Calcium in PDB 1qiv: Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd), 1:2 Complex
Protein crystallography data
The structure of Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd), 1:2 Complex, PDB code: 1qiv
was solved by
V.Harmat,
Z.S.Bocskei,
B.G.Vertessy,
G.Naray-Szabo,
J.Ovadi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.58 /
2.64
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
40.125,
40.125,
173.814,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20.7 /
30.1
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd), 1:2 Complex
(pdb code 1qiv). 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 Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd), 1:2 Complex, PDB code: 1qiv:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1qiv
Go back to
Calcium Binding Sites List in 1qiv
Calcium binding site 1 out
of 4 in the Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd), 1:2 Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd), 1:2 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca149
b:17.9
occ:1.00
|
O
|
A:THR26
|
2.3
|
14.4
|
1.0
|
OD1
|
A:ASP20
|
2.3
|
16.8
|
1.0
|
OE2
|
A:GLU31
|
2.3
|
18.7
|
1.0
|
OD1
|
A:ASP22
|
2.3
|
25.4
|
1.0
|
OD1
|
A:ASP24
|
2.3
|
23.1
|
1.0
|
OE1
|
A:GLU31
|
2.3
|
11.7
|
1.0
|
CD
|
A:GLU31
|
2.6
|
5.1
|
1.0
|
CG
|
A:ASP22
|
3.2
|
16.0
|
1.0
|
OD2
|
A:ASP22
|
3.4
|
23.4
|
1.0
|
CG
|
A:ASP20
|
3.4
|
15.2
|
1.0
|
CG
|
A:ASP24
|
3.4
|
21.0
|
1.0
|
C
|
A:THR26
|
3.5
|
15.5
|
1.0
|
OG1
|
A:THR26
|
3.9
|
13.4
|
1.0
|
CA
|
A:ASP20
|
3.9
|
17.4
|
1.0
|
CB
|
A:ASP20
|
4.1
|
16.8
|
1.0
|
OD2
|
A:ASP24
|
4.1
|
18.1
|
1.0
|
CG
|
A:GLU31
|
4.1
|
8.6
|
1.0
|
N
|
A:THR26
|
4.2
|
27.3
|
1.0
|
N
|
A:ASP24
|
4.3
|
20.5
|
1.0
|
C
|
A:ASP20
|
4.3
|
16.3
|
1.0
|
N
|
A:ASP22
|
4.3
|
19.9
|
1.0
|
CA
|
A:THR26
|
4.4
|
17.1
|
1.0
|
N
|
A:ILE27
|
4.4
|
11.6
|
1.0
|
OD2
|
A:ASP20
|
4.4
|
23.0
|
1.0
|
CA
|
A:ILE27
|
4.4
|
9.2
|
1.0
|
CB
|
A:ASP22
|
4.5
|
15.0
|
1.0
|
CB
|
A:ASP24
|
4.5
|
9.5
|
1.0
|
N
|
A:LYS21
|
4.6
|
17.5
|
1.0
|
CG2
|
A:THR28
|
4.7
|
13.4
|
1.0
|
N
|
A:GLY23
|
4.7
|
11.7
|
1.0
|
CA
|
A:ASP22
|
4.8
|
12.9
|
1.0
|
CB
|
A:THR26
|
4.8
|
10.2
|
1.0
|
CA
|
A:ASP24
|
4.8
|
15.4
|
1.0
|
O
|
A:ASP20
|
4.8
|
18.1
|
1.0
|
N
|
A:THR28
|
4.9
|
18.1
|
1.0
|
C
|
A:ASP22
|
4.9
|
17.0
|
1.0
|
N
|
A:GLY25
|
4.9
|
26.3
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1qiv
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Calcium Binding Sites List in 1qiv
Calcium binding site 2 out
of 4 in the Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd), 1:2 Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd), 1:2 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca150
b:30.2
occ:1.00
|
OD1
|
A:ASP56
|
2.3
|
27.0
|
1.0
|
OD1
|
A:ASN60
|
2.3
|
40.9
|
1.0
|
OD1
|
A:ASP58
|
2.3
|
34.2
|
1.0
|
OE1
|
A:GLU67
|
2.3
|
25.7
|
1.0
|
O
|
A:THR62
|
2.3
|
26.4
|
1.0
|
OE2
|
A:GLU67
|
2.3
|
24.6
|
1.0
|
ND2
|
A:ASN60
|
2.5
|
27.2
|
1.0
|
CD
|
A:GLU67
|
2.5
|
20.7
|
1.0
|
CG
|
A:ASN60
|
2.6
|
37.9
|
1.0
|
CG
|
A:ASP58
|
3.4
|
36.3
|
1.0
|
C
|
A:THR62
|
3.5
|
26.8
|
1.0
|
CG
|
A:ASP56
|
3.5
|
25.9
|
1.0
|
CG
|
A:GLU67
|
3.9
|
15.2
|
1.0
|
CB
|
A:ASN60
|
4.0
|
31.0
|
1.0
|
CA
|
A:ILE63
|
4.1
|
22.5
|
1.0
|
OD2
|
A:ASP58
|
4.1
|
43.7
|
1.0
|
N
|
A:ILE63
|
4.2
|
23.6
|
1.0
|
N
|
A:ASP64
|
4.2
|
17.7
|
1.0
|
N
|
A:ASN60
|
4.3
|
32.0
|
1.0
|
CA
|
A:ASP56
|
4.3
|
28.0
|
1.0
|
OD2
|
A:ASP56
|
4.3
|
26.6
|
1.0
|
N
|
A:THR62
|
4.4
|
31.1
|
1.0
|
N
|
A:ASP58
|
4.4
|
34.0
|
1.0
|
CB
|
A:ASP56
|
4.4
|
26.4
|
1.0
|
CB
|
A:ASP58
|
4.5
|
27.8
|
1.0
|
CD1
|
A:ILE63
|
4.5
|
3.6
|
1.0
|
CA
|
A:THR62
|
4.5
|
27.4
|
1.0
|
CA
|
A:ASN60
|
4.6
|
31.1
|
1.0
|
C
|
A:ILE63
|
4.7
|
20.8
|
1.0
|
C
|
A:ASP56
|
4.7
|
30.1
|
1.0
|
CG
|
A:ASP64
|
4.7
|
28.3
|
1.0
|
N
|
A:GLY61
|
4.7
|
28.5
|
1.0
|
OD2
|
A:ASP64
|
4.8
|
21.1
|
1.0
|
OD1
|
A:ASP64
|
4.8
|
30.7
|
1.0
|
CA
|
A:ASP58
|
4.8
|
30.8
|
1.0
|
N
|
A:ALA57
|
4.8
|
30.6
|
1.0
|
OG1
|
A:THR62
|
4.8
|
21.6
|
1.0
|
CB
|
A:GLU67
|
4.8
|
8.2
|
1.0
|
C
|
A:ASP58
|
4.8
|
33.1
|
1.0
|
N
|
A:GLY59
|
4.9
|
30.1
|
1.0
|
C
|
A:ASN60
|
5.0
|
29.4
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1qiv
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Calcium Binding Sites List in 1qiv
Calcium binding site 3 out
of 4 in the Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd), 1:2 Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd), 1:2 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca151
b:27.0
occ:1.00
|
OD1
|
A:ASP93
|
2.3
|
20.6
|
1.0
|
O
|
A:TYR99
|
2.3
|
7.5
|
1.0
|
OD1
|
A:ASP95
|
2.3
|
31.7
|
1.0
|
OD1
|
A:ASN97
|
2.3
|
18.5
|
1.0
|
OE2
|
A:GLU104
|
2.3
|
33.5
|
1.0
|
OE1
|
A:GLU104
|
2.3
|
30.8
|
1.0
|
OD2
|
A:ASP95
|
2.5
|
41.6
|
1.0
|
CD
|
A:GLU104
|
2.6
|
27.1
|
1.0
|
CG
|
A:ASP95
|
2.7
|
34.3
|
1.0
|
CG
|
A:ASP93
|
3.3
|
16.8
|
1.0
|
CG
|
A:ASN97
|
3.4
|
14.3
|
1.0
|
C
|
A:TYR99
|
3.4
|
11.3
|
1.0
|
CA
|
A:ASP93
|
4.0
|
8.2
|
1.0
|
OD2
|
A:ASP93
|
4.0
|
11.0
|
1.0
|
N
|
A:TYR99
|
4.0
|
17.7
|
1.0
|
CG
|
A:GLU104
|
4.1
|
15.5
|
1.0
|
CB
|
A:ASP93
|
4.1
|
4.6
|
1.0
|
ND2
|
A:ASN97
|
4.1
|
12.4
|
1.0
|
CB
|
A:ASP95
|
4.2
|
27.1
|
1.0
|
CA
|
A:TYR99
|
4.2
|
12.8
|
1.0
|
N
|
A:ASN97
|
4.3
|
15.7
|
1.0
|
N
|
A:ILE100
|
4.4
|
11.3
|
1.0
|
CB
|
A:ASN97
|
4.4
|
9.9
|
1.0
|
N
|
A:ASP95
|
4.4
|
26.9
|
1.0
|
C
|
A:ASP93
|
4.5
|
9.2
|
1.0
|
CA
|
A:ILE100
|
4.5
|
14.4
|
1.0
|
N
|
A:GLY96
|
4.7
|
14.1
|
1.0
|
N
|
A:LYS94
|
4.7
|
15.4
|
1.0
|
N
|
A:GLY98
|
4.7
|
18.4
|
1.0
|
CB
|
A:TYR99
|
4.7
|
8.4
|
1.0
|
CA
|
A:ASP95
|
4.7
|
22.5
|
1.0
|
CA
|
A:ASN97
|
4.8
|
12.5
|
1.0
|
N
|
A:SER101
|
4.8
|
16.2
|
1.0
|
C
|
A:ASP95
|
4.9
|
19.2
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1qiv
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Calcium Binding Sites List in 1qiv
Calcium binding site 4 out
of 4 in the Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd), 1:2 Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd), 1:2 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca152
b:15.1
occ:1.00
|
OD1
|
A:ASP129
|
2.3
|
9.6
|
1.0
|
O
|
A:GLN135
|
2.3
|
13.6
|
1.0
|
OD1
|
A:ASP133
|
2.3
|
18.9
|
1.0
|
OE2
|
A:GLU140
|
2.3
|
9.9
|
1.0
|
OE1
|
A:GLU140
|
2.3
|
13.3
|
1.0
|
OD1
|
A:ASP131
|
2.3
|
17.7
|
1.0
|
CD
|
A:GLU140
|
2.6
|
11.4
|
1.0
|
CG
|
A:ASP133
|
3.2
|
16.9
|
1.0
|
CG
|
A:ASP131
|
3.2
|
21.9
|
1.0
|
C
|
A:GLN135
|
3.3
|
11.9
|
1.0
|
CG
|
A:ASP129
|
3.4
|
16.4
|
1.0
|
OD2
|
A:ASP131
|
3.5
|
23.5
|
1.0
|
OD2
|
A:ASP133
|
3.6
|
15.2
|
1.0
|
N
|
A:GLN135
|
4.1
|
11.6
|
1.0
|
OD2
|
A:ASP129
|
4.1
|
23.1
|
1.0
|
CG
|
A:GLU140
|
4.1
|
9.7
|
1.0
|
CA
|
A:VAL136
|
4.1
|
7.4
|
1.0
|
N
|
A:VAL136
|
4.2
|
13.2
|
1.0
|
CA
|
A:ASP129
|
4.3
|
10.7
|
1.0
|
CA
|
A:GLN135
|
4.3
|
4.5
|
1.0
|
N
|
A:ILE130
|
4.3
|
15.6
|
1.0
|
N
|
A:ASP133
|
4.3
|
10.7
|
1.0
|
N
|
A:ASP131
|
4.4
|
20.9
|
1.0
|
CB
|
A:ASP129
|
4.4
|
9.7
|
1.0
|
CB
|
A:ASP133
|
4.4
|
4.7
|
1.0
|
N
|
A:ASN137
|
4.4
|
8.9
|
1.0
|
CB
|
A:ASP131
|
4.6
|
19.8
|
1.0
|
N
|
A:GLY132
|
4.6
|
19.1
|
1.0
|
C
|
A:VAL136
|
4.7
|
4.8
|
1.0
|
N
|
A:GLY134
|
4.8
|
11.5
|
1.0
|
CA
|
A:ASP133
|
4.8
|
7.0
|
1.0
|
CB
|
A:GLN135
|
4.8
|
4.3
|
1.0
|
C
|
A:ASP129
|
4.9
|
16.6
|
1.0
|
CA
|
A:ASP131
|
4.9
|
21.8
|
1.0
|
CG
|
A:ASN137
|
4.9
|
11.1
|
1.0
|
CB
|
A:GLU140
|
5.0
|
13.9
|
1.0
|
C
|
A:ASP133
|
5.0
|
11.5
|
1.0
|
|
Reference:
V.Harmat,
Z.S.Bocskei,
G.Naray-Szabo,
I.Bata,
A.S.Csutor,
I.Hermecz,
P.Aranyi,
B.Szabo,
K.Liliom,
B.G.Vertessy,
J.Ovadi.
A New Potent Calmodulin Antagonist with Arylalkylamine Structure: Crystallographic, Spectroscopic and Functional Studies J.Mol.Biol. V. 297 747 2000.
ISSN: ISSN 0022-2836
PubMed: 10731425
DOI: 10.1006/JMBI.2000.3607
Page generated: Thu Jul 11 21:48:51 2024
|