Calcium in PDB 6o20: Cryo-Em Structure of TRPV5 with Calmodulin Bound
Calcium Binding Sites:
The binding sites of Calcium atom in the Cryo-Em Structure of TRPV5 with Calmodulin Bound
(pdb code 6o20). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Cryo-Em Structure of TRPV5 with Calmodulin Bound, PDB code: 6o20:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6o20
Go back to
Calcium Binding Sites List in 6o20
Calcium binding site 1 out
of 4 in the Cryo-Em Structure of TRPV5 with Calmodulin Bound
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Cryo-Em Structure of TRPV5 with Calmodulin Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca201
b:0.2
occ:1.00
|
OD1
|
F:ASP129
|
2.5
|
0.5
|
1.0
|
OD1
|
F:ASP131
|
2.5
|
0.5
|
1.0
|
OD1
|
F:ASP133
|
2.6
|
0.7
|
1.0
|
O
|
F:GLN135
|
2.6
|
0.9
|
1.0
|
OD2
|
F:ASP131
|
3.0
|
0.5
|
1.0
|
CG
|
F:ASP131
|
3.1
|
0.5
|
1.0
|
OD2
|
F:ASP133
|
3.2
|
0.7
|
1.0
|
CG
|
F:ASP133
|
3.3
|
0.7
|
1.0
|
N
|
F:ASN137
|
3.4
|
0.6
|
1.0
|
CG
|
F:ASP129
|
3.6
|
0.5
|
1.0
|
C
|
F:GLN135
|
3.8
|
0.9
|
1.0
|
CB
|
F:ASN137
|
3.9
|
0.6
|
1.0
|
C
|
F:VAL136
|
3.9
|
0.5
|
1.0
|
CA
|
F:VAL136
|
4.0
|
0.5
|
1.0
|
OD2
|
F:ASP129
|
4.1
|
0.5
|
1.0
|
CA
|
F:ASN137
|
4.2
|
0.6
|
1.0
|
N
|
F:VAL136
|
4.4
|
0.5
|
1.0
|
CB
|
F:ASP131
|
4.6
|
0.5
|
1.0
|
CB
|
F:ASP133
|
4.7
|
0.7
|
1.0
|
O
|
F:VAL136
|
4.8
|
0.5
|
1.0
|
N
|
F:ASP133
|
4.8
|
0.7
|
1.0
|
CB
|
F:ASP129
|
4.8
|
0.5
|
1.0
|
N
|
F:ASP131
|
4.9
|
0.5
|
1.0
|
N
|
F:GLN135
|
4.9
|
0.9
|
1.0
|
CA
|
F:GLN135
|
4.9
|
0.9
|
1.0
|
CA
|
F:ASP129
|
4.9
|
0.5
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6o20
Go back to
Calcium Binding Sites List in 6o20
Calcium binding site 2 out
of 4 in the Cryo-Em Structure of TRPV5 with Calmodulin Bound
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Cryo-Em Structure of TRPV5 with Calmodulin Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca202
b:95.8
occ:1.00
|
O
|
F:TYR99
|
2.5
|
0.2
|
1.0
|
OD1
|
F:ASP95
|
2.5
|
99.3
|
1.0
|
OE1
|
F:GLU104
|
2.6
|
0.3
|
1.0
|
OD2
|
F:ASP95
|
2.6
|
99.3
|
1.0
|
OD1
|
F:ASP93
|
2.6
|
0.1
|
1.0
|
CG
|
F:ASP95
|
2.9
|
99.3
|
1.0
|
OD1
|
F:ASN97
|
3.0
|
98.2
|
1.0
|
CG
|
F:ASP93
|
3.5
|
0.1
|
1.0
|
C
|
F:TYR99
|
3.5
|
0.2
|
1.0
|
O
|
F:ILE100
|
3.6
|
0.9
|
1.0
|
OD2
|
F:ASP93
|
3.6
|
0.1
|
1.0
|
CD
|
F:GLU104
|
3.6
|
0.3
|
1.0
|
C
|
F:ILE100
|
3.7
|
0.9
|
1.0
|
CB
|
F:SER101
|
3.8
|
0.5
|
1.0
|
CG
|
F:ASN97
|
3.9
|
98.2
|
1.0
|
ND2
|
F:ASN97
|
4.0
|
98.2
|
1.0
|
N
|
F:SER101
|
4.1
|
0.5
|
1.0
|
CA
|
F:ILE100
|
4.2
|
0.9
|
1.0
|
OE2
|
F:GLU104
|
4.2
|
0.3
|
1.0
|
N
|
F:ILE100
|
4.2
|
0.9
|
1.0
|
CB
|
F:ASP95
|
4.3
|
99.3
|
1.0
|
CA
|
F:SER101
|
4.6
|
0.5
|
1.0
|
CA
|
F:TYR99
|
4.6
|
0.2
|
1.0
|
CG
|
F:GLU104
|
4.7
|
0.3
|
1.0
|
N
|
F:TYR99
|
4.8
|
0.2
|
1.0
|
CB
|
F:ASP93
|
4.8
|
0.1
|
1.0
|
CB
|
F:TYR99
|
4.8
|
0.2
|
1.0
|
N
|
F:ASP95
|
4.9
|
99.3
|
1.0
|
OG
|
F:SER101
|
5.0
|
0.5
|
1.0
|
CB
|
F:GLU104
|
5.0
|
0.3
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6o20
Go back to
Calcium Binding Sites List in 6o20
Calcium binding site 3 out
of 4 in the Cryo-Em Structure of TRPV5 with Calmodulin Bound
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Cryo-Em Structure of TRPV5 with Calmodulin Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca203
b:0.3
occ:1.00
|
O
|
F:GLY25
|
2.5
|
0.4
|
1.0
|
O
|
F:THR26
|
2.5
|
0.3
|
1.0
|
OE2
|
F:GLU31
|
2.5
|
0.7
|
1.0
|
OE1
|
F:GLU31
|
2.6
|
0.7
|
1.0
|
CD
|
F:GLU31
|
2.9
|
0.7
|
1.0
|
OD2
|
F:ASP20
|
3.4
|
0.5
|
1.0
|
C
|
F:GLY25
|
3.4
|
0.4
|
1.0
|
C
|
F:THR26
|
3.6
|
0.3
|
1.0
|
O
|
F:ASP22
|
3.8
|
0.1
|
1.0
|
N
|
F:THR26
|
4.1
|
0.3
|
1.0
|
CB
|
F:THR28
|
4.1
|
0.3
|
1.0
|
CA
|
F:THR26
|
4.3
|
0.3
|
1.0
|
CG
|
F:ASP20
|
4.3
|
0.5
|
1.0
|
CA
|
F:GLY23
|
4.3
|
0.1
|
1.0
|
CG
|
F:GLU31
|
4.4
|
0.7
|
1.0
|
CA
|
F:GLY25
|
4.5
|
0.4
|
1.0
|
N
|
F:THR28
|
4.5
|
0.3
|
1.0
|
OD1
|
F:ASP20
|
4.5
|
0.5
|
1.0
|
C
|
F:GLY23
|
4.6
|
0.1
|
1.0
|
N
|
F:GLY25
|
4.6
|
0.4
|
1.0
|
N
|
F:ILE27
|
4.6
|
0.6
|
1.0
|
C
|
F:ILE27
|
4.7
|
0.6
|
1.0
|
C
|
F:ASP22
|
4.8
|
0.1
|
1.0
|
CA
|
F:ILE27
|
4.8
|
0.6
|
1.0
|
N
|
F:ASP24
|
4.9
|
0.2
|
1.0
|
CA
|
F:THR28
|
4.9
|
0.3
|
1.0
|
O
|
F:GLY23
|
5.0
|
0.1
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6o20
Go back to
Calcium Binding Sites List in 6o20
Calcium binding site 4 out
of 4 in the Cryo-Em Structure of TRPV5 with Calmodulin Bound
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Cryo-Em Structure of TRPV5 with Calmodulin Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca204
b:0.9
occ:1.00
|
OE1
|
F:GLU67
|
2.5
|
0.8
|
1.0
|
O
|
F:THR62
|
2.5
|
0.1
|
1.0
|
OD1
|
F:ASP58
|
2.6
|
0.4
|
1.0
|
OD1
|
F:ASN60
|
3.0
|
0.6
|
1.0
|
OD2
|
F:ASP56
|
3.2
|
0.5
|
1.0
|
OD2
|
F:ASP64
|
3.4
|
1.0
|
1.0
|
OD1
|
F:ASP56
|
3.6
|
0.5
|
1.0
|
CD
|
F:GLU67
|
3.7
|
0.8
|
1.0
|
CG
|
F:ASP58
|
3.7
|
0.4
|
1.0
|
C
|
F:THR62
|
3.7
|
0.1
|
1.0
|
CG
|
F:ASP56
|
3.8
|
0.5
|
1.0
|
CA
|
F:ILE63
|
4.0
|
0.2
|
1.0
|
CG
|
F:ASN60
|
4.0
|
0.6
|
1.0
|
OD2
|
F:ASP58
|
4.0
|
0.4
|
1.0
|
O
|
F:ASN60
|
4.1
|
0.6
|
1.0
|
CG
|
F:ASP64
|
4.2
|
1.0
|
1.0
|
N
|
F:ASP64
|
4.3
|
1.0
|
1.0
|
OE2
|
F:GLU67
|
4.3
|
0.8
|
1.0
|
N
|
F:ILE63
|
4.3
|
0.2
|
1.0
|
OG1
|
F:THR62
|
4.3
|
0.1
|
1.0
|
O
|
F:GLY59
|
4.4
|
0.4
|
1.0
|
C
|
F:ILE63
|
4.5
|
0.2
|
1.0
|
ND2
|
F:ASN60
|
4.6
|
0.6
|
1.0
|
CG
|
F:GLU67
|
4.7
|
0.8
|
1.0
|
CB
|
F:ASP64
|
4.9
|
1.0
|
1.0
|
CA
|
F:THR62
|
4.9
|
0.1
|
1.0
|
OD1
|
F:ASP64
|
4.9
|
1.0
|
1.0
|
C
|
F:ASN60
|
4.9
|
0.6
|
1.0
|
O
|
F:ASP58
|
4.9
|
0.4
|
1.0
|
CG2
|
F:ILE63
|
5.0
|
0.2
|
1.0
|
CB
|
F:ASP58
|
5.0
|
0.4
|
1.0
|
|
Reference:
S.Dang,
M.K.Van Goor,
D.Asarnow,
Y.Wang,
D.Julius,
Y.Cheng,
J.Van Der Wijst.
Structural Insight Into TRPV5 Channel Function and Modulation. Proc.Natl.Acad.Sci.Usa V. 116 8869 2019.
ISSN: ESSN 1091-6490
PubMed: 30975749
DOI: 10.1073/PNAS.1820323116
Page generated: Tue Jul 16 12:19:30 2024
|