Calcium in PDB 7plp: Human Teneurin-4 C-Rich Domain
Protein crystallography data
The structure of Human Teneurin-4 C-Rich Domain, PDB code: 7plp
was solved by
J.W.Beugelink,
D.H.Meijer,
B.J.C.Janssen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
33.19 /
1.40
|
|
Space group
|
P 21 3
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.343,
66.343,
66.343,
90,
90,
90
|
|
R / Rfree (%)
|
15.5 /
17.1
|
Other elements in 7plp:
The structure of Human Teneurin-4 C-Rich Domain also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Human Teneurin-4 C-Rich Domain
(pdb code 7plp). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Human Teneurin-4 C-Rich Domain, PDB code: 7plp:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 7plp
Go back to
Calcium Binding Sites List in 7plp
Calcium binding site 1 out
of 6 in the Human Teneurin-4 C-Rich Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Human Teneurin-4 C-Rich Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca101
b:14.5
occ:1.00
|
O
|
A:ALA12
|
2.2
|
16.8
|
1.0
|
|
OD1
|
A:ASP26
|
2.3
|
15.3
|
1.0
|
|
OD1
|
A:ASN19
|
2.3
|
14.5
|
1.0
|
|
OE2
|
A:GLU10
|
2.3
|
14.5
|
1.0
|
|
O
|
A:LYS17
|
2.3
|
14.7
|
1.0
|
|
OD1
|
A:ASP15
|
2.3
|
15.1
|
1.0
|
|
CD
|
A:GLU10
|
3.2
|
14.2
|
1.0
|
|
CG
|
A:ASP15
|
3.4
|
17.0
|
1.0
|
|
CG
|
A:ASN19
|
3.4
|
15.2
|
1.0
|
|
C
|
A:ALA12
|
3.4
|
15.4
|
1.0
|
|
C
|
A:LYS17
|
3.5
|
14.8
|
1.0
|
|
CG
|
A:ASP26
|
3.5
|
15.5
|
1.0
|
|
CG
|
A:GLU10
|
3.8
|
15.5
|
1.0
|
|
N
|
A:LYS17
|
3.9
|
14.6
|
1.0
|
|
OD2
|
A:ASP15
|
3.9
|
18.0
|
1.0
|
|
ND2
|
A:ASN19
|
4.0
|
16.9
|
1.0
|
|
N
|
A:ASP26
|
4.1
|
14.4
|
1.0
|
|
OE1
|
A:GLU10
|
4.1
|
15.8
|
1.0
|
|
CA
|
A:LYS17
|
4.2
|
14.4
|
1.0
|
|
CA
|
A:CYS13
|
4.3
|
17.4
|
1.0
|
|
OD2
|
A:ASP26
|
4.3
|
16.3
|
1.0
|
|
N
|
A:CYS13
|
4.3
|
16.5
|
1.0
|
|
CA
|
A:ASP26
|
4.3
|
14.8
|
1.0
|
|
N
|
A:ASP15
|
4.3
|
17.1
|
1.0
|
|
N
|
A:ASN19
|
4.4
|
14.3
|
1.0
|
|
CB
|
A:ALA12
|
4.4
|
16.7
|
1.0
|
|
CA
|
A:ALA12
|
4.5
|
16.5
|
1.0
|
|
N
|
A:SER16
|
4.5
|
15.2
|
1.0
|
|
CB
|
A:ASP26
|
4.5
|
14.2
|
1.0
|
|
N
|
A:ASP18
|
4.5
|
14.1
|
1.0
|
|
CB
|
A:LYS17
|
4.6
|
19.2
|
1.0
|
|
CB
|
A:ASP15
|
4.6
|
17.5
|
1.0
|
|
C
|
A:CYS13
|
4.6
|
18.0
|
1.0
|
|
CB
|
A:ASN19
|
4.6
|
14.1
|
1.0
|
|
N
|
A:GLY14
|
4.7
|
18.3
|
1.0
|
|
CA
|
A:ASP15
|
4.8
|
16.8
|
1.0
|
|
C
|
A:ASP15
|
4.8
|
15.9
|
1.0
|
|
CA
|
A:ASP18
|
4.8
|
14.3
|
1.0
|
|
CG1
|
A:VAL25
|
4.8
|
17.8
|
1.0
|
|
C
|
A:SER16
|
4.9
|
16.2
|
1.0
|
|
N
|
A:ALA12
|
4.9
|
17.0
|
1.0
|
|
Calcium binding site 2 out
of 6 in 7plp
Go back to
Calcium Binding Sites List in 7plp
Calcium binding site 2 out
of 6 in the Human Teneurin-4 C-Rich Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Human Teneurin-4 C-Rich Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca102
b:15.6
occ:1.00
|
OD1
|
A:ASP20
|
2.3
|
16.1
|
1.0
|
|
O
|
A:LEU24
|
2.3
|
17.3
|
1.0
|
|
OD2
|
A:ASP29
|
2.3
|
16.0
|
1.0
|
|
OE1
|
A:GLU10
|
2.3
|
15.8
|
1.0
|
|
OD1
|
A:ASP18
|
2.3
|
16.5
|
1.0
|
|
OD1
|
A:ASP22
|
2.3
|
16.7
|
1.0
|
|
CG
|
A:ASP22
|
3.3
|
18.8
|
1.0
|
|
CG
|
A:ASP20
|
3.3
|
16.2
|
1.0
|
|
CG
|
A:ASP29
|
3.3
|
16.9
|
1.0
|
|
C
|
A:LEU24
|
3.4
|
17.6
|
1.0
|
|
CG
|
A:ASP18
|
3.5
|
15.8
|
1.0
|
|
CD
|
A:GLU10
|
3.5
|
14.2
|
1.0
|
|
OD2
|
A:ASP22
|
3.7
|
19.1
|
1.0
|
|
CB
|
A:ASP29
|
3.8
|
16.8
|
1.0
|
|
OD2
|
A:ASP20
|
3.8
|
17.1
|
1.0
|
|
N
|
A:LEU24
|
4.0
|
18.3
|
1.0
|
|
CB
|
A:GLU10
|
4.1
|
15.5
|
1.0
|
|
CA
|
A:LEU24
|
4.1
|
17.6
|
1.0
|
|
CA
|
A:CA103
|
4.1
|
17.3
|
1.0
|
|
CA
|
A:ASP18
|
4.2
|
14.3
|
1.0
|
|
CB
|
A:LEU24
|
4.2
|
17.9
|
1.0
|
|
N
|
A:ASP22
|
4.2
|
17.1
|
1.0
|
|
CB
|
A:ASP18
|
4.3
|
14.7
|
1.0
|
|
OD2
|
A:ASP18
|
4.3
|
18.7
|
1.0
|
|
N
|
A:ASP20
|
4.3
|
15.5
|
1.0
|
|
OE2
|
A:GLU10
|
4.3
|
14.5
|
1.0
|
|
CG
|
A:GLU10
|
4.4
|
15.5
|
1.0
|
|
C
|
A:ASP18
|
4.4
|
13.9
|
1.0
|
|
OD1
|
A:ASP29
|
4.4
|
17.8
|
1.0
|
|
CB
|
A:ASP22
|
4.5
|
19.5
|
1.0
|
|
N
|
A:ASN19
|
4.5
|
14.3
|
1.0
|
|
N
|
A:VAL25
|
4.5
|
16.3
|
1.0
|
|
CB
|
A:ASP20
|
4.6
|
15.4
|
1.0
|
|
N
|
A:GLY21
|
4.6
|
16.5
|
1.0
|
|
CA
|
A:ASP22
|
4.7
|
18.2
|
1.0
|
|
CA
|
A:VAL25
|
4.8
|
14.6
|
1.0
|
|
N
|
A:GLY23
|
4.8
|
19.6
|
1.0
|
|
CA
|
A:ASP20
|
4.8
|
15.1
|
1.0
|
|
C
|
A:ASP20
|
4.9
|
15.4
|
1.0
|
|
C
|
A:ASP22
|
4.9
|
19.5
|
1.0
|
|
Calcium binding site 3 out
of 6 in 7plp
Go back to
Calcium Binding Sites List in 7plp
Calcium binding site 3 out
of 6 in the Human Teneurin-4 C-Rich Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Human Teneurin-4 C-Rich Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca103
b:17.3
occ:1.00
|
OD2
|
A:ASP22
|
2.3
|
19.1
|
1.0
|
|
OD2
|
A:ASP31
|
2.3
|
19.6
|
1.0
|
|
OD2
|
A:ASP20
|
2.3
|
17.1
|
1.0
|
|
O
|
A:HOH222
|
2.4
|
26.3
|
1.0
|
|
O
|
A:HOH212
|
2.4
|
21.2
|
1.0
|
|
OD1
|
A:ASP29
|
2.5
|
17.8
|
1.0
|
|
OD2
|
A:ASP29
|
2.5
|
16.0
|
1.0
|
|
CG
|
A:ASP29
|
2.8
|
16.9
|
1.0
|
|
CG
|
A:ASP31
|
3.2
|
18.7
|
1.0
|
|
CG
|
A:ASP22
|
3.3
|
18.8
|
1.0
|
|
CG
|
A:ASP20
|
3.4
|
16.2
|
1.0
|
|
OD1
|
A:ASP31
|
3.7
|
24.7
|
1.0
|
|
OD1
|
A:ASP20
|
3.7
|
16.1
|
1.0
|
|
OD1
|
A:ASP22
|
3.9
|
16.7
|
1.0
|
|
CA
|
A:CA102
|
4.1
|
15.6
|
1.0
|
|
CB
|
A:ASP31
|
4.2
|
16.8
|
1.0
|
|
CB
|
A:ASP22
|
4.3
|
19.5
|
1.0
|
|
CB
|
A:ASP29
|
4.3
|
16.8
|
1.0
|
|
N
|
A:GLU10
|
4.3
|
15.1
|
1.0
|
|
O
|
A:HOH215
|
4.3
|
55.5
|
1.0
|
|
O
|
A:HOH224
|
4.4
|
58.9
|
1.0
|
|
CA
|
A:MET9
|
4.6
|
17.0
|
0.5
|
|
O
|
A:SER8
|
4.6
|
17.7
|
1.0
|
|
CB
|
A:ASP20
|
4.7
|
15.4
|
1.0
|
|
CA
|
A:MET9
|
4.7
|
15.8
|
0.5
|
|
CB
|
A:GLU10
|
4.7
|
15.5
|
1.0
|
|
N
|
A:ASP31
|
4.8
|
18.4
|
1.0
|
|
Calcium binding site 4 out
of 6 in 7plp
Go back to
Calcium Binding Sites List in 7plp
Calcium binding site 4 out
of 6 in the Human Teneurin-4 C-Rich Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Human Teneurin-4 C-Rich Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca101
b:15.5
occ:1.00
|
OD2
|
B:ASP22
|
2.3
|
17.9
|
1.0
|
|
OD2
|
B:ASP20
|
2.3
|
16.2
|
1.0
|
|
OD2
|
B:ASP31
|
2.3
|
16.6
|
1.0
|
|
O
|
B:HOH216
|
2.4
|
18.5
|
1.0
|
|
O
|
B:HOH224
|
2.4
|
23.1
|
1.0
|
|
OD2
|
B:ASP29
|
2.5
|
14.3
|
1.0
|
|
OD1
|
B:ASP29
|
2.5
|
16.4
|
1.0
|
|
CG
|
B:ASP29
|
2.8
|
13.6
|
1.0
|
|
CG
|
B:ASP31
|
3.2
|
18.0
|
1.0
|
|
CG
|
B:ASP22
|
3.3
|
16.5
|
1.0
|
|
CG
|
B:ASP20
|
3.3
|
14.3
|
1.0
|
|
OD1
|
B:ASP20
|
3.7
|
15.9
|
1.0
|
|
OD1
|
B:ASP31
|
3.8
|
23.1
|
1.0
|
|
OD1
|
B:ASP22
|
3.9
|
15.4
|
1.0
|
|
O
|
B:HOH218
|
4.1
|
49.6
|
1.0
|
|
CA
|
B:CA102
|
4.1
|
14.0
|
1.0
|
|
O
|
B:HOH217
|
4.2
|
45.4
|
1.0
|
|
CB
|
B:ASP31
|
4.2
|
16.7
|
1.0
|
|
N
|
B:GLU10
|
4.3
|
14.4
|
1.0
|
|
CB
|
B:ASP29
|
4.3
|
13.6
|
1.0
|
|
CB
|
B:ASP22
|
4.4
|
18.0
|
1.0
|
|
O
|
B:HOH231
|
4.6
|
54.7
|
1.0
|
|
CA
|
B:MET9
|
4.6
|
16.5
|
0.5
|
|
O
|
B:SER8
|
4.6
|
17.3
|
1.0
|
|
CB
|
B:GLU10
|
4.6
|
14.5
|
1.0
|
|
CB
|
B:ASP20
|
4.7
|
14.8
|
1.0
|
|
CA
|
B:MET9
|
4.7
|
17.6
|
0.5
|
|
N
|
B:ASP31
|
4.9
|
15.5
|
1.0
|
|
C
|
B:MET9
|
5.0
|
15.7
|
0.5
|
|
Calcium binding site 5 out
of 6 in 7plp
Go back to
Calcium Binding Sites List in 7plp
Calcium binding site 5 out
of 6 in the Human Teneurin-4 C-Rich Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Human Teneurin-4 C-Rich Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca102
b:14.0
occ:1.00
|
OD1
|
B:ASP20
|
2.3
|
15.9
|
1.0
|
|
O
|
B:LEU24
|
2.3
|
15.7
|
1.0
|
|
OD2
|
B:ASP29
|
2.3
|
14.3
|
1.0
|
|
OE1
|
B:GLU10
|
2.3
|
14.7
|
1.0
|
|
OD1
|
B:ASP18
|
2.3
|
16.3
|
1.0
|
|
OD1
|
B:ASP22
|
2.3
|
15.4
|
1.0
|
|
CG
|
B:ASP22
|
3.3
|
16.5
|
1.0
|
|
CG
|
B:ASP20
|
3.3
|
14.3
|
1.0
|
|
C
|
B:LEU24
|
3.4
|
14.6
|
1.0
|
|
CG
|
B:ASP29
|
3.4
|
13.6
|
1.0
|
|
CD
|
B:GLU10
|
3.5
|
13.3
|
1.0
|
|
CG
|
B:ASP18
|
3.5
|
14.8
|
1.0
|
|
OD2
|
B:ASP22
|
3.7
|
17.9
|
1.0
|
|
OD2
|
B:ASP20
|
3.8
|
16.2
|
1.0
|
|
CB
|
B:ASP29
|
3.9
|
13.6
|
1.0
|
|
N
|
B:LEU24
|
3.9
|
15.7
|
1.0
|
|
CA
|
B:LEU24
|
4.0
|
14.5
|
1.0
|
|
CB
|
B:GLU10
|
4.0
|
14.5
|
1.0
|
|
CB
|
B:LEU24
|
4.0
|
15.4
|
1.0
|
|
CA
|
B:CA101
|
4.1
|
15.5
|
1.0
|
|
CA
|
B:ASP18
|
4.2
|
14.5
|
1.0
|
|
CB
|
B:ASP18
|
4.3
|
14.7
|
1.0
|
|
N
|
B:ASP20
|
4.3
|
13.9
|
1.0
|
|
OE2
|
B:GLU10
|
4.3
|
12.0
|
1.0
|
|
N
|
B:ASP22
|
4.3
|
17.2
|
1.0
|
|
CG
|
B:GLU10
|
4.4
|
13.4
|
1.0
|
|
C
|
B:ASP18
|
4.4
|
13.8
|
1.0
|
|
OD2
|
B:ASP18
|
4.4
|
16.8
|
1.0
|
|
N
|
B:ASN19
|
4.4
|
13.4
|
1.0
|
|
OD1
|
B:ASP29
|
4.5
|
16.4
|
1.0
|
|
N
|
B:VAL25
|
4.5
|
14.3
|
1.0
|
|
CB
|
B:ASP22
|
4.5
|
18.0
|
1.0
|
|
N
|
B:GLY21
|
4.5
|
16.5
|
1.0
|
|
CB
|
B:ASP20
|
4.6
|
14.8
|
1.0
|
|
N
|
B:GLY23
|
4.8
|
15.8
|
1.0
|
|
CA
|
B:VAL25
|
4.8
|
13.7
|
1.0
|
|
CA
|
B:ASP20
|
4.8
|
14.5
|
1.0
|
|
CA
|
B:ASP22
|
4.8
|
17.1
|
1.0
|
|
C
|
B:ASP20
|
4.9
|
16.8
|
1.0
|
|
C
|
B:ASP22
|
5.0
|
16.4
|
1.0
|
|
CG
|
B:LEU24
|
5.0
|
18.5
|
1.0
|
|
Calcium binding site 6 out
of 6 in 7plp
Go back to
Calcium Binding Sites List in 7plp
Calcium binding site 6 out
of 6 in the Human Teneurin-4 C-Rich Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Human Teneurin-4 C-Rich Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca103
b:13.6
occ:1.00
|
O
|
B:ALA12
|
2.2
|
15.9
|
1.0
|
|
OD1
|
B:ASN19
|
2.3
|
14.4
|
1.0
|
|
OD1
|
B:ASP26
|
2.3
|
13.4
|
1.0
|
|
O
|
B:LYS17
|
2.3
|
14.5
|
1.0
|
|
OD1
|
B:ASP15
|
2.3
|
14.8
|
1.0
|
|
OE2
|
B:GLU10
|
2.3
|
12.0
|
1.0
|
|
CD
|
B:GLU10
|
3.2
|
13.3
|
1.0
|
|
CG
|
B:ASP15
|
3.4
|
15.5
|
1.0
|
|
CG
|
B:ASN19
|
3.4
|
14.4
|
1.0
|
|
C
|
B:LYS17
|
3.4
|
13.9
|
1.0
|
|
C
|
B:ALA12
|
3.5
|
13.8
|
1.0
|
|
CG
|
B:ASP26
|
3.5
|
13.7
|
1.0
|
|
CG
|
B:GLU10
|
3.9
|
13.4
|
1.0
|
|
N
|
B:LYS17
|
3.9
|
13.8
|
1.0
|
|
OD2
|
B:ASP15
|
3.9
|
16.3
|
1.0
|
|
N
|
B:ASP26
|
4.0
|
13.7
|
1.0
|
|
ND2
|
B:ASN19
|
4.1
|
15.1
|
1.0
|
|
OE1
|
B:GLU10
|
4.1
|
14.7
|
1.0
|
|
CA
|
B:LYS17
|
4.1
|
13.9
|
1.0
|
|
CA
|
B:CYS13
|
4.3
|
14.9
|
1.0
|
|
OD2
|
B:ASP26
|
4.3
|
15.3
|
1.0
|
|
CA
|
B:ASP26
|
4.3
|
13.3
|
1.0
|
|
N
|
B:CYS13
|
4.3
|
14.5
|
1.0
|
|
N
|
B:ASP15
|
4.4
|
14.6
|
1.0
|
|
N
|
B:ASN19
|
4.4
|
13.4
|
1.0
|
|
CB
|
B:ALA12
|
4.4
|
15.8
|
1.0
|
|
CB
|
B:LYS17
|
4.4
|
15.5
|
1.0
|
|
CA
|
B:ALA12
|
4.5
|
13.8
|
1.0
|
|
CB
|
B:ASP26
|
4.5
|
14.0
|
1.0
|
|
N
|
B:ASP18
|
4.5
|
13.0
|
1.0
|
|
N
|
B:SER16
|
4.6
|
14.7
|
1.0
|
|
CB
|
B:ASP15
|
4.6
|
15.7
|
1.0
|
|
CB
|
B:ASN19
|
4.6
|
14.4
|
1.0
|
|
C
|
B:CYS13
|
4.6
|
15.3
|
1.0
|
|
N
|
B:GLY14
|
4.7
|
14.0
|
1.0
|
|
CA
|
B:ASP15
|
4.8
|
15.1
|
1.0
|
|
CG1
|
B:VAL25
|
4.8
|
15.5
|
1.0
|
|
CA
|
B:ASP18
|
4.8
|
14.5
|
1.0
|
|
C
|
B:ASP15
|
4.9
|
13.9
|
1.0
|
|
N
|
B:ALA12
|
5.0
|
14.1
|
1.0
|
|
C
|
B:SER16
|
5.0
|
14.8
|
1.0
|
|
Reference:
D.H.Meijer,
C.P.Frias,
J.W.Beugelink,
Y.N.Deurloo,
B.J.C.Janssen.
TENEURIN4 Dimer Structures Reveal A Calcium-Stabilized Compact Conformation Supporting Homomeric Trans-Interactions. Embo J. V. 41 07505 2022.
ISSN: ESSN 1460-2075
PubMed: 35099835
DOI: 10.15252/EMBJ.2020107505
Page generated: Fri Jul 19 03:06:51 2024
|
