|
B:LEU225
|
4.9
|
57.8
|
1.0
|
|
Calcium binding site 6 out
of 10 in 3vi4
Go back to
Calcium Binding Sites List in 3vi4
Calcium binding site 6 out
of 10 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2001
b:59.0
occ:1.00
|
O
|
C:THR245
|
2.3
|
58.7
|
1.0
|
|
OG
|
C:SER241
|
2.3
|
62.2
|
1.0
|
|
OD1
|
C:ASP243
|
2.3
|
69.5
|
1.0
|
|
OE2
|
C:GLU239
|
2.3
|
53.8
|
1.0
|
|
OD2
|
C:ASP247
|
2.3
|
64.0
|
1.0
|
|
OE1
|
C:GLU239
|
2.9
|
58.9
|
1.0
|
|
CD
|
C:GLU239
|
2.9
|
55.2
|
1.0
|
|
CG
|
C:ASP247
|
2.9
|
64.4
|
1.0
|
|
OD1
|
C:ASP247
|
3.0
|
70.5
|
1.0
|
|
CG
|
C:ASP243
|
3.0
|
66.1
|
1.0
|
|
OD2
|
C:ASP243
|
3.2
|
66.2
|
1.0
|
|
C
|
C:THR245
|
3.5
|
57.9
|
1.0
|
|
CB
|
C:SER241
|
3.7
|
62.0
|
1.0
|
|
OG1
|
C:THR245
|
3.9
|
62.5
|
1.0
|
|
N
|
C:SER241
|
4.3
|
59.3
|
1.0
|
|
N
|
C:THR245
|
4.3
|
61.6
|
1.0
|
|
CB
|
C:ASP247
|
4.3
|
59.7
|
1.0
|
|
CA
|
C:THR245
|
4.4
|
59.7
|
1.0
|
|
N
|
C:ASP247
|
4.4
|
58.0
|
1.0
|
|
CB
|
C:ASP243
|
4.4
|
58.5
|
1.0
|
|
C
|
C:GLU246
|
4.4
|
56.0
|
1.0
|
|
CG
|
C:GLU239
|
4.4
|
52.6
|
1.0
|
|
CA
|
C:SER241
|
4.5
|
61.2
|
1.0
|
|
N
|
C:GLU246
|
4.5
|
53.5
|
1.0
|
|
OD1
|
C:ASN266
|
4.5
|
58.3
|
1.0
|
|
CA
|
C:GLU246
|
4.6
|
54.9
|
1.0
|
|
N
|
C:ASP243
|
4.6
|
59.6
|
1.0
|
|
N
|
C:GLY267
|
4.7
|
53.1
|
1.0
|
|
C
|
C:ASP243
|
4.7
|
55.1
|
1.0
|
|
C
|
C:SER241
|
4.7
|
62.2
|
1.0
|
|
CB
|
C:THR245
|
4.7
|
60.0
|
1.0
|
|
CA
|
C:ASP243
|
4.8
|
57.2
|
1.0
|
|
CA
|
C:ASP247
|
4.8
|
58.8
|
1.0
|
|
O
|
C:GLU246
|
4.8
|
56.7
|
1.0
|
|
O
|
C:SER241
|
4.8
|
66.7
|
1.0
|
|
N
|
C:ASP244
|
4.8
|
59.3
|
1.0
|
|
N
|
C:PHE240
|
4.9
|
58.3
|
1.0
|
|
Calcium binding site 7 out
of 10 in 3vi4
Go back to
Calcium Binding Sites List in 3vi4
Calcium binding site 7 out
of 10 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2002
b:80.1
occ:1.00
|
OD2
|
C:ASP293
|
2.3
|
67.9
|
1.0
|
|
O
|
C:LEU299
|
2.3
|
76.2
|
1.0
|
|
OD1
|
C:ASN295
|
2.3
|
79.7
|
1.0
|
|
OD1
|
C:ASP301
|
2.3
|
67.9
|
1.0
|
|
OD1
|
C:ASP297
|
2.6
|
84.4
|
1.0
|
|
OD2
|
C:ASP301
|
2.6
|
70.3
|
1.0
|
|
CG
|
C:ASP301
|
2.8
|
68.7
|
1.0
|
|
CG
|
C:ASN295
|
3.3
|
80.5
|
1.0
|
|
CG
|
C:ASP297
|
3.5
|
86.3
|
1.0
|
|
C
|
C:LEU299
|
3.5
|
74.7
|
1.0
|
|
ND2
|
C:ASN295
|
3.5
|
81.2
|
1.0
|
|
CG
|
C:ASP293
|
3.6
|
65.5
|
1.0
|
|
OD2
|
C:ASP297
|
3.7
|
85.2
|
1.0
|
|
CB
|
C:LEU299
|
4.0
|
71.1
|
1.0
|
|
O
|
C:ASP297
|
4.1
|
88.0
|
1.0
|
|
O
|
C:GLN329
|
4.1
|
63.1
|
1.0
|
|
CA
|
C:LEU299
|
4.2
|
72.3
|
1.0
|
|
OD1
|
C:ASP293
|
4.3
|
68.9
|
1.0
|
|
CB
|
C:ASP301
|
4.3
|
69.4
|
1.0
|
|
N
|
C:LEU299
|
4.4
|
72.0
|
1.0
|
|
N
|
C:VAL294
|
4.5
|
70.1
|
1.0
|
|
N
|
C:GLN329
|
4.5
|
66.2
|
1.0
|
|
CB
|
C:ASP293
|
4.6
|
65.2
|
1.0
|
|
N
|
C:ASP300
|
4.6
|
75.3
|
1.0
|
|
CD2
|
C:LEU328
|
4.6
|
59.1
|
1.0
|
|
N
|
C:ASP301
|
4.6
|
70.6
|
1.0
|
|
N
|
C:ASN295
|
4.6
|
78.0
|
1.0
|
|
C
|
C:ASP300
|
4.6
|
71.5
|
1.0
|
|
CB
|
C:ASN295
|
4.6
|
78.9
|
1.0
|
|
CA
|
C:ASP293
|
4.7
|
65.9
|
1.0
|
|
CB
|
C:ASP297
|
4.8
|
85.3
|
1.0
|
|
C
|
C:ASP297
|
4.9
|
82.5
|
1.0
|
|
CA
|
C:ASP300
|
4.9
|
72.9
|
1.0
|
|
CA
|
C:ASP301
|
5.0
|
68.6
|
1.0
|
|
C
|
C:GLN329
|
5.0
|
66.2
|
1.0
|
|
Calcium binding site 8 out
of 10 in 3vi4
Go back to
Calcium Binding Sites List in 3vi4
Calcium binding site 8 out
of 10 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2003
b:78.7
occ:1.00
|
O
|
C:TYR366
|
2.3
|
75.3
|
1.0
|
|
OD1
|
C:ASP362
|
2.3
|
77.8
|
1.0
|
|
OD2
|
C:ASP364
|
2.3
|
82.7
|
1.0
|
|
OD2
|
C:ASP368
|
2.3
|
76.6
|
1.0
|
|
OD2
|
C:ASP360
|
2.3
|
89.0
|
1.0
|
|
OD1
|
C:ASP368
|
2.7
|
80.5
|
1.0
|
|
CG
|
C:ASP368
|
2.8
|
76.6
|
1.0
|
|
CG
|
C:ASP364
|
3.3
|
84.0
|
1.0
|
|
CG
|
C:ASP362
|
3.4
|
82.7
|
1.0
|
|
C
|
C:TYR366
|
3.5
|
72.2
|
1.0
|
|
CG
|
C:ASP360
|
3.6
|
88.1
|
1.0
|
|
OD1
|
C:ASP364
|
3.8
|
80.0
|
1.0
|
|
OD2
|
C:ASP362
|
3.8
|
85.7
|
1.0
|
|
N
|
C:LEU361
|
4.1
|
77.2
|
1.0
|
|
N
|
C:TYR366
|
4.1
|
74.5
|
1.0
|
|
CA
|
C:TYR366
|
4.1
|
71.5
|
1.0
|
|
CA
|
C:ASP360
|
4.2
|
81.2
|
1.0
|
|
CB
|
C:TYR366
|
4.2
|
69.5
|
1.0
|
|
N
|
C:ASP362
|
4.2
|
83.9
|
1.0
|
|
C
|
C:ASP360
|
4.3
|
78.2
|
1.0
|
|
CB
|
C:ASP368
|
4.4
|
72.5
|
1.0
|
|
CB
|
C:ASP364
|
4.4
|
83.4
|
1.0
|
|
OD1
|
C:ASP360
|
4.4
|
88.8
|
1.0
|
|
N
|
C:ASP364
|
4.4
|
79.2
|
1.0
|
|
CB
|
C:ASP360
|
4.4
|
86.0
|
1.0
|
|
N
|
C:ASN367
|
4.5
|
67.9
|
1.0
|
|
N
|
C:ASP368
|
4.5
|
65.9
|
1.0
|
|
C
|
C:ASN367
|
4.6
|
68.6
|
1.0
|
|
N
|
C:GLN363
|
4.7
|
77.1
|
1.0
|
|
CB
|
C:ASP362
|
4.7
|
83.0
|
1.0
|
|
CA
|
C:ASN367
|
4.8
|
67.6
|
1.0
|
|
N
|
C:GLY389
|
4.8
|
80.0
|
1.0
|
|
CA
|
C:ASP362
|
4.9
|
83.2
|
1.0
|
|
CA
|
C:ASP364
|
4.9
|
80.1
|
1.0
|
|
N
|
C:GLY365
|
4.9
|
73.7
|
1.0
|
|
CA
|
C:ASP368
|
5.0
|
66.3
|
1.0
|
|
Calcium binding site 9 out
of 10 in 3vi4
Go back to
Calcium Binding Sites List in 3vi4
Calcium binding site 9 out
of 10 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2004
b:76.8
occ:1.00
|
O
|
C:TYR430
|
2.3
|
73.2
|
1.0
|
|
OD1
|
C:ASP426
|
2.3
|
74.6
|
1.0
|
|
OD1
|
C:ASN428
|
2.3
|
83.4
|
1.0
|
|
OD2
|
C:ASP432
|
2.3
|
84.3
|
1.0
|
|
OD1
|
C:ASP424
|
2.3
|
82.2
|
1.0
|
|
CG
|
C:ASP432
|
3.2
|
85.6
|
1.0
|
|
CG
|
C:ASN428
|
3.3
|
84.1
|
1.0
|
|
O
|
C:ASN428
|
3.3
|
78.2
|
1.0
|
|
OD1
|
C:ASP432
|
3.4
|
91.5
|
1.0
|
|
C
|
C:TYR430
|
3.4
|
75.6
|
1.0
|
|
CG
|
C:ASP424
|
3.6
|
80.1
|
1.0
|
|
CG
|
C:ASP426
|
3.6
|
74.5
|
1.0
|
|
ND2
|
C:ASN428
|
3.8
|
84.8
|
1.0
|
|
N
|
C:TYR430
|
3.9
|
77.9
|
1.0
|
|
N
|
C:ASP426
|
4.0
|
79.9
|
1.0
|
|
CA
|
C:TYR430
|
4.1
|
79.0
|
1.0
|
|
O
|
C:ASP426
|
4.1
|
87.0
|
1.0
|
|
C
|
C:ASN428
|
4.1
|
77.3
|
1.0
|
|
CB
|
C:TYR430
|
4.3
|
81.8
|
1.0
|
|
OD2
|
C:ASP426
|
4.3
|
71.1
|
1.0
|
|
OD2
|
C:ASP424
|
4.3
|
73.8
|
1.0
|
|
O
|
C:GLY448
|
4.3
|
99.2
|
1.0
|
|
N
|
C:LEU425
|
4.4
|
74.2
|
1.0
|
|
C
|
C:ASP426
|
4.4
|
86.6
|
1.0
|
|
CA
|
C:ASP424
|
4.4
|
81.7
|
1.0
|
|
CB
|
C:ASN428
|
4.4
|
84.5
|
1.0
|
|
N
|
C:ASN428
|
4.5
|
85.5
|
1.0
|
|
N
|
C:PRO431
|
4.5
|
72.9
|
1.0
|
|
CA
|
C:ASP426
|
4.5
|
82.3
|
1.0
|
|
CA
|
C:ASN428
|
4.5
|
81.7
|
1.0
|
|
C
|
C:ASP424
|
4.6
|
77.6
|
1.0
|
|
CB
|
C:ASP424
|
4.6
|
80.0
|
1.0
|
|
C
|
C:PRO431
|
4.6
|
72.2
|
1.0
|
|
CB
|
C:ASP426
|
4.6
|
80.0
|
1.0
|
|
N
|
C:GLY448
|
4.6
|
84.8
|
1.0
|
|
CB
|
C:ASP432
|
4.7
|
78.4
|
1.0
|
|
CA
|
C:PRO431
|
4.8
|
72.6
|
1.0
|
|
O
|
C:PRO431
|
4.8
|
74.4
|
1.0
|
|
CA
|
C:GLY448
|
4.8
|
88.9
|
1.0
|
|
N
|
C:ASP432
|
4.9
|
74.5
|
1.0
|
|
Calcium binding site 10 out
of 10 in 3vi4
Go back to
Calcium Binding Sites List in 3vi4
Calcium binding site 10 out
of 10 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca501
b:50.9
occ:1.00
|
O
|
D:PRO228
|
2.3
|
46.4
|
1.0
|
|
OD1
|
D:ASN224
|
2.3
|
53.1
|
1.0
|
|
OE1
|
D:GLU169
|
2.3
|
54.2
|
1.0
|
|
O
|
D:ASP226
|
2.3
|
52.6
|
1.0
|
|
OE2
|
D:GLU229
|
2.3
|
53.3
|
1.0
|
|
OD1
|
D:ASP226
|
2.4
|
64.0
|
1.0
|
|
CG
|
D:ASN224
|
3.0
|
56.8
|
1.0
|
|
ND2
|
D:ASN224
|
3.1
|
57.0
|
1.0
|
|
CD
|
D:GLU169
|
3.4
|
58.3
|
1.0
|
|
C
|
D:PRO228
|
3.4
|
47.7
|
1.0
|
|
C
|
D:ASP226
|
3.4
|
54.8
|
1.0
|
|
CD
|
D:GLU229
|
3.5
|
51.8
|
1.0
|
|
CG
|
D:ASP226
|
3.6
|
61.6
|
1.0
|
|
CG
|
D:GLU169
|
3.7
|
55.4
|
1.0
|
|
CA
|
D:GLU229
|
3.7
|
52.1
|
1.0
|
|
N
|
D:GLU229
|
4.0
|
49.9
|
1.0
|
|
N
|
D:ASP226
|
4.0
|
56.1
|
1.0
|
|
CA
|
D:ASP226
|
4.0
|
57.3
|
1.0
|
|
CB
|
D:GLU169
|
4.2
|
54.9
|
1.0
|
|
C
|
D:SER227
|
4.3
|
49.3
|
1.0
|
|
O
|
D:SER227
|
4.3
|
48.7
|
1.0
|
|
NE2
|
D:HIS263
|
4.3
|
51.6
|
1.0
|
|
OE1
|
D:GLU229
|
4.3
|
56.6
|
1.0
|
|
CB
|
D:ASP226
|
4.4
|
59.5
|
1.0
|
|
CB
|
D:GLU229
|
4.4
|
51.2
|
1.0
|
|
N
|
D:PRO228
|
4.4
|
47.7
|
1.0
|
|
CB
|
D:ASN224
|
4.4
|
56.9
|
1.0
|
|
N
|
D:SER227
|
4.5
|
53.8
|
1.0
|
|
CG
|
D:GLU229
|
4.5
|
52.4
|
1.0
|
|
OE2
|
D:GLU169
|
4.5
|
57.4
|
1.0
|
|
CA
|
D:PRO228
|
4.5
|
49.1
|
1.0
|
|
OD2
|
D:ASP226
|
4.5
|
64.1
|
1.0
|
|
O
|
D:VAL168
|
4.6
|
57.8
|
1.0
|
|
CD2
|
D:HIS263
|
4.6
|
51.3
|
1.0
|
|
O
|
D:TYR175
|
4.6
|
50.4
|
1.0
|
|
C
|
D:GLU229
|
4.7
|
49.6
|
1.0
|
|
CA
|
D:SER227
|
4.9
|
52.8
|
1.0
|
|
C
|
D:LEU225
|
4.9
|
57.7
|
1.0
|
|
N
|
D:LEU225
|
4.9
|
61.5
|
1.0
|
|
Reference:
M.Nagae,
S.Re,
E.Mihara,
T.Nogi,
Y.Sugita,
J.Takagi.
Crystal Structure of ALPHA5BETA1 Integrin Ectodomain: Atomic Details of the Fibronectin Receptor J.Cell Biol. V. 197 131 2012.
ISSN: ISSN 0021-9525
PubMed: 22451694
DOI: 10.1083/JCB.201111077
Page generated: Tue Jul 8 17:34:45 2025
|
