Calcium in PDB 8t2v: Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids
Other elements in 8t2v:
The structure of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids
(pdb code 8t2v). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the
Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids, PDB code: 8t2v:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
Calcium binding site 1 out
of 7 in 8t2v
Go back to
Calcium Binding Sites List in 8t2v
Calcium binding site 1 out
of 7 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1101
b:148.8
occ:1.00
|
OD1
|
A:ASN299
|
2.0
|
205.3
|
1.0
|
OD1
|
A:ASP301
|
2.2
|
174.9
|
1.0
|
OD2
|
A:ASP305
|
2.3
|
95.5
|
1.0
|
OD1
|
A:ASP297
|
2.3
|
165.9
|
1.0
|
OD2
|
A:ASP301
|
2.3
|
181.6
|
1.0
|
O
|
A:ARG303
|
2.4
|
94.1
|
1.0
|
ND2
|
A:ASN299
|
2.5
|
176.0
|
1.0
|
CG
|
A:ASN299
|
2.5
|
178.2
|
1.0
|
OD1
|
A:ASP305
|
2.6
|
96.7
|
1.0
|
CG
|
A:ASP301
|
2.6
|
151.9
|
1.0
|
CG
|
A:ASP305
|
2.7
|
90.7
|
1.0
|
CG
|
A:ASP297
|
3.5
|
131.6
|
1.0
|
C
|
A:ARG303
|
3.6
|
86.9
|
1.0
|
CB
|
A:ASN299
|
3.9
|
125.7
|
1.0
|
CB
|
A:ASP301
|
4.1
|
139.5
|
1.0
|
CB
|
A:ASP305
|
4.1
|
86.0
|
1.0
|
OD2
|
A:ASP297
|
4.2
|
144.1
|
1.0
|
N
|
A:ASN299
|
4.2
|
100.2
|
1.0
|
N
|
A:ASP305
|
4.2
|
70.5
|
1.0
|
CA
|
A:ASP297
|
4.3
|
89.7
|
1.0
|
N
|
A:ARG303
|
4.3
|
115.5
|
1.0
|
CA
|
A:ARG303
|
4.3
|
116.4
|
1.0
|
CB
|
A:ARG303
|
4.4
|
134.2
|
1.0
|
CD2
|
A:LEU332
|
4.4
|
119.5
|
1.0
|
CB
|
A:ASP297
|
4.5
|
90.7
|
1.0
|
C
|
A:HIS304
|
4.5
|
61.0
|
1.0
|
CA
|
A:ASN299
|
4.5
|
102.4
|
1.0
|
N
|
A:ASP301
|
4.6
|
130.9
|
1.0
|
N
|
A:HIS304
|
4.6
|
73.1
|
1.0
|
N
|
A:VAL298
|
4.6
|
64.3
|
1.0
|
CA
|
A:ASP305
|
4.6
|
84.7
|
1.0
|
C
|
A:ASP297
|
4.7
|
84.9
|
1.0
|
N
|
A:GLY300
|
4.7
|
94.2
|
1.0
|
CA
|
A:HIS304
|
4.8
|
74.6
|
1.0
|
CA
|
A:ASP301
|
4.9
|
140.0
|
1.0
|
C
|
A:ASN299
|
4.9
|
96.2
|
1.0
|
N
|
A:GLN333
|
4.9
|
92.2
|
1.0
|
|
Calcium binding site 2 out
of 7 in 8t2v
Go back to
Calcium Binding Sites List in 8t2v
Calcium binding site 2 out
of 7 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1102
b:206.3
occ:1.00
|
OE1
|
A:GLU243
|
1.8
|
212.2
|
1.0
|
OE1
|
A:GLU252
|
1.8
|
162.2
|
1.0
|
OD1
|
A:ASP245
|
2.1
|
188.7
|
1.0
|
CD
|
A:GLU243
|
2.4
|
198.4
|
1.0
|
CD
|
A:GLU252
|
2.4
|
142.1
|
1.0
|
O
|
A:ASP247
|
2.4
|
186.8
|
1.0
|
OE2
|
A:GLU252
|
2.5
|
165.4
|
1.0
|
OE2
|
A:GLU243
|
2.5
|
231.5
|
1.0
|
OG1
|
A:THR250
|
2.5
|
191.6
|
1.0
|
O
|
A:THR250
|
2.6
|
152.9
|
1.0
|
CG
|
A:ASP245
|
3.0
|
164.6
|
1.0
|
CB
|
A:THR250
|
3.2
|
197.8
|
1.0
|
C
|
A:THR250
|
3.3
|
142.4
|
1.0
|
C
|
A:ASP247
|
3.6
|
202.9
|
1.0
|
CB
|
A:ASP245
|
3.7
|
162.3
|
1.0
|
CA
|
A:THR250
|
3.7
|
149.7
|
1.0
|
CG
|
A:GLU243
|
3.8
|
158.2
|
1.0
|
OD2
|
A:ASP245
|
3.9
|
164.1
|
1.0
|
CG
|
A:GLU252
|
3.9
|
148.8
|
1.0
|
N
|
A:ASP245
|
4.0
|
133.2
|
1.0
|
N
|
A:ASP247
|
4.0
|
171.0
|
1.0
|
CA
|
A:GLU243
|
4.2
|
133.8
|
1.0
|
N
|
A:THR251
|
4.2
|
143.4
|
1.0
|
N
|
A:THR250
|
4.2
|
152.1
|
1.0
|
CA
|
A:ASP245
|
4.3
|
150.1
|
1.0
|
N
|
A:GLY246
|
4.3
|
123.2
|
1.0
|
CA
|
A:ASP247
|
4.3
|
207.4
|
1.0
|
N
|
A:PHE244
|
4.4
|
144.8
|
1.0
|
N
|
A:GLU252
|
4.4
|
103.3
|
1.0
|
CB
|
A:GLU243
|
4.5
|
145.4
|
1.0
|
CG2
|
A:THR250
|
4.6
|
217.0
|
1.0
|
C
|
A:GLU243
|
4.6
|
118.9
|
1.0
|
CA
|
A:THR251
|
4.6
|
145.8
|
1.0
|
N
|
A:LEU248
|
4.6
|
214.0
|
1.0
|
C
|
A:ASP245
|
4.7
|
158.0
|
1.0
|
CB
|
A:ASP247
|
4.8
|
241.9
|
1.0
|
O
|
A:GLY242
|
4.8
|
147.4
|
1.0
|
CA
|
A:LEU248
|
4.9
|
230.1
|
1.0
|
CB
|
A:GLU252
|
4.9
|
97.6
|
1.0
|
C
|
A:LEU248
|
5.0
|
218.7
|
1.0
|
|
Calcium binding site 3 out
of 7 in 8t2v
Go back to
Calcium Binding Sites List in 8t2v
Calcium binding site 3 out
of 7 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1103
b:158.1
occ:1.00
|
OD1
|
A:ASP373
|
2.0
|
143.0
|
1.0
|
OD2
|
A:ASP369
|
2.1
|
172.9
|
1.0
|
OD1
|
A:ASP367
|
2.2
|
203.3
|
1.0
|
OD2
|
A:ASP373
|
2.3
|
128.7
|
1.0
|
CG
|
A:ASP373
|
2.4
|
118.4
|
1.0
|
OD1
|
A:ASP369
|
2.5
|
154.6
|
1.0
|
O
|
A:TYR371
|
2.5
|
121.4
|
1.0
|
CG
|
A:ASP369
|
2.5
|
195.3
|
1.0
|
OD1
|
A:ASP365
|
3.2
|
140.2
|
1.0
|
CG
|
A:ASP367
|
3.3
|
167.1
|
1.0
|
OD2
|
A:ASP367
|
3.7
|
173.6
|
1.0
|
C
|
A:TYR371
|
3.7
|
98.4
|
1.0
|
CB
|
A:ASP373
|
3.9
|
81.5
|
1.0
|
CB
|
A:ASP369
|
4.0
|
179.1
|
1.0
|
N
|
A:ASP367
|
4.2
|
116.7
|
1.0
|
CD2
|
A:LEU393
|
4.3
|
105.6
|
1.0
|
CG
|
A:ASP365
|
4.3
|
159.2
|
1.0
|
N
|
A:LEU366
|
4.3
|
71.2
|
1.0
|
N
|
A:ASP369
|
4.4
|
159.2
|
1.0
|
CA
|
A:ASP365
|
4.4
|
113.2
|
1.0
|
N
|
A:GLY394
|
4.5
|
91.3
|
1.0
|
C
|
A:ASN372
|
4.5
|
99.8
|
1.0
|
N
|
A:ASP373
|
4.5
|
92.9
|
1.0
|
N
|
A:TYR371
|
4.6
|
82.7
|
1.0
|
CA
|
A:TYR371
|
4.6
|
96.5
|
1.0
|
CB
|
A:ASP367
|
4.6
|
116.8
|
1.0
|
C
|
A:ASP365
|
4.6
|
94.2
|
1.0
|
O
|
A:ASN372
|
4.7
|
101.3
|
1.0
|
N
|
A:ASN372
|
4.7
|
85.8
|
1.0
|
CB
|
A:LEU393
|
4.7
|
121.5
|
1.0
|
CA
|
A:ASP369
|
4.7
|
165.0
|
1.0
|
CA
|
A:ASN372
|
4.8
|
94.8
|
1.0
|
CA
|
A:ASP367
|
4.8
|
110.9
|
1.0
|
N
|
A:ARG368
|
4.8
|
97.7
|
1.0
|
O
|
A:GLY394
|
4.8
|
120.3
|
1.0
|
CA
|
A:ASP373
|
4.8
|
73.5
|
1.0
|
CB
|
A:TYR371
|
4.8
|
115.8
|
1.0
|
O
|
A:GLY364
|
5.0
|
76.4
|
1.0
|
CB
|
A:ASP365
|
5.0
|
136.9
|
1.0
|
|
Calcium binding site 4 out
of 7 in 8t2v
Go back to
Calcium Binding Sites List in 8t2v
Calcium binding site 4 out
of 7 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1104
b:154.5
occ:1.00
|
OD1
|
A:ASN430
|
1.9
|
130.8
|
1.0
|
OD1
|
A:ASP434
|
2.0
|
111.9
|
1.0
|
OD1
|
A:ASP428
|
2.0
|
190.4
|
1.0
|
OD2
|
A:ASP434
|
2.0
|
100.0
|
1.0
|
CG
|
A:ASP434
|
2.3
|
97.8
|
1.0
|
OD2
|
A:ASP428
|
2.3
|
135.4
|
1.0
|
O
|
A:TYR432
|
2.3
|
99.6
|
1.0
|
CG
|
A:ASP428
|
2.4
|
187.1
|
1.0
|
CG
|
A:ASN430
|
2.8
|
134.1
|
1.0
|
OD1
|
A:ASP426
|
3.2
|
156.3
|
1.0
|
ND2
|
A:ASN430
|
3.2
|
181.1
|
1.0
|
C
|
A:TYR432
|
3.5
|
86.7
|
1.0
|
CB
|
A:ASP434
|
3.8
|
74.2
|
1.0
|
CB
|
A:ASP428
|
3.9
|
158.3
|
1.0
|
CB
|
A:ASN430
|
4.0
|
109.8
|
1.0
|
N
|
A:TYR432
|
4.2
|
85.5
|
1.0
|
CA
|
A:TYR432
|
4.2
|
87.3
|
1.0
|
N
|
A:ASP434
|
4.3
|
78.5
|
1.0
|
CB
|
A:TYR432
|
4.3
|
101.4
|
1.0
|
C
|
A:PRO433
|
4.4
|
75.9
|
1.0
|
N
|
A:ASP428
|
4.4
|
148.3
|
1.0
|
N
|
A:ALA450
|
4.4
|
122.9
|
1.0
|
CG
|
A:ASP426
|
4.4
|
198.7
|
1.0
|
N
|
A:ASN430
|
4.4
|
121.3
|
1.0
|
O
|
A:ALA450
|
4.4
|
172.0
|
1.0
|
CA
|
A:ASP434
|
4.5
|
70.2
|
1.0
|
N
|
A:PRO433
|
4.5
|
86.9
|
1.0
|
CB
|
A:ALA450
|
4.5
|
106.1
|
1.0
|
CA
|
A:ASP428
|
4.6
|
139.9
|
1.0
|
CA
|
A:PRO433
|
4.6
|
92.6
|
1.0
|
CA
|
A:ASN430
|
4.7
|
114.7
|
1.0
|
O
|
A:PRO433
|
4.7
|
73.8
|
1.0
|
N
|
A:ILE427
|
4.8
|
97.7
|
1.0
|
CA
|
A:ASP426
|
4.8
|
136.3
|
1.0
|
CA
|
A:ALA450
|
4.9
|
103.3
|
1.0
|
|
Calcium binding site 5 out
of 7 in 8t2v
Go back to
Calcium Binding Sites List in 8t2v
Calcium binding site 5 out
of 7 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1109
b:297.0
occ:1.00
|
OE1
|
A:GLU642
|
1.8
|
305.3
|
1.0
|
OD2
|
A:ASP605
|
2.0
|
295.2
|
1.0
|
OD1
|
A:ASP605
|
2.1
|
292.5
|
1.0
|
CG
|
A:ASP605
|
2.2
|
311.1
|
1.0
|
O
|
A:CYS602
|
2.4
|
275.8
|
1.0
|
CD
|
A:GLU642
|
2.5
|
301.6
|
1.0
|
O
|
A:VAL607
|
2.5
|
268.5
|
1.0
|
OE2
|
A:GLU642
|
2.5
|
285.5
|
1.0
|
C
|
A:CYS602
|
3.5
|
266.7
|
1.0
|
C
|
A:VAL607
|
3.5
|
258.1
|
1.0
|
CB
|
A:ASP605
|
3.6
|
306.3
|
1.0
|
CG
|
A:GLU642
|
3.9
|
299.6
|
1.0
|
N
|
A:VAL607
|
4.1
|
272.5
|
1.0
|
N
|
A:GLY603
|
4.3
|
242.0
|
1.0
|
CA
|
A:CYS602
|
4.3
|
274.6
|
1.0
|
N
|
A:VAL609
|
4.4
|
266.1
|
1.0
|
N
|
A:CYS608
|
4.4
|
251.7
|
1.0
|
CA
|
A:VAL607
|
4.4
|
274.9
|
1.0
|
CA
|
A:GLY603
|
4.4
|
247.1
|
1.0
|
CA
|
A:CYS608
|
4.4
|
271.2
|
1.0
|
CA
|
A:ASP605
|
4.5
|
297.3
|
1.0
|
N
|
A:ASP605
|
4.5
|
279.7
|
1.0
|
CG2
|
A:VAL609
|
4.6
|
261.5
|
1.0
|
N
|
A:ASP606
|
4.6
|
283.9
|
1.0
|
CB
|
A:CYS602
|
4.8
|
276.7
|
1.0
|
C
|
A:ASP605
|
4.8
|
291.2
|
1.0
|
C
|
A:GLY603
|
4.8
|
286.6
|
1.0
|
C
|
A:CYS608
|
4.9
|
257.1
|
1.0
|
CB
|
A:VAL607
|
4.9
|
277.8
|
1.0
|
CB
|
A:VAL609
|
5.0
|
281.2
|
1.0
|
|
Calcium binding site 6 out
of 7 in 8t2v
Go back to
Calcium Binding Sites List in 8t2v
Calcium binding site 6 out
of 7 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca805
b:111.7
occ:1.00
|
OE1
|
B:GLU220
|
1.8
|
138.5
|
1.0
|
OD2
|
B:ASP158
|
2.0
|
130.8
|
1.0
|
OD1
|
B:ASN215
|
2.0
|
86.8
|
1.0
|
OD1
|
B:ASP217
|
2.1
|
77.4
|
1.0
|
O
|
B:PRO219
|
2.1
|
98.7
|
1.0
|
CG
|
B:ASP217
|
2.5
|
109.1
|
1.0
|
O
|
B:ASP217
|
2.5
|
95.1
|
1.0
|
CG
|
B:ASN215
|
2.7
|
100.7
|
1.0
|
OD2
|
B:ASP217
|
2.8
|
76.1
|
1.0
|
CD
|
B:GLU220
|
2.9
|
103.3
|
1.0
|
ND2
|
B:ASN215
|
3.2
|
112.5
|
1.0
|
CG
|
B:ASP158
|
3.2
|
150.1
|
1.0
|
C
|
B:PRO219
|
3.3
|
71.1
|
1.0
|
C
|
B:ASP217
|
3.4
|
98.8
|
1.0
|
CB
|
B:ASP217
|
3.6
|
109.4
|
1.0
|
OE2
|
B:GLU220
|
3.6
|
135.5
|
1.0
|
CA
|
B:ASP217
|
3.8
|
103.7
|
1.0
|
N
|
B:ASP217
|
3.8
|
117.8
|
1.0
|
CB
|
B:ASN215
|
3.9
|
87.8
|
1.0
|
CA
|
B:GLU220
|
4.0
|
78.7
|
1.0
|
N
|
B:GLU220
|
4.0
|
69.6
|
1.0
|
OD1
|
B:ASP158
|
4.0
|
147.5
|
1.0
|
CG
|
B:GLU220
|
4.1
|
80.5
|
1.0
|
CB
|
B:ASP158
|
4.2
|
113.3
|
1.0
|
CB
|
B:GLU220
|
4.4
|
64.1
|
1.0
|
C
|
B:ALA218
|
4.4
|
121.4
|
1.0
|
O
|
B:ALA218
|
4.4
|
97.0
|
1.0
|
CA
|
B:PRO219
|
4.4
|
74.9
|
1.0
|
N
|
B:PRO219
|
4.5
|
86.2
|
1.0
|
N
|
B:ALA218
|
4.5
|
93.6
|
1.0
|
C
|
B:ARG216
|
4.6
|
96.9
|
1.0
|
C
|
B:ASN215
|
4.7
|
69.0
|
1.0
|
N
|
B:ARG216
|
4.7
|
64.4
|
1.0
|
O
|
B:HOH904
|
4.7
|
72.8
|
1.0
|
O
|
B:ASN215
|
4.9
|
76.5
|
1.0
|
CA
|
B:ALA218
|
5.0
|
141.1
|
1.0
|
CA
|
B:ASN215
|
5.0
|
66.5
|
1.0
|
|
Calcium binding site 7 out
of 7 in 8t2v
Go back to
Calcium Binding Sites List in 8t2v
Calcium binding site 7 out
of 7 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca806
b:221.0
occ:1.00
|
O
|
B:HOH903
|
1.9
|
108.7
|
1.0
|
OD1
|
B:ASP126
|
1.9
|
246.0
|
1.0
|
OD2
|
B:ASP126
|
2.0
|
222.7
|
1.0
|
O
|
B:HOH901
|
2.1
|
126.1
|
1.0
|
OD1
|
B:ASP127
|
2.1
|
199.7
|
1.0
|
CG
|
B:ASP126
|
2.2
|
221.7
|
1.0
|
O
|
B:SER123
|
2.4
|
201.2
|
1.0
|
O
|
B:MET335
|
2.6
|
179.9
|
1.0
|
CG
|
B:ASP127
|
2.8
|
156.8
|
1.0
|
OD2
|
B:ASP127
|
3.2
|
133.5
|
1.0
|
C
|
B:SER123
|
3.6
|
147.1
|
1.0
|
CB
|
B:ASP126
|
3.7
|
198.1
|
1.0
|
C
|
B:MET335
|
3.8
|
148.0
|
1.0
|
N
|
B:ASP127
|
3.8
|
149.7
|
1.0
|
CB
|
B:ASP127
|
4.0
|
141.3
|
1.0
|
CA
|
B:MET124
|
4.0
|
156.1
|
1.0
|
CE
|
B:MET335
|
4.2
|
252.6
|
1.0
|
N
|
B:MET124
|
4.3
|
123.7
|
1.0
|
CA
|
B:ASP126
|
4.4
|
176.5
|
1.0
|
N
|
B:ASP126
|
4.4
|
177.2
|
1.0
|
CA
|
B:ASP127
|
4.5
|
136.9
|
1.0
|
C
|
B:MET124
|
4.5
|
109.7
|
1.0
|
C
|
B:ASP126
|
4.5
|
145.4
|
1.0
|
CA
|
B:ASP336
|
4.6
|
142.9
|
1.0
|
N
|
B:ASP336
|
4.6
|
144.2
|
1.0
|
CA
|
B:SER123
|
4.7
|
155.0
|
1.0
|
CA
|
B:MET335
|
4.8
|
153.5
|
1.0
|
O
|
B:MET124
|
4.9
|
103.0
|
1.0
|
N
|
B:LYS125
|
5.0
|
119.4
|
1.0
|
|
Reference:
B.D.Adair,
J.P.Xiong,
M.Yeager,
M.A.Arnaout.
Cryo-Em Structures of Full-Length Integrin Alpha Iib Beta 3 in Native Lipids. Nat Commun V. 14 4168 2023.
ISSN: ESSN 2041-1723
PubMed: 37443315
DOI: 10.1038/S41467-023-39763-0
Page generated: Fri Jul 19 11:59:32 2024
|