Calcium in PDB 6y4o: Calmodulin Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain
Protein crystallography data
The structure of Calmodulin Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain, PDB code: 6y4o
was solved by
K.Lau,
L.H.Nielsen,
C.Holt,
M.Brohus,
A.B.Sorensen,
K.T.Larsen,
C.Sommer,
F.Van Petegem,
M.T.Overgaard,
R.Wimmer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
27.30 /
1.84
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
38.037,
43.557,
90.102,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
17.7 /
20.8
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Calmodulin Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain
(pdb code 6y4o). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Calmodulin Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain, PDB code: 6y4o:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6y4o
Go back to
Calcium Binding Sites List in 6y4o
Calcium binding site 1 out
of 4 in the Calmodulin Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Calmodulin Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca201
b:29.3
occ:1.00
|
O
|
A:HOH304
|
2.3
|
39.2
|
1.0
|
|
O
|
A:THR26
|
2.3
|
33.1
|
1.0
|
|
OD1
|
A:ASP20
|
2.3
|
28.9
|
1.0
|
|
OD1
|
A:ASP22
|
2.4
|
38.0
|
1.0
|
|
OE2
|
A:GLU31
|
2.4
|
34.3
|
1.0
|
|
OD1
|
A:ASP24
|
2.5
|
37.0
|
1.0
|
|
OE1
|
A:GLU31
|
2.5
|
33.4
|
1.0
|
|
CD
|
A:GLU31
|
2.8
|
33.1
|
1.0
|
|
HG1
|
A:THR26
|
3.2
|
52.1
|
1.0
|
|
CG
|
A:ASP22
|
3.2
|
43.0
|
1.0
|
|
H
|
A:THR26
|
3.3
|
36.5
|
1.0
|
|
OD2
|
A:ASP22
|
3.4
|
47.2
|
1.0
|
|
C
|
A:THR26
|
3.5
|
31.5
|
1.0
|
|
CG
|
A:ASP24
|
3.5
|
42.3
|
1.0
|
|
CG
|
A:ASP20
|
3.5
|
32.5
|
1.0
|
|
H
|
A:ASP22
|
3.6
|
39.9
|
1.0
|
|
H
|
A:ASP24
|
3.6
|
42.0
|
1.0
|
|
HA
|
A:ASP20
|
3.6
|
37.9
|
1.0
|
|
OG1
|
A:THR26
|
3.6
|
43.3
|
1.0
|
|
HA
|
A:ILE27
|
3.9
|
30.9
|
1.0
|
|
HG23
|
A:THR28
|
3.9
|
45.4
|
1.0
|
|
N
|
A:THR26
|
4.0
|
30.3
|
1.0
|
|
OD2
|
A:ASP24
|
4.1
|
38.8
|
1.0
|
|
CA
|
A:THR26
|
4.2
|
30.6
|
1.0
|
|
CA
|
A:ASP20
|
4.3
|
31.5
|
1.0
|
|
H
|
A:GLY23
|
4.3
|
35.9
|
1.0
|
|
N
|
A:ASP24
|
4.3
|
34.9
|
1.0
|
|
OD2
|
A:ASP20
|
4.3
|
30.9
|
1.0
|
|
H
|
A:LYS21
|
4.3
|
39.5
|
1.0
|
|
CG
|
A:GLU31
|
4.3
|
32.3
|
1.0
|
|
N
|
A:ASP22
|
4.4
|
33.2
|
1.0
|
|
H
|
A:THR28
|
4.4
|
33.0
|
1.0
|
|
CB
|
A:ASP20
|
4.4
|
31.2
|
1.0
|
|
N
|
A:ILE27
|
4.5
|
27.3
|
1.0
|
|
CB
|
A:ASP24
|
4.5
|
37.6
|
1.0
|
|
C
|
A:ASP20
|
4.5
|
32.0
|
1.0
|
|
HB3
|
A:ASP24
|
4.5
|
45.2
|
1.0
|
|
H
|
A:GLY25
|
4.5
|
37.3
|
1.0
|
|
N
|
A:LYS21
|
4.6
|
32.9
|
1.0
|
|
CB
|
A:ASP22
|
4.6
|
40.6
|
1.0
|
|
CB
|
A:THR26
|
4.6
|
35.6
|
1.0
|
|
CA
|
A:ILE27
|
4.6
|
25.6
|
1.0
|
|
N
|
A:GLY23
|
4.7
|
29.9
|
1.0
|
|
HG3
|
A:GLU31
|
4.7
|
38.9
|
1.0
|
|
HB2
|
A:ASP20
|
4.7
|
37.5
|
1.0
|
|
HG2
|
A:GLU31
|
4.7
|
38.9
|
1.0
|
|
CA
|
A:ASP24
|
4.8
|
31.9
|
1.0
|
|
N
|
A:GLY25
|
4.8
|
31.0
|
1.0
|
|
CG2
|
A:THR28
|
4.9
|
37.8
|
1.0
|
|
CA
|
A:ASP22
|
4.9
|
34.4
|
1.0
|
|
O
|
A:HOH311
|
4.9
|
40.0
|
1.0
|
|
C
|
A:ASP24
|
4.9
|
36.4
|
1.0
|
|
N
|
A:THR28
|
4.9
|
27.4
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6y4o
Go back to
Calcium Binding Sites List in 6y4o
Calcium binding site 2 out
of 4 in the Calmodulin Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Calmodulin Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca202
b:30.3
occ:1.00
|
OD1
|
A:ASP56
|
2.2
|
35.9
|
1.0
|
|
O
|
A:HOH302
|
2.3
|
47.0
|
1.0
|
|
O
|
A:THR62
|
2.4
|
29.4
|
1.0
|
|
OD1
|
A:ASN60
|
2.4
|
35.2
|
1.0
|
|
OD1
|
A:ASP58
|
2.4
|
42.3
|
1.0
|
|
OE2
|
A:GLU67
|
2.5
|
34.4
|
1.0
|
|
OE1
|
A:GLU67
|
2.5
|
31.2
|
1.0
|
|
CD
|
A:GLU67
|
2.8
|
35.6
|
1.0
|
|
O
|
A:HOH338
|
3.0
|
45.0
|
1.0
|
|
CG
|
A:ASP58
|
3.2
|
49.6
|
1.0
|
|
CG
|
A:ASP56
|
3.3
|
37.8
|
1.0
|
|
CG
|
A:ASN60
|
3.3
|
44.2
|
1.0
|
|
HD21
|
A:ASN60
|
3.5
|
56.3
|
1.0
|
|
OD2
|
A:ASP58
|
3.5
|
49.4
|
1.0
|
|
C
|
A:THR62
|
3.6
|
28.8
|
1.0
|
|
H
|
A:THR62
|
3.6
|
39.7
|
1.0
|
|
H
|
A:ASP58
|
3.6
|
49.0
|
1.0
|
|
H
|
A:ASN60
|
3.6
|
48.6
|
1.0
|
|
HA
|
A:ILE63
|
3.7
|
30.9
|
1.0
|
|
HA
|
A:ASP56
|
3.7
|
40.9
|
1.0
|
|
ND2
|
A:ASN60
|
3.8
|
46.9
|
1.0
|
|
H
|
A:ASP64
|
3.8
|
33.7
|
1.0
|
|
OD2
|
A:ASP56
|
4.0
|
38.7
|
1.0
|
|
H
|
A:GLY59
|
4.2
|
52.8
|
1.0
|
|
N
|
A:THR62
|
4.3
|
33.0
|
1.0
|
|
CB
|
A:ASP56
|
4.3
|
37.4
|
1.0
|
|
CA
|
A:ASP56
|
4.3
|
34.0
|
1.0
|
|
H
|
A:GLY61
|
4.3
|
40.3
|
1.0
|
|
CG
|
A:GLU67
|
4.4
|
33.6
|
1.0
|
|
N
|
A:ASN60
|
4.4
|
40.5
|
1.0
|
|
N
|
A:ASP58
|
4.4
|
40.8
|
1.0
|
|
CA
|
A:ILE63
|
4.4
|
25.6
|
1.0
|
|
N
|
A:ILE63
|
4.4
|
27.9
|
1.0
|
|
N
|
A:ASP64
|
4.4
|
28.0
|
1.0
|
|
OD2
|
A:ASP64
|
4.5
|
46.4
|
1.0
|
|
CB
|
A:ASP58
|
4.5
|
46.6
|
1.0
|
|
HB2
|
A:ASP56
|
4.5
|
44.9
|
1.0
|
|
CA
|
A:THR62
|
4.5
|
30.0
|
1.0
|
|
OG1
|
A:THR62
|
4.5
|
34.0
|
1.0
|
|
H
|
A:ALA57
|
4.5
|
48.4
|
1.0
|
|
CB
|
A:ASN60
|
4.5
|
44.5
|
1.0
|
|
HD22
|
A:ASN60
|
4.6
|
56.3
|
1.0
|
|
C
|
A:ASP56
|
4.6
|
41.2
|
1.0
|
|
N
|
A:GLY59
|
4.7
|
43.9
|
1.0
|
|
N
|
A:ALA57
|
4.7
|
40.3
|
1.0
|
|
HG3
|
A:GLU67
|
4.7
|
40.4
|
1.0
|
|
N
|
A:GLY61
|
4.7
|
33.5
|
1.0
|
|
HG2
|
A:GLU67
|
4.8
|
40.4
|
1.0
|
|
HB3
|
A:ASN60
|
4.8
|
53.5
|
1.0
|
|
CG
|
A:ASP64
|
4.8
|
42.2
|
1.0
|
|
HB3
|
A:ASP58
|
4.8
|
56.0
|
1.0
|
|
CA
|
A:ASP58
|
4.8
|
45.9
|
1.0
|
|
CA
|
A:ASN60
|
4.9
|
43.6
|
1.0
|
|
C
|
A:ILE63
|
4.9
|
27.9
|
1.0
|
|
HB3
|
A:ASP64
|
4.9
|
38.2
|
1.0
|
|
HB2
|
A:GLU67
|
5.0
|
38.2
|
1.0
|
|
C
|
A:ASP58
|
5.0
|
46.5
|
1.0
|
|
C
|
A:ASN60
|
5.0
|
39.8
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6y4o
Go back to
Calcium Binding Sites List in 6y4o
Calcium binding site 3 out
of 4 in the Calmodulin Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Calmodulin Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca203
b:24.7
occ:1.00
|
O
|
A:TYR99
|
2.2
|
25.1
|
1.0
|
|
OD1
|
A:ASP93
|
2.3
|
31.2
|
1.0
|
|
OD1
|
A:ASP95
|
2.3
|
38.1
|
1.0
|
|
OE2
|
A:GLU104
|
2.4
|
27.1
|
1.0
|
|
O
|
A:HOH322
|
2.4
|
28.8
|
1.0
|
|
OD1
|
A:ASN97
|
2.5
|
24.8
|
1.0
|
|
OE1
|
A:GLU104
|
2.6
|
30.0
|
1.0
|
|
CD
|
A:GLU104
|
2.8
|
25.4
|
1.0
|
|
CG
|
A:ASP95
|
3.2
|
40.4
|
1.0
|
|
CG
|
A:ASN97
|
3.4
|
26.0
|
1.0
|
|
CG
|
A:ASP93
|
3.4
|
29.3
|
1.0
|
|
H
|
A:TYR99
|
3.5
|
27.8
|
1.0
|
|
C
|
A:TYR99
|
3.5
|
25.2
|
1.0
|
|
HA
|
A:ASP93
|
3.5
|
33.7
|
1.0
|
|
OD2
|
A:ASP95
|
3.5
|
43.6
|
1.0
|
|
H
|
A:ASN97
|
3.6
|
36.5
|
1.0
|
|
HD21
|
A:ASN97
|
3.6
|
31.0
|
1.0
|
|
H
|
A:ASP95
|
3.7
|
38.6
|
1.0
|
|
HA
|
A:ILE100
|
3.8
|
26.7
|
1.0
|
|
ND2
|
A:ASN97
|
3.8
|
25.8
|
1.0
|
|
H
|
A:SER101
|
4.1
|
27.8
|
1.0
|
|
HB2
|
A:TYR99
|
4.1
|
29.6
|
1.0
|
|
N
|
A:TYR99
|
4.2
|
23.1
|
1.0
|
|
CA
|
A:ASP93
|
4.2
|
28.0
|
1.0
|
|
H
|
A:GLY96
|
4.2
|
41.5
|
1.0
|
|
CB
|
A:ASP93
|
4.2
|
32.4
|
1.0
|
|
HB2
|
A:ASP93
|
4.3
|
38.9
|
1.0
|
|
O
|
A:HOH334
|
4.3
|
43.1
|
1.0
|
|
CG
|
A:GLU104
|
4.3
|
27.7
|
1.0
|
|
OD2
|
A:ASP93
|
4.3
|
30.6
|
1.0
|
|
CA
|
A:TYR99
|
4.3
|
23.7
|
1.0
|
|
N
|
A:ASN97
|
4.4
|
30.4
|
1.0
|
|
N
|
A:ILE100
|
4.4
|
23.5
|
1.0
|
|
N
|
A:ASP95
|
4.4
|
32.1
|
1.0
|
|
C
|
A:ASP93
|
4.5
|
24.9
|
1.0
|
|
CB
|
A:ASP95
|
4.5
|
38.8
|
1.0
|
|
CA
|
A:ILE100
|
4.5
|
22.2
|
1.0
|
|
H
|
A:GLY98
|
4.6
|
30.4
|
1.0
|
|
N
|
A:GLY96
|
4.6
|
34.5
|
1.0
|
|
HB3
|
A:SER101
|
4.6
|
32.7
|
1.0
|
|
HG3
|
A:GLU104
|
4.6
|
33.4
|
1.0
|
|
CB
|
A:ASN97
|
4.6
|
27.6
|
1.0
|
|
HD22
|
A:ASN97
|
4.6
|
31.0
|
1.0
|
|
OE1
|
A:GLN135
|
4.6
|
26.6
|
1.0
|
|
H
|
A:LYS94
|
4.6
|
38.0
|
1.0
|
|
N
|
A:SER101
|
4.7
|
23.1
|
1.0
|
|
CB
|
A:TYR99
|
4.7
|
24.6
|
1.0
|
|
N
|
A:LYS94
|
4.8
|
31.6
|
1.0
|
|
HG2
|
A:GLU104
|
4.8
|
33.4
|
1.0
|
|
HB3
|
A:ASN97
|
4.8
|
33.2
|
1.0
|
|
CA
|
A:ASP95
|
4.8
|
32.7
|
1.0
|
|
O
|
A:HOH313
|
4.8
|
49.4
|
1.0
|
|
HB3
|
A:ASP95
|
4.8
|
46.7
|
1.0
|
|
C
|
A:ASP95
|
4.8
|
35.8
|
1.0
|
|
N
|
A:GLY98
|
4.9
|
25.3
|
1.0
|
|
CA
|
A:ASN97
|
4.9
|
25.7
|
1.0
|
|
O
|
A:ASP93
|
5.0
|
29.8
|
1.0
|
|
HB2
|
A:GLU104
|
5.0
|
28.7
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6y4o
Go back to
Calcium Binding Sites List in 6y4o
Calcium binding site 4 out
of 4 in the Calmodulin Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Calmodulin Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca204
b:24.8
occ:1.00
|
O
|
A:HOH316
|
2.2
|
27.6
|
1.0
|
|
OD1
|
A:ASP129
|
2.2
|
29.7
|
1.0
|
|
O
|
A:GLN135
|
2.3
|
27.8
|
1.0
|
|
OD1
|
A:ASP133
|
2.3
|
28.2
|
1.0
|
|
OD1
|
A:ASP131
|
2.3
|
28.8
|
1.0
|
|
OE1
|
A:GLU140
|
2.4
|
24.7
|
1.0
|
|
OE2
|
A:GLU140
|
2.6
|
28.5
|
1.0
|
|
CD
|
A:GLU140
|
2.9
|
26.4
|
1.0
|
|
CG
|
A:ASP133
|
3.2
|
32.8
|
1.0
|
|
CG
|
A:ASP131
|
3.2
|
34.7
|
1.0
|
|
H
|
A:ASP133
|
3.3
|
37.1
|
1.0
|
|
CG
|
A:ASP129
|
3.3
|
33.3
|
1.0
|
|
HA
|
A:ASP129
|
3.4
|
36.6
|
1.0
|
|
C
|
A:GLN135
|
3.5
|
23.3
|
1.0
|
|
H
|
A:GLN135
|
3.5
|
28.0
|
1.0
|
|
H
|
A:ASP131
|
3.5
|
43.7
|
1.0
|
|
OD2
|
A:ASP131
|
3.6
|
39.9
|
1.0
|
|
HA
|
A:VAL136
|
3.6
|
23.4
|
1.0
|
|
OD2
|
A:ASP133
|
3.6
|
32.8
|
1.0
|
|
H
|
A:ASN137
|
3.7
|
30.9
|
1.0
|
|
N
|
A:ASP133
|
4.1
|
30.9
|
1.0
|
|
CA
|
A:ASP129
|
4.1
|
30.5
|
1.0
|
|
CB
|
A:ASP129
|
4.2
|
33.8
|
1.0
|
|
H
|
A:GLY132
|
4.2
|
38.8
|
1.0
|
|
OD2
|
A:ASP129
|
4.2
|
34.5
|
1.0
|
|
H
|
A:ILE130
|
4.2
|
41.3
|
1.0
|
|
N
|
A:GLN135
|
4.2
|
23.3
|
1.0
|
|
HB2
|
A:ASP129
|
4.3
|
40.7
|
1.0
|
|
N
|
A:ASP131
|
4.3
|
36.3
|
1.0
|
|
N
|
A:ASN137
|
4.3
|
25.7
|
1.0
|
|
CA
|
A:VAL136
|
4.3
|
19.4
|
1.0
|
|
N
|
A:VAL136
|
4.3
|
21.5
|
1.0
|
|
CB
|
A:ASP133
|
4.4
|
29.6
|
1.0
|
|
CG
|
A:GLU140
|
4.4
|
24.4
|
1.0
|
|
H
|
A:GLY134
|
4.4
|
29.5
|
1.0
|
|
C
|
A:ASP129
|
4.4
|
34.1
|
1.0
|
|
CA
|
A:GLN135
|
4.5
|
26.1
|
1.0
|
|
N
|
A:ILE130
|
4.5
|
34.3
|
1.0
|
|
CB
|
A:ASP131
|
4.5
|
37.5
|
1.0
|
|
N
|
A:GLY132
|
4.5
|
32.3
|
1.0
|
|
HB3
|
A:ASP133
|
4.5
|
35.5
|
1.0
|
|
HB3
|
A:ASN137
|
4.6
|
31.0
|
1.0
|
|
CA
|
A:ASP133
|
4.7
|
28.1
|
1.0
|
|
HB2
|
A:GLN135
|
4.7
|
29.2
|
1.0
|
|
HG3
|
A:GLU140
|
4.7
|
29.3
|
1.0
|
|
HD1
|
A:TYR99
|
4.7
|
29.4
|
1.0
|
|
N
|
A:GLY134
|
4.8
|
24.5
|
1.0
|
|
CA
|
A:ASP131
|
4.8
|
36.2
|
1.0
|
|
C
|
A:VAL136
|
4.8
|
23.8
|
1.0
|
|
HG2
|
A:GLU140
|
4.8
|
29.3
|
1.0
|
|
C
|
A:ASP131
|
4.9
|
37.6
|
1.0
|
|
HB3
|
A:ASP131
|
4.9
|
45.1
|
1.0
|
|
C
|
A:ASP133
|
4.9
|
29.0
|
1.0
|
|
CG
|
A:ASN137
|
4.9
|
28.3
|
1.0
|
|
HB2
|
A:GLU140
|
4.9
|
29.6
|
1.0
|
|
O
|
A:HOH331
|
5.0
|
44.0
|
1.0
|
|
Reference:
C.Holt,
L.Hamborg,
K.Lau,
M.Brohus,
A.B.Sorensen,
K.T.Larsen,
C.Sommer,
F.V.Petegem,
M.T.Overgaard,
R.Wimmer.
The Arrhythmogenic N53I Variant Subtly Changes the Structure and Dynamics in the Calmodulin N-Domain, Altering Its Interaction with the Cardiac Ryanodine Receptor J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
Page generated: Tue Jul 16 18:26:14 2024
|
