Calcium in PDB 5nin: Crystal Structure of AKAP79 Calmodulin Binding Domain Peptide in Complex with CA2+/Calmodulin
Protein crystallography data
The structure of Crystal Structure of AKAP79 Calmodulin Binding Domain Peptide in Complex with CA2+/Calmodulin, PDB code: 5nin
was solved by
M.G.Gold,
N.Patel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
54.07 /
1.70
|
|
Space group
|
P 42 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.460,
76.460,
128.990,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
16.4 /
19.4
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of AKAP79 Calmodulin Binding Domain Peptide in Complex with CA2+/Calmodulin
(pdb code 5nin). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Crystal Structure of AKAP79 Calmodulin Binding Domain Peptide in Complex with CA2+/Calmodulin, PDB code: 5nin:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 5nin
Go back to
Calcium Binding Sites List in 5nin
Calcium binding site 1 out
of 4 in the Crystal Structure of AKAP79 Calmodulin Binding Domain Peptide in Complex with CA2+/Calmodulin
 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 AKAP79 Calmodulin Binding Domain Peptide in Complex with CA2+/Calmodulin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca201
b:4.9
occ:1.00
|
O
|
B:TYR99
|
2.2
|
9.8
|
1.0
|
|
OD1
|
B:ASP93
|
2.3
|
7.5
|
1.0
|
|
O
|
B:HOH450
|
2.3
|
14.1
|
1.0
|
|
OD1
|
B:ASP95
|
2.4
|
6.3
|
1.0
|
|
OE1
|
B:GLU104
|
2.5
|
8.2
|
1.0
|
|
OD1
|
B:ASN97
|
2.5
|
6.8
|
1.0
|
|
OE2
|
B:GLU104
|
2.6
|
9.0
|
1.0
|
|
CD
|
B:GLU104
|
2.8
|
6.5
|
1.0
|
|
CG
|
B:ASP95
|
3.4
|
12.9
|
1.0
|
|
H
|
B:ASN97
|
3.4
|
9.7
|
1.0
|
|
CG
|
B:ASN97
|
3.5
|
6.5
|
1.0
|
|
C
|
B:TYR99
|
3.5
|
6.0
|
1.0
|
|
CG
|
B:ASP93
|
3.5
|
8.8
|
1.0
|
|
H
|
B:TYR99
|
3.5
|
5.7
|
1.0
|
|
H
|
B:ASP95
|
3.5
|
12.3
|
1.0
|
|
HA
|
B:ASP93
|
3.5
|
7.3
|
1.0
|
|
OD2
|
B:ASP95
|
3.7
|
11.9
|
1.0
|
|
HA
|
B:ILE100
|
3.8
|
3.6
|
1.0
|
|
H
|
B:SER101
|
3.9
|
7.8
|
1.0
|
|
HD21
|
B:ASN97
|
4.0
|
11.7
|
1.0
|
|
ND2
|
B:ASN97
|
4.1
|
9.8
|
1.0
|
|
HB2
|
B:TYR99
|
4.2
|
6.1
|
1.0
|
|
N
|
B:TYR99
|
4.2
|
4.7
|
1.0
|
|
CA
|
B:ASP93
|
4.2
|
6.1
|
1.0
|
|
N
|
B:ASN97
|
4.2
|
8.1
|
1.0
|
|
H
|
B:GLY96
|
4.2
|
10.9
|
1.0
|
|
H
|
B:LYS94
|
4.2
|
9.8
|
1.0
|
|
N
|
B:ASP95
|
4.3
|
10.3
|
1.0
|
|
OD2
|
B:ASP93
|
4.3
|
8.9
|
1.0
|
|
CB
|
B:ASP93
|
4.3
|
5.8
|
1.0
|
|
CA
|
B:TYR99
|
4.3
|
5.7
|
1.0
|
|
C
|
B:ASP93
|
4.4
|
5.4
|
1.0
|
|
CG
|
B:GLU104
|
4.4
|
5.3
|
1.0
|
|
N
|
B:ILE100
|
4.4
|
3.5
|
1.0
|
|
N
|
B:LYS94
|
4.4
|
8.1
|
1.0
|
|
O
|
B:HOH443
|
4.5
|
20.8
|
1.0
|
|
CB
|
B:ASN97
|
4.5
|
6.9
|
1.0
|
|
CA
|
B:ILE100
|
4.5
|
3.0
|
1.0
|
|
HB3
|
B:ASN97
|
4.5
|
8.2
|
1.0
|
|
N
|
B:SER101
|
4.6
|
6.5
|
1.0
|
|
N
|
B:GLY96
|
4.6
|
9.1
|
1.0
|
|
HB3
|
B:SER101
|
4.6
|
11.3
|
1.0
|
|
HB2
|
B:ASP93
|
4.6
|
6.9
|
1.0
|
|
H
|
B:GLY98
|
4.6
|
6.7
|
1.0
|
|
CB
|
B:ASP95
|
4.6
|
9.7
|
1.0
|
|
HG3
|
B:GLU104
|
4.7
|
6.3
|
1.0
|
|
CA
|
B:ASN97
|
4.8
|
7.0
|
1.0
|
|
CB
|
B:TYR99
|
4.8
|
5.1
|
1.0
|
|
CA
|
B:ASP95
|
4.8
|
10.0
|
1.0
|
|
HG2
|
B:GLU104
|
4.8
|
6.3
|
1.0
|
|
C
|
B:ASP95
|
4.9
|
9.9
|
1.0
|
|
O
|
B:HOH342
|
4.9
|
10.9
|
1.0
|
|
HD22
|
B:ASN97
|
4.9
|
11.7
|
1.0
|
|
N
|
B:GLY98
|
4.9
|
5.6
|
1.0
|
|
O
|
B:ASP93
|
4.9
|
11.0
|
1.0
|
|
HB2
|
B:GLU104
|
4.9
|
7.7
|
1.0
|
|
C
|
B:ILE100
|
5.0
|
5.3
|
1.0
|
|
Calcium binding site 2 out
of 4 in 5nin
Go back to
Calcium Binding Sites List in 5nin
Calcium binding site 2 out
of 4 in the Crystal Structure of AKAP79 Calmodulin Binding Domain Peptide in Complex with CA2+/Calmodulin
 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 AKAP79 Calmodulin Binding Domain Peptide in Complex with CA2+/Calmodulin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca202
b:6.2
occ:1.00
|
OD1
|
B:ASP129
|
2.2
|
11.5
|
1.0
|
|
OD1
|
B:ASP131
|
2.3
|
10.3
|
1.0
|
|
O
|
B:GLN135
|
2.3
|
6.9
|
1.0
|
|
OD1
|
B:ASP133
|
2.4
|
9.1
|
1.0
|
|
O
|
B:HOH360
|
2.4
|
10.0
|
1.0
|
|
OE1
|
B:GLU140
|
2.4
|
7.5
|
1.0
|
|
OE2
|
B:GLU140
|
2.6
|
8.4
|
1.0
|
|
CD
|
B:GLU140
|
2.8
|
8.4
|
1.0
|
|
CG
|
B:ASP131
|
3.3
|
12.7
|
1.0
|
|
CG
|
B:ASP133
|
3.3
|
15.6
|
1.0
|
|
CG
|
B:ASP129
|
3.4
|
12.5
|
1.0
|
|
HA
|
B:ASP129
|
3.4
|
12.2
|
1.0
|
|
H
|
B:GLN135
|
3.4
|
11.9
|
1.0
|
|
H
|
B:ASP133
|
3.5
|
10.3
|
1.0
|
|
C
|
B:GLN135
|
3.5
|
7.1
|
1.0
|
|
H
|
B:ASP131
|
3.5
|
10.8
|
1.0
|
|
OD2
|
B:ASP131
|
3.6
|
16.4
|
1.0
|
|
HA
|
B:VAL136
|
3.7
|
7.6
|
1.0
|
|
OD2
|
B:ASP133
|
3.7
|
13.4
|
1.0
|
|
H
|
B:ASN137
|
3.8
|
5.8
|
1.0
|
|
H
|
B:ILE130
|
4.1
|
11.8
|
1.0
|
|
CA
|
B:ASP129
|
4.1
|
10.2
|
1.0
|
|
N
|
B:GLN135
|
4.2
|
9.9
|
1.0
|
|
CB
|
B:ASP129
|
4.2
|
8.0
|
1.0
|
|
HG3
|
B:GLN135
|
4.2
|
31.8
|
1.0
|
|
H
|
B:GLY132
|
4.2
|
16.9
|
1.0
|
|
N
|
B:ASP133
|
4.2
|
8.6
|
1.0
|
|
OD2
|
B:ASP129
|
4.2
|
13.2
|
1.0
|
|
HB2
|
B:ASP129
|
4.3
|
9.6
|
1.0
|
|
N
|
B:ASP131
|
4.3
|
9.0
|
1.0
|
|
CG
|
B:GLU140
|
4.4
|
4.6
|
1.0
|
|
H
|
B:GLY134
|
4.4
|
13.2
|
1.0
|
|
N
|
B:VAL136
|
4.4
|
5.0
|
1.0
|
|
CA
|
B:VAL136
|
4.4
|
6.3
|
1.0
|
|
N
|
B:ASN137
|
4.4
|
4.8
|
1.0
|
|
HG2
|
B:GLN135
|
4.4
|
31.8
|
1.0
|
|
CA
|
B:GLN135
|
4.5
|
10.5
|
1.0
|
|
CB
|
B:ASP133
|
4.5
|
14.7
|
1.0
|
|
N
|
B:ILE130
|
4.5
|
9.9
|
1.0
|
|
CB
|
B:ASP131
|
4.6
|
9.8
|
1.0
|
|
C
|
B:ASP129
|
4.6
|
16.3
|
1.0
|
|
HB3
|
B:ASN137
|
4.6
|
6.9
|
1.0
|
|
N
|
B:GLY132
|
4.6
|
14.1
|
1.0
|
|
HB3
|
B:ASP133
|
4.7
|
17.6
|
1.0
|
|
N
|
B:GLY134
|
4.7
|
11.0
|
1.0
|
|
CG
|
B:GLN135
|
4.7
|
26.5
|
1.0
|
|
HG3
|
B:GLU140
|
4.7
|
5.5
|
1.0
|
|
CA
|
B:ASP133
|
4.7
|
8.3
|
1.0
|
|
HG2
|
B:GLU140
|
4.8
|
5.5
|
1.0
|
|
HD1
|
B:TYR99
|
4.8
|
13.7
|
1.0
|
|
CA
|
B:ASP131
|
4.8
|
10.6
|
1.0
|
|
C
|
B:VAL136
|
4.9
|
4.6
|
1.0
|
|
HB2
|
B:GLU140
|
4.9
|
4.2
|
1.0
|
|
C
|
B:ASP133
|
4.9
|
10.6
|
1.0
|
|
C
|
B:ASP131
|
4.9
|
12.7
|
1.0
|
|
HB3
|
B:ASP131
|
5.0
|
11.8
|
1.0
|
|
CG
|
B:ASN137
|
5.0
|
7.1
|
1.0
|
|
Calcium binding site 3 out
of 4 in 5nin
Go back to
Calcium Binding Sites List in 5nin
Calcium binding site 3 out
of 4 in the Crystal Structure of AKAP79 Calmodulin Binding Domain Peptide in Complex with CA2+/Calmodulin
 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 AKAP79 Calmodulin Binding Domain Peptide in Complex with CA2+/Calmodulin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca201
b:8.0
occ:1.00
|
O
|
A:TYR99
|
2.2
|
9.5
|
1.0
|
|
OD1
|
A:ASP93
|
2.3
|
14.0
|
1.0
|
|
OD1
|
A:ASP95
|
2.4
|
11.7
|
1.0
|
|
OD1
|
A:ASN97
|
2.4
|
10.0
|
1.0
|
|
O
|
A:HOH354
|
2.4
|
13.1
|
1.0
|
|
OE1
|
A:GLU104
|
2.5
|
11.3
|
1.0
|
|
OE2
|
A:GLU104
|
2.6
|
9.3
|
1.0
|
|
CD
|
A:GLU104
|
2.9
|
6.9
|
1.0
|
|
CG
|
A:ASP95
|
3.3
|
13.0
|
1.0
|
|
H
|
A:ASN97
|
3.3
|
13.4
|
1.0
|
|
CG
|
A:ASN97
|
3.4
|
11.0
|
1.0
|
|
H
|
A:TYR99
|
3.4
|
8.2
|
1.0
|
|
C
|
A:TYR99
|
3.5
|
8.5
|
1.0
|
|
CG
|
A:ASP93
|
3.5
|
10.7
|
1.0
|
|
H
|
A:ASP95
|
3.5
|
8.3
|
1.0
|
|
OD2
|
A:ASP95
|
3.7
|
11.2
|
1.0
|
|
HA
|
A:ASP93
|
3.7
|
9.3
|
1.0
|
|
HA
|
A:ILE100
|
3.8
|
6.3
|
1.0
|
|
H
|
A:SER101
|
4.0
|
9.7
|
1.0
|
|
HD21
|
A:ASN97
|
4.0
|
15.2
|
1.0
|
|
H
|
A:GLY96
|
4.1
|
16.2
|
1.0
|
|
HB2
|
A:TYR99
|
4.1
|
11.2
|
1.0
|
|
ND2
|
A:ASN97
|
4.1
|
12.7
|
1.0
|
|
N
|
A:TYR99
|
4.1
|
6.8
|
1.0
|
|
N
|
A:ASN97
|
4.2
|
11.2
|
1.0
|
|
N
|
A:ASP95
|
4.2
|
6.9
|
1.0
|
|
OD2
|
A:ASP93
|
4.2
|
9.8
|
1.0
|
|
CA
|
A:ASP93
|
4.3
|
7.8
|
1.0
|
|
CA
|
A:TYR99
|
4.3
|
5.3
|
1.0
|
|
CG
|
A:GLU104
|
4.4
|
9.5
|
1.0
|
|
C
|
A:ASP93
|
4.4
|
8.2
|
1.0
|
|
N
|
A:ILE100
|
4.4
|
5.0
|
1.0
|
|
H
|
A:LYS94
|
4.4
|
13.8
|
1.0
|
|
CB
|
A:ASP93
|
4.4
|
8.5
|
1.0
|
|
CB
|
A:ASN97
|
4.4
|
10.8
|
1.0
|
|
HB3
|
A:ASN97
|
4.4
|
13.0
|
1.0
|
|
O
|
A:HOH308
|
4.4
|
17.7
|
1.0
|
|
N
|
A:GLY96
|
4.5
|
13.5
|
1.0
|
|
CA
|
A:ILE100
|
4.5
|
5.2
|
1.0
|
|
CB
|
A:ASP95
|
4.5
|
12.0
|
1.0
|
|
H
|
A:GLY98
|
4.5
|
13.5
|
1.0
|
|
N
|
A:LYS94
|
4.5
|
11.5
|
1.0
|
|
N
|
A:SER101
|
4.6
|
8.1
|
1.0
|
|
HB3
|
A:SER101
|
4.6
|
13.0
|
1.0
|
|
HB2
|
A:ASP93
|
4.6
|
10.2
|
1.0
|
|
HG3
|
A:GLU104
|
4.7
|
11.4
|
1.0
|
|
CA
|
A:ASP95
|
4.7
|
9.2
|
1.0
|
|
CA
|
A:ASN97
|
4.7
|
11.0
|
1.0
|
|
CB
|
A:TYR99
|
4.8
|
9.3
|
1.0
|
|
C
|
A:ASP95
|
4.8
|
17.6
|
1.0
|
|
HG2
|
A:GLU104
|
4.8
|
11.4
|
1.0
|
|
O
|
A:ASP93
|
4.8
|
9.3
|
1.0
|
|
HB3
|
A:ASP95
|
4.8
|
14.4
|
1.0
|
|
N
|
A:GLY98
|
4.8
|
11.3
|
1.0
|
|
HD22
|
A:ASN97
|
4.9
|
15.2
|
1.0
|
|
HB2
|
A:GLU104
|
5.0
|
7.0
|
1.0
|
|
C
|
A:ILE100
|
5.0
|
7.9
|
1.0
|
|
C
|
A:ASN97
|
5.0
|
11.1
|
1.0
|
|
Calcium binding site 4 out
of 4 in 5nin
Go back to
Calcium Binding Sites List in 5nin
Calcium binding site 4 out
of 4 in the Crystal Structure of AKAP79 Calmodulin Binding Domain Peptide in Complex with CA2+/Calmodulin
 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 AKAP79 Calmodulin Binding Domain Peptide in Complex with CA2+/Calmodulin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca202
b:8.0
occ:1.00
|
O
|
A:HOH347
|
2.2
|
14.5
|
1.0
|
|
OD1
|
A:ASP129
|
2.2
|
12.1
|
1.0
|
|
O
|
A:GLN135
|
2.3
|
9.7
|
1.0
|
|
OD1
|
A:ASP131
|
2.3
|
14.9
|
1.0
|
|
OD1
|
A:ASP133
|
2.3
|
13.4
|
1.0
|
|
OE1
|
A:GLU140
|
2.4
|
6.3
|
1.0
|
|
OE2
|
A:GLU140
|
2.5
|
9.6
|
1.0
|
|
CD
|
A:GLU140
|
2.8
|
10.9
|
1.0
|
|
CG
|
A:ASP131
|
3.2
|
19.3
|
1.0
|
|
CG
|
A:ASP133
|
3.3
|
21.5
|
1.0
|
|
CG
|
A:ASP129
|
3.4
|
13.1
|
1.0
|
|
H
|
A:ASP133
|
3.4
|
16.4
|
1.0
|
|
HA
|
A:ASP129
|
3.5
|
9.2
|
1.0
|
|
H
|
A:GLN135
|
3.5
|
10.8
|
1.0
|
|
OD2
|
A:ASP131
|
3.5
|
24.7
|
1.0
|
|
H
|
A:ASP131
|
3.5
|
14.8
|
1.0
|
|
C
|
A:GLN135
|
3.5
|
7.1
|
1.0
|
|
HA
|
A:VAL136
|
3.7
|
6.0
|
1.0
|
|
OD2
|
A:ASP133
|
3.7
|
17.0
|
1.0
|
|
H
|
A:ASN137
|
3.7
|
6.5
|
1.0
|
|
H
|
A:GLY132
|
4.1
|
19.1
|
1.0
|
|
CA
|
A:ASP129
|
4.2
|
7.6
|
1.0
|
|
CB
|
A:ASP129
|
4.2
|
11.0
|
1.0
|
|
OD2
|
A:ASP129
|
4.2
|
17.1
|
1.0
|
|
N
|
A:ASP133
|
4.2
|
13.7
|
1.0
|
|
HB2
|
A:ASP129
|
4.2
|
13.2
|
1.0
|
|
N
|
A:GLN135
|
4.2
|
9.0
|
1.0
|
|
N
|
A:ASP131
|
4.3
|
12.3
|
1.0
|
|
H
|
A:ILE130
|
4.4
|
10.8
|
1.0
|
|
CG
|
A:GLU140
|
4.4
|
7.0
|
1.0
|
|
N
|
A:VAL136
|
4.4
|
6.2
|
1.0
|
|
CA
|
A:VAL136
|
4.4
|
5.0
|
1.0
|
|
N
|
A:ASN137
|
4.4
|
5.4
|
1.0
|
|
CB
|
A:ASP133
|
4.5
|
17.1
|
1.0
|
|
CB
|
A:ASP131
|
4.5
|
9.8
|
1.0
|
|
CA
|
A:GLN135
|
4.5
|
8.8
|
1.0
|
|
C
|
A:ASP129
|
4.5
|
10.9
|
1.0
|
|
H
|
A:GLY134
|
4.5
|
18.1
|
1.0
|
|
N
|
A:GLY132
|
4.6
|
15.9
|
1.0
|
|
HB3
|
A:ASN137
|
4.6
|
6.5
|
1.0
|
|
N
|
A:ILE130
|
4.6
|
9.0
|
1.0
|
|
HG3
|
A:GLN135
|
4.6
|
39.3
|
1.0
|
|
HB3
|
A:ASP133
|
4.7
|
20.5
|
1.0
|
|
HG3
|
A:GLU140
|
4.7
|
8.4
|
1.0
|
|
CA
|
A:ASP131
|
4.8
|
14.1
|
1.0
|
|
CA
|
A:ASP133
|
4.8
|
16.6
|
1.0
|
|
HG2
|
A:GLU140
|
4.8
|
8.4
|
1.0
|
|
HD1
|
A:TYR99
|
4.8
|
15.9
|
1.0
|
|
N
|
A:GLY134
|
4.8
|
15.1
|
1.0
|
|
C
|
A:VAL136
|
4.9
|
7.8
|
1.0
|
|
C
|
A:ASP131
|
4.9
|
19.4
|
1.0
|
|
HB3
|
A:ASP131
|
4.9
|
11.7
|
1.0
|
|
HB2
|
A:GLU140
|
4.9
|
6.7
|
1.0
|
|
C
|
A:ASP133
|
5.0
|
13.2
|
1.0
|
|
Reference:
N.Patel,
F.Stengel,
R.Aebersold,
M.G.Gold.
Molecular Basis of AKAP79 Regulation By Calmodulin. Nat Commun V. 8 1681 2017.
ISSN: ESSN 2041-1723
PubMed: 29162807
DOI: 10.1038/S41467-017-01715-W
Page generated: Mon Jul 15 09:05:02 2024
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