Calcium in PDB 7nyc: Cryoem Structure of 3C9-Smac
Calcium Binding Sites:
The binding sites of Calcium atom in the Cryoem Structure of 3C9-Smac
(pdb code 7nyc). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Cryoem Structure of 3C9-Smac, PDB code: 7nyc:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 7nyc
Go back to
Calcium Binding Sites List in 7nyc
Calcium binding site 1 out
of 3 in the Cryoem Structure of 3C9-Smac
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Cryoem Structure of 3C9-Smac within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca603
b:131.9
occ:1.00
|
OD2
|
D:ASP97
|
2.2
|
116.9
|
1.0
|
|
OD2
|
D:ASP91
|
2.3
|
13.4
|
1.0
|
|
O
|
D:ASP89
|
2.3
|
79.3
|
1.0
|
|
OE2
|
D:GLU98
|
2.3
|
323.4
|
1.0
|
|
OD1
|
D:ASN87
|
2.3
|
79.2
|
1.0
|
|
O
|
D:LEU84
|
2.5
|
206.4
|
1.0
|
|
CD
|
D:GLU98
|
2.8
|
310.6
|
1.0
|
|
CG
|
D:ASN87
|
3.2
|
210.2
|
1.0
|
|
OE1
|
D:GLU98
|
3.2
|
79.8
|
1.0
|
|
CG
|
D:ASP91
|
3.3
|
137.9
|
1.0
|
|
CG
|
D:ASP97
|
3.3
|
166.9
|
1.0
|
|
C
|
D:ASP89
|
3.4
|
88.4
|
1.0
|
|
ND2
|
D:ASN87
|
3.5
|
246.6
|
1.0
|
|
C
|
D:LEU84
|
3.6
|
244.2
|
1.0
|
|
CG
|
D:GLU98
|
3.8
|
378.6
|
1.0
|
|
CB
|
D:ASP97
|
3.9
|
91.4
|
1.0
|
|
N
|
D:ASP91
|
4.0
|
127.5
|
1.0
|
|
N
|
D:ASP89
|
4.0
|
76.1
|
1.0
|
|
CB
|
D:ASP91
|
4.0
|
115.2
|
1.0
|
|
OD1
|
D:ASP91
|
4.1
|
272.3
|
1.0
|
|
CA
|
D:ASP89
|
4.1
|
125.3
|
1.0
|
|
N
|
D:ASN87
|
4.1
|
274.9
|
1.0
|
|
N
|
D:CYS86
|
4.1
|
179.4
|
1.0
|
|
CA
|
D:LEU85
|
4.3
|
158.6
|
1.0
|
|
OD1
|
D:ASP97
|
4.3
|
52.9
|
1.0
|
|
N
|
D:ASN90
|
4.3
|
125.5
|
1.0
|
|
CB
|
D:ASN87
|
4.4
|
85.8
|
1.0
|
|
N
|
D:LEU85
|
4.4
|
423.6
|
1.0
|
|
CB
|
D:ASP89
|
4.4
|
162.3
|
1.0
|
|
C
|
D:LEU85
|
4.5
|
294.2
|
1.0
|
|
CA
|
D:LEU84
|
4.6
|
219.1
|
1.0
|
|
CA
|
D:ASN90
|
4.6
|
44.2
|
1.0
|
|
CA
|
D:ASP91
|
4.7
|
64.5
|
1.0
|
|
CB
|
D:LEU84
|
4.7
|
58.7
|
1.0
|
|
CA
|
D:ASN87
|
4.7
|
77.3
|
1.0
|
|
C
|
D:ASN90
|
4.7
|
176.4
|
1.0
|
|
N
|
D:GLY88
|
4.8
|
150.5
|
1.0
|
|
C
|
D:ASP97
|
4.8
|
168.4
|
1.0
|
|
CA
|
D:CYS86
|
5.0
|
174.3
|
1.0
|
|
N
|
D:GLU98
|
5.0
|
129.4
|
1.0
|
|
Calcium binding site 2 out
of 3 in 7nyc
Go back to
Calcium Binding Sites List in 7nyc
Calcium binding site 2 out
of 3 in the Cryoem Structure of 3C9-Smac
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Cryoem Structure of 3C9-Smac within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca605
b:344.5
occ:1.00
|
OD2
|
E:ASP90
|
2.3
|
95.0
|
1.0
|
|
O
|
E:ASP88
|
2.4
|
71.0
|
1.0
|
|
OD1
|
E:ASP96
|
2.4
|
342.8
|
1.0
|
|
OE2
|
E:GLU97
|
2.4
|
440.0
|
1.0
|
|
OD1
|
E:ASN86
|
2.4
|
107.2
|
1.0
|
|
O
|
E:LEU83
|
2.5
|
427.8
|
1.0
|
|
O
|
E:ASP96
|
2.6
|
440.0
|
1.0
|
|
CD
|
E:GLU97
|
3.2
|
440.0
|
1.0
|
|
CG
|
E:GLU97
|
3.2
|
440.0
|
1.0
|
|
CG
|
E:ASN86
|
3.2
|
97.3
|
1.0
|
|
CG
|
E:ASP90
|
3.3
|
180.3
|
1.0
|
|
CG
|
E:ASP96
|
3.4
|
270.2
|
1.0
|
|
C
|
E:ASP96
|
3.5
|
350.4
|
1.0
|
|
C
|
E:ASP88
|
3.5
|
176.8
|
1.0
|
|
ND2
|
E:ASN86
|
3.6
|
309.0
|
1.0
|
|
C
|
E:LEU83
|
3.6
|
337.5
|
1.0
|
|
CB
|
E:ASP96
|
3.8
|
218.6
|
1.0
|
|
N
|
E:ASN86
|
3.8
|
288.5
|
1.0
|
|
N
|
E:CYS85
|
3.9
|
350.2
|
1.0
|
|
N
|
E:ASP88
|
4.0
|
295.2
|
1.0
|
|
OD1
|
E:ASP90
|
4.1
|
139.6
|
1.0
|
|
N
|
E:ASP90
|
4.2
|
240.9
|
1.0
|
|
N
|
E:GLU97
|
4.2
|
317.4
|
1.0
|
|
CB
|
E:ASP90
|
4.3
|
221.6
|
1.0
|
|
CA
|
E:ASP96
|
4.3
|
267.5
|
1.0
|
|
CB
|
E:ASN86
|
4.4
|
98.2
|
1.0
|
|
CA
|
E:ASP88
|
4.4
|
119.3
|
1.0
|
|
OE1
|
E:GLU97
|
4.4
|
440.0
|
1.0
|
|
N
|
E:GLY87
|
4.4
|
259.3
|
1.0
|
|
CB
|
E:GLU97
|
4.4
|
429.5
|
1.0
|
|
CA
|
E:VAL84
|
4.4
|
334.5
|
1.0
|
|
N
|
E:VAL84
|
4.4
|
423.2
|
1.0
|
|
C
|
E:VAL84
|
4.5
|
330.4
|
1.0
|
|
CA
|
E:ASN86
|
4.5
|
279.6
|
1.0
|
|
CA
|
E:CYS85
|
4.5
|
389.7
|
1.0
|
|
N
|
E:GLN89
|
4.5
|
411.2
|
1.0
|
|
OD2
|
E:ASP96
|
4.6
|
164.7
|
1.0
|
|
CA
|
E:GLU97
|
4.6
|
437.8
|
1.0
|
|
CA
|
E:LEU83
|
4.6
|
167.8
|
1.0
|
|
C
|
E:CYS85
|
4.6
|
272.3
|
1.0
|
|
CA
|
E:GLN89
|
4.7
|
438.8
|
1.0
|
|
C
|
E:ASN86
|
4.9
|
317.8
|
1.0
|
|
C
|
E:GLN89
|
4.9
|
114.1
|
1.0
|
|
CA
|
E:ASP90
|
4.9
|
288.4
|
1.0
|
|
Calcium binding site 3 out
of 3 in 7nyc
Go back to
Calcium Binding Sites List in 7nyc
Calcium binding site 3 out
of 3 in the Cryoem Structure of 3C9-Smac
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Cryoem Structure of 3C9-Smac within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca602
b:299.4
occ:1.00
|
OE2
|
H:GLU110
|
2.3
|
440.0
|
1.0
|
|
O
|
H:ASP101
|
2.3
|
266.9
|
1.0
|
|
OD1
|
H:ASP103
|
2.3
|
135.8
|
1.0
|
|
O
|
H:LEU96
|
2.4
|
328.3
|
1.0
|
|
O
|
H:ASN99
|
2.4
|
179.2
|
1.0
|
|
OD2
|
H:ASP103
|
2.4
|
326.1
|
1.0
|
|
CG
|
H:ASP103
|
2.6
|
263.3
|
1.0
|
|
CD
|
H:GLU110
|
2.7
|
440.0
|
1.0
|
|
OE1
|
H:GLU110
|
2.7
|
440.0
|
1.0
|
|
C
|
H:LEU96
|
3.3
|
295.5
|
1.0
|
|
C
|
H:ASP101
|
3.3
|
264.6
|
1.0
|
|
C
|
H:ASN99
|
3.5
|
263.3
|
1.0
|
|
N
|
H:ASP103
|
3.9
|
188.1
|
1.0
|
|
CG
|
H:GLU110
|
3.9
|
440.0
|
1.0
|
|
CB
|
H:ASP101
|
3.9
|
269.8
|
1.0
|
|
N
|
H:ASP101
|
4.0
|
295.8
|
1.0
|
|
CA
|
H:ASP101
|
4.0
|
264.6
|
1.0
|
|
N
|
H:ARG97
|
4.0
|
287.9
|
1.0
|
|
CB
|
H:ASP103
|
4.0
|
362.1
|
1.0
|
|
CA
|
H:ARG97
|
4.0
|
440.0
|
1.0
|
|
N
|
H:ASN99
|
4.2
|
169.8
|
1.0
|
|
CA
|
H:ASN99
|
4.2
|
276.2
|
1.0
|
|
C
|
H:ARG97
|
4.2
|
440.0
|
1.0
|
|
CA
|
H:LEU96
|
4.3
|
392.2
|
1.0
|
|
CB
|
H:ASN99
|
4.3
|
440.0
|
1.0
|
|
N
|
H:ASN102
|
4.3
|
204.2
|
1.0
|
|
CB
|
H:LEU96
|
4.4
|
332.6
|
1.0
|
|
CA
|
H:ASN102
|
4.5
|
244.1
|
1.0
|
|
N
|
H:GLY100
|
4.5
|
222.9
|
1.0
|
|
CB
|
H:GLU110
|
4.6
|
318.1
|
1.0
|
|
O
|
H:ARG97
|
4.6
|
440.0
|
1.0
|
|
C
|
H:GLY100
|
4.6
|
243.3
|
1.0
|
|
CA
|
H:ASP103
|
4.6
|
184.5
|
1.0
|
|
N
|
H:CYS98
|
4.6
|
440.0
|
1.0
|
|
C
|
H:ASN102
|
4.7
|
212.7
|
1.0
|
|
C
|
H:CYS98
|
4.7
|
244.3
|
1.0
|
|
CG
|
H:ASP101
|
4.8
|
381.9
|
1.0
|
|
CA
|
H:GLY100
|
4.9
|
164.9
|
1.0
|
|
Reference:
A.Menny,
M.V.Lukassen,
E.C.Couves,
V.Franc,
A.J.R.Heck,
D.Bubeck.
Structural Basis For How Smac Is Packaged For Clearance To Be Published.
Page generated: Wed Jul 9 23:45:17 2025
|
