Calcium in PDB 7d7e: Structure of PKD1L3-Ctd/PKD2L1 in Apo State
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of PKD1L3-Ctd/PKD2L1 in Apo State
(pdb code 7d7e). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Structure of PKD1L3-Ctd/PKD2L1 in Apo State, PDB code: 7d7e:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 7d7e
Go back to
Calcium Binding Sites List in 7d7e
Calcium binding site 1 out
of 3 in the Structure of PKD1L3-Ctd/PKD2L1 in Apo State
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of PKD1L3-Ctd/PKD2L1 in Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca704
b:30.0
occ:1.00
|
ND2
|
B:ASN387
|
2.6
|
100.5
|
1.0
|
OD1
|
B:ASP390
|
2.7
|
92.6
|
1.0
|
OE1
|
B:GLU373
|
2.8
|
115.0
|
1.0
|
OE2
|
B:GLU370
|
3.4
|
107.9
|
1.0
|
NZ
|
B:LYS455
|
3.4
|
92.4
|
1.0
|
CD
|
B:GLU373
|
3.6
|
115.0
|
1.0
|
OE1
|
B:GLU370
|
3.6
|
107.9
|
1.0
|
OE2
|
B:GLU373
|
3.7
|
115.0
|
1.0
|
CG
|
B:ASN387
|
3.9
|
100.5
|
1.0
|
CD
|
B:GLU370
|
3.9
|
107.9
|
1.0
|
CG
|
B:ASP390
|
3.9
|
92.6
|
1.0
|
CA
|
B:ASN387
|
4.6
|
100.5
|
1.0
|
CB
|
B:ASN387
|
4.6
|
100.5
|
1.0
|
CB
|
B:ASP390
|
4.7
|
92.6
|
1.0
|
OD1
|
B:ASN387
|
4.7
|
100.5
|
1.0
|
CE
|
B:LYS455
|
4.8
|
92.4
|
1.0
|
OD2
|
B:ASP390
|
4.8
|
92.6
|
1.0
|
N
|
B:ASN387
|
4.9
|
100.5
|
1.0
|
|
Calcium binding site 2 out
of 3 in 7d7e
Go back to
Calcium Binding Sites List in 7d7e
Calcium binding site 2 out
of 3 in the Structure of PKD1L3-Ctd/PKD2L1 in Apo State
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of PKD1L3-Ctd/PKD2L1 in Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca704
b:30.0
occ:1.00
|
OE2
|
C:GLU373
|
2.4
|
105.2
|
1.0
|
OE2
|
C:GLU370
|
2.5
|
100.2
|
1.0
|
OD1
|
C:ASP390
|
2.5
|
89.4
|
1.0
|
OD1
|
C:ASN387
|
2.7
|
96.8
|
1.0
|
NZ
|
C:LYS455
|
3.0
|
88.6
|
1.0
|
CD
|
C:GLU373
|
3.3
|
105.2
|
1.0
|
CD
|
C:GLU370
|
3.6
|
100.2
|
1.0
|
CG
|
C:ASP390
|
3.6
|
89.4
|
1.0
|
OE1
|
C:GLU373
|
3.6
|
105.2
|
1.0
|
CG
|
C:ASN387
|
3.9
|
96.8
|
1.0
|
OE1
|
C:GLU370
|
3.9
|
100.2
|
1.0
|
CE
|
C:LYS455
|
4.1
|
88.6
|
1.0
|
CB
|
C:ASP390
|
4.2
|
89.4
|
1.0
|
OD2
|
C:ASP390
|
4.5
|
89.4
|
1.0
|
CA
|
C:ASN387
|
4.6
|
96.8
|
1.0
|
CG
|
C:GLU373
|
4.6
|
105.2
|
1.0
|
OE1
|
C:GLU369
|
4.7
|
98.8
|
1.0
|
ND2
|
C:ASN387
|
4.7
|
96.8
|
1.0
|
CB
|
C:ASN387
|
4.8
|
96.8
|
1.0
|
CG
|
C:GLU370
|
4.8
|
100.2
|
1.0
|
|
Calcium binding site 3 out
of 3 in 7d7e
Go back to
Calcium Binding Sites List in 7d7e
Calcium binding site 3 out
of 3 in the Structure of PKD1L3-Ctd/PKD2L1 in Apo State
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of PKD1L3-Ctd/PKD2L1 in Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca803
b:30.0
occ:1.00
|
OD1
|
D:ASN387
|
1.9
|
119.9
|
1.0
|
OD2
|
D:ASP390
|
2.7
|
115.1
|
1.0
|
OE2
|
D:GLU373
|
2.8
|
123.0
|
1.0
|
OE1
|
D:GLU370
|
3.0
|
120.8
|
1.0
|
CG
|
D:ASN387
|
3.1
|
119.9
|
1.0
|
OE2
|
D:GLU370
|
3.4
|
120.8
|
1.0
|
CD
|
D:GLU370
|
3.6
|
120.8
|
1.0
|
ND2
|
D:ASN387
|
3.8
|
119.9
|
1.0
|
CG
|
D:ASP390
|
3.8
|
115.1
|
1.0
|
NZ
|
D:LYS455
|
4.0
|
109.1
|
1.0
|
CD
|
D:GLU373
|
4.0
|
123.0
|
1.0
|
CB
|
D:ASN387
|
4.2
|
119.9
|
1.0
|
CA
|
D:ASN387
|
4.2
|
119.9
|
1.0
|
N
|
D:ASN387
|
4.5
|
119.9
|
1.0
|
CB
|
D:ASP390
|
4.6
|
115.1
|
1.0
|
OE1
|
D:GLU373
|
4.6
|
123.0
|
1.0
|
O
|
D:TRP386
|
4.7
|
116.6
|
1.0
|
OD1
|
D:ASP390
|
4.7
|
115.1
|
1.0
|
C
|
D:TRP386
|
4.7
|
116.6
|
1.0
|
CE
|
D:LYS455
|
5.0
|
109.1
|
1.0
|
|
Reference:
Q.Su,
M.Chen,
Y.Wang,
B.Li,
D.Jing,
X.Zhan,
Y.Yu,
Y.Shi.
Structural Basis For Ca 2+ Activation of the Heteromeric PKD1L3/PKD2L1 Channel. Nat Commun V. 12 4871 2021.
ISSN: ESSN 2041-1723
PubMed: 34381056
DOI: 10.1038/S41467-021-25216-Z
Page generated: Fri Sep 24 12:13:35 2021
|