Calcium in PDB 7mbs: Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State)
Calcium Binding Sites:
The binding sites of Calcium atom in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State)
(pdb code 7mbs). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State), PDB code: 7mbs:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 7mbs
Go back to
Calcium Binding Sites List in 7mbs
Calcium binding site 1 out
of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State)
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 Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1502
b:37.5
occ:1.00
|
O
|
A:HOH1604
|
2.4
|
30.0
|
1.0
|
O
|
A:HOH1603
|
2.5
|
30.0
|
1.0
|
OE1
|
A:GLU768
|
2.5
|
36.4
|
1.0
|
OD1
|
A:ASN794
|
2.5
|
33.8
|
1.0
|
OE1
|
A:GLN771
|
2.6
|
39.5
|
1.0
|
OD2
|
A:ASP797
|
2.6
|
33.4
|
1.0
|
CD
|
A:GLU768
|
3.4
|
36.4
|
1.0
|
CD
|
A:GLN771
|
3.6
|
39.5
|
1.0
|
NH1
|
A:ARG834
|
3.6
|
26.4
|
1.0
|
CG
|
A:ASN794
|
3.7
|
33.8
|
1.0
|
OE2
|
A:GLU768
|
3.8
|
36.4
|
1.0
|
CG
|
A:ASP797
|
3.8
|
33.4
|
1.0
|
NE2
|
A:GLN771
|
3.9
|
39.5
|
1.0
|
CA
|
A:ASN794
|
4.3
|
33.8
|
1.0
|
OH
|
A:TYR788
|
4.4
|
37.4
|
1.0
|
CB
|
A:ASP797
|
4.5
|
33.4
|
1.0
|
CE1
|
A:TYR788
|
4.5
|
37.4
|
1.0
|
CB
|
A:ASN794
|
4.6
|
33.8
|
1.0
|
ND2
|
A:ASN794
|
4.6
|
33.8
|
1.0
|
CG
|
A:GLU768
|
4.8
|
36.4
|
1.0
|
N
|
A:ASN794
|
4.8
|
33.8
|
1.0
|
OD1
|
A:ASP797
|
4.8
|
33.4
|
1.0
|
CZ
|
A:ARG834
|
4.9
|
26.4
|
1.0
|
O
|
A:TRP793
|
4.9
|
31.2
|
1.0
|
CZ
|
A:TYR788
|
4.9
|
37.4
|
1.0
|
CG
|
A:GLN771
|
4.9
|
39.5
|
1.0
|
C
|
A:TRP793
|
5.0
|
31.2
|
1.0
|
|
Calcium binding site 2 out
of 8 in 7mbs
Go back to
Calcium Binding Sites List in 7mbs
Calcium binding site 2 out
of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State)
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 Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1503
b:56.6
occ:1.00
|
O
|
A:ASP333
|
2.5
|
57.8
|
1.0
|
OE1
|
A:GLU337
|
2.5
|
46.7
|
1.0
|
OE1
|
A:GLU212
|
2.5
|
56.2
|
1.0
|
OE2
|
A:GLU337
|
2.8
|
46.7
|
1.0
|
OD1
|
A:ASP336
|
2.8
|
49.8
|
1.0
|
OD2
|
A:ASP336
|
3.0
|
49.8
|
1.0
|
CD
|
A:GLU337
|
3.0
|
46.7
|
1.0
|
CG
|
A:ASP336
|
3.3
|
49.8
|
1.0
|
SG
|
A:CYS324
|
3.3
|
56.0
|
1.0
|
C
|
A:ASP333
|
3.7
|
57.8
|
1.0
|
CD
|
A:GLU212
|
3.7
|
56.2
|
1.0
|
OE2
|
A:GLU212
|
4.4
|
56.2
|
1.0
|
CB
|
A:CYS324
|
4.4
|
56.0
|
1.0
|
CA
|
A:ASP333
|
4.5
|
57.8
|
1.0
|
CG
|
A:GLU337
|
4.5
|
46.7
|
1.0
|
N
|
A:PHE334
|
4.6
|
52.7
|
1.0
|
CB
|
A:GLU212
|
4.7
|
56.2
|
1.0
|
CB
|
A:ASP333
|
4.7
|
57.8
|
1.0
|
CB
|
A:ASP336
|
4.7
|
49.8
|
1.0
|
CA
|
A:PHE334
|
4.7
|
52.7
|
1.0
|
CG
|
A:GLU212
|
4.8
|
56.2
|
1.0
|
N
|
A:GLU337
|
4.9
|
46.7
|
1.0
|
|
Calcium binding site 3 out
of 8 in 7mbs
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Calcium Binding Sites List in 7mbs
Calcium binding site 3 out
of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State)
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 Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1502
b:37.5
occ:1.00
|
O
|
B:HOH1604
|
2.4
|
30.0
|
1.0
|
O
|
B:HOH1603
|
2.5
|
30.0
|
1.0
|
OE1
|
B:GLU768
|
2.5
|
36.4
|
1.0
|
OD1
|
B:ASN794
|
2.5
|
33.8
|
1.0
|
OE1
|
B:GLN771
|
2.6
|
39.5
|
1.0
|
OD2
|
B:ASP797
|
2.6
|
33.4
|
1.0
|
CD
|
B:GLU768
|
3.4
|
36.4
|
1.0
|
CD
|
B:GLN771
|
3.6
|
39.5
|
1.0
|
NH1
|
B:ARG834
|
3.6
|
26.4
|
1.0
|
CG
|
B:ASN794
|
3.7
|
33.8
|
1.0
|
OE2
|
B:GLU768
|
3.8
|
36.4
|
1.0
|
CG
|
B:ASP797
|
3.8
|
33.4
|
1.0
|
NE2
|
B:GLN771
|
3.9
|
39.5
|
1.0
|
CA
|
B:ASN794
|
4.3
|
33.8
|
1.0
|
OH
|
B:TYR788
|
4.4
|
37.4
|
1.0
|
CB
|
B:ASP797
|
4.5
|
33.4
|
1.0
|
CE1
|
B:TYR788
|
4.5
|
37.4
|
1.0
|
CB
|
B:ASN794
|
4.6
|
33.8
|
1.0
|
ND2
|
B:ASN794
|
4.6
|
33.8
|
1.0
|
CG
|
B:GLU768
|
4.8
|
36.4
|
1.0
|
N
|
B:ASN794
|
4.8
|
33.8
|
1.0
|
OD1
|
B:ASP797
|
4.8
|
33.4
|
1.0
|
CZ
|
B:ARG834
|
4.9
|
26.4
|
1.0
|
O
|
B:TRP793
|
4.9
|
31.2
|
1.0
|
CZ
|
B:TYR788
|
4.9
|
37.4
|
1.0
|
CG
|
B:GLN771
|
4.9
|
39.5
|
1.0
|
C
|
B:TRP793
|
5.0
|
31.2
|
1.0
|
|
Calcium binding site 4 out
of 8 in 7mbs
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Calcium Binding Sites List in 7mbs
Calcium binding site 4 out
of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State)
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 Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1503
b:56.6
occ:1.00
|
O
|
B:ASP333
|
2.5
|
57.8
|
1.0
|
OE1
|
B:GLU337
|
2.5
|
46.7
|
1.0
|
OE1
|
B:GLU212
|
2.5
|
56.2
|
1.0
|
OE2
|
B:GLU337
|
2.8
|
46.7
|
1.0
|
OD1
|
B:ASP336
|
2.8
|
49.8
|
1.0
|
OD2
|
B:ASP336
|
3.0
|
49.8
|
1.0
|
CD
|
B:GLU337
|
3.0
|
46.7
|
1.0
|
CG
|
B:ASP336
|
3.3
|
49.8
|
1.0
|
SG
|
B:CYS324
|
3.3
|
56.0
|
1.0
|
C
|
B:ASP333
|
3.7
|
57.8
|
1.0
|
CD
|
B:GLU212
|
3.7
|
56.2
|
1.0
|
OE2
|
B:GLU212
|
4.4
|
56.2
|
1.0
|
CB
|
B:CYS324
|
4.4
|
56.0
|
1.0
|
CA
|
B:ASP333
|
4.5
|
57.8
|
1.0
|
CG
|
B:GLU337
|
4.5
|
46.7
|
1.0
|
N
|
B:PHE334
|
4.6
|
52.7
|
1.0
|
CB
|
B:GLU212
|
4.7
|
56.2
|
1.0
|
CB
|
B:ASP333
|
4.7
|
57.8
|
1.0
|
CB
|
B:ASP336
|
4.7
|
49.8
|
1.0
|
CA
|
B:PHE334
|
4.7
|
52.7
|
1.0
|
CG
|
B:GLU212
|
4.8
|
56.2
|
1.0
|
N
|
B:GLU337
|
4.9
|
46.7
|
1.0
|
|
Calcium binding site 5 out
of 8 in 7mbs
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Calcium Binding Sites List in 7mbs
Calcium binding site 5 out
of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca1502
b:37.5
occ:1.00
|
O
|
C:HOH1604
|
2.4
|
30.0
|
1.0
|
O
|
C:HOH1603
|
2.5
|
30.0
|
1.0
|
OE1
|
C:GLU768
|
2.5
|
36.4
|
1.0
|
OD1
|
C:ASN794
|
2.5
|
33.8
|
1.0
|
OE1
|
C:GLN771
|
2.6
|
39.5
|
1.0
|
OD2
|
C:ASP797
|
2.6
|
33.4
|
1.0
|
CD
|
C:GLU768
|
3.4
|
36.4
|
1.0
|
CD
|
C:GLN771
|
3.6
|
39.5
|
1.0
|
NH1
|
C:ARG834
|
3.6
|
26.4
|
1.0
|
CG
|
C:ASN794
|
3.7
|
33.8
|
1.0
|
OE2
|
C:GLU768
|
3.8
|
36.4
|
1.0
|
CG
|
C:ASP797
|
3.8
|
33.4
|
1.0
|
NE2
|
C:GLN771
|
3.9
|
39.5
|
1.0
|
CA
|
C:ASN794
|
4.3
|
33.8
|
1.0
|
OH
|
C:TYR788
|
4.4
|
37.4
|
1.0
|
CB
|
C:ASP797
|
4.5
|
33.4
|
1.0
|
CE1
|
C:TYR788
|
4.5
|
37.4
|
1.0
|
CB
|
C:ASN794
|
4.6
|
33.8
|
1.0
|
ND2
|
C:ASN794
|
4.6
|
33.8
|
1.0
|
CG
|
C:GLU768
|
4.8
|
36.4
|
1.0
|
N
|
C:ASN794
|
4.8
|
33.8
|
1.0
|
OD1
|
C:ASP797
|
4.8
|
33.4
|
1.0
|
CZ
|
C:ARG834
|
4.9
|
26.4
|
1.0
|
O
|
C:TRP793
|
4.9
|
31.2
|
1.0
|
CZ
|
C:TYR788
|
4.9
|
37.4
|
1.0
|
CG
|
C:GLN771
|
4.9
|
39.5
|
1.0
|
C
|
C:TRP793
|
5.0
|
31.2
|
1.0
|
|
Calcium binding site 6 out
of 8 in 7mbs
Go back to
Calcium Binding Sites List in 7mbs
Calcium binding site 6 out
of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca1503
b:56.6
occ:1.00
|
O
|
C:ASP333
|
2.5
|
57.8
|
1.0
|
OE1
|
C:GLU337
|
2.5
|
46.7
|
1.0
|
OE1
|
C:GLU212
|
2.5
|
56.2
|
1.0
|
OE2
|
C:GLU337
|
2.8
|
46.7
|
1.0
|
OD1
|
C:ASP336
|
2.8
|
49.8
|
1.0
|
OD2
|
C:ASP336
|
3.0
|
49.8
|
1.0
|
CD
|
C:GLU337
|
3.0
|
46.7
|
1.0
|
CG
|
C:ASP336
|
3.3
|
49.8
|
1.0
|
SG
|
C:CYS324
|
3.3
|
56.0
|
1.0
|
C
|
C:ASP333
|
3.7
|
57.8
|
1.0
|
CD
|
C:GLU212
|
3.7
|
56.2
|
1.0
|
OE2
|
C:GLU212
|
4.4
|
56.2
|
1.0
|
CB
|
C:CYS324
|
4.4
|
56.0
|
1.0
|
CA
|
C:ASP333
|
4.5
|
57.8
|
1.0
|
CG
|
C:GLU337
|
4.5
|
46.7
|
1.0
|
N
|
C:PHE334
|
4.7
|
52.7
|
1.0
|
CB
|
C:GLU212
|
4.7
|
56.2
|
1.0
|
CB
|
C:ASP333
|
4.7
|
57.8
|
1.0
|
CB
|
C:ASP336
|
4.7
|
49.8
|
1.0
|
CA
|
C:PHE334
|
4.7
|
52.7
|
1.0
|
CG
|
C:GLU212
|
4.8
|
56.2
|
1.0
|
N
|
C:GLU337
|
4.9
|
46.7
|
1.0
|
|
Calcium binding site 7 out
of 8 in 7mbs
Go back to
Calcium Binding Sites List in 7mbs
Calcium binding site 7 out
of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca3003
b:37.5
occ:1.00
|
O
|
D:HOH3104
|
2.4
|
30.0
|
1.0
|
O
|
D:HOH3103
|
2.5
|
30.0
|
1.0
|
OE1
|
D:GLU768
|
2.5
|
36.4
|
1.0
|
OD1
|
D:ASN794
|
2.5
|
33.8
|
1.0
|
OE1
|
D:GLN771
|
2.6
|
39.5
|
1.0
|
OD2
|
D:ASP797
|
2.6
|
33.4
|
1.0
|
CD
|
D:GLU768
|
3.4
|
36.4
|
1.0
|
CD
|
D:GLN771
|
3.6
|
39.5
|
1.0
|
NH1
|
D:ARG834
|
3.6
|
26.4
|
1.0
|
CG
|
D:ASN794
|
3.7
|
33.8
|
1.0
|
OE2
|
D:GLU768
|
3.8
|
36.4
|
1.0
|
CG
|
D:ASP797
|
3.8
|
33.4
|
1.0
|
NE2
|
D:GLN771
|
3.9
|
39.5
|
1.0
|
CA
|
D:ASN794
|
4.3
|
33.8
|
1.0
|
OH
|
D:TYR788
|
4.4
|
37.4
|
1.0
|
CB
|
D:ASP797
|
4.5
|
33.4
|
1.0
|
CE1
|
D:TYR788
|
4.5
|
37.4
|
1.0
|
CB
|
D:ASN794
|
4.6
|
33.8
|
1.0
|
ND2
|
D:ASN794
|
4.6
|
33.8
|
1.0
|
CG
|
D:GLU768
|
4.8
|
36.4
|
1.0
|
N
|
D:ASN794
|
4.8
|
33.8
|
1.0
|
OD1
|
D:ASP797
|
4.8
|
33.4
|
1.0
|
CZ
|
D:ARG834
|
4.9
|
26.4
|
1.0
|
O
|
D:TRP793
|
4.9
|
31.2
|
1.0
|
CZ
|
D:TYR788
|
4.9
|
37.4
|
1.0
|
CG
|
D:GLN771
|
4.9
|
39.5
|
1.0
|
C
|
D:TRP793
|
5.0
|
31.2
|
1.0
|
|
Calcium binding site 8 out
of 8 in 7mbs
Go back to
Calcium Binding Sites List in 7mbs
Calcium binding site 8 out
of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 6 Um Calcium (Open State) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca3004
b:56.6
occ:1.00
|
O
|
D:ASP333
|
2.5
|
57.8
|
1.0
|
OE1
|
D:GLU337
|
2.5
|
46.7
|
1.0
|
OE1
|
D:GLU212
|
2.5
|
56.2
|
1.0
|
OE2
|
D:GLU337
|
2.8
|
46.7
|
1.0
|
OD1
|
D:ASP336
|
2.8
|
49.8
|
1.0
|
OD2
|
D:ASP336
|
3.0
|
49.8
|
1.0
|
CD
|
D:GLU337
|
3.0
|
46.7
|
1.0
|
CG
|
D:ASP336
|
3.3
|
49.8
|
1.0
|
SG
|
D:CYS324
|
3.3
|
56.0
|
1.0
|
C
|
D:ASP333
|
3.7
|
57.8
|
1.0
|
CD
|
D:GLU212
|
3.7
|
56.2
|
1.0
|
OE2
|
D:GLU212
|
4.4
|
56.2
|
1.0
|
CB
|
D:CYS324
|
4.4
|
56.0
|
1.0
|
CA
|
D:ASP333
|
4.5
|
57.8
|
1.0
|
CG
|
D:GLU337
|
4.5
|
46.7
|
1.0
|
N
|
D:PHE334
|
4.6
|
52.7
|
1.0
|
CB
|
D:GLU212
|
4.7
|
56.2
|
1.0
|
CB
|
D:ASP333
|
4.7
|
57.8
|
1.0
|
CB
|
D:ASP336
|
4.7
|
49.8
|
1.0
|
CA
|
D:PHE334
|
4.7
|
52.7
|
1.0
|
CG
|
D:GLU212
|
4.8
|
56.2
|
1.0
|
N
|
D:GLU337
|
4.9
|
46.7
|
1.0
|
|
Reference:
Z.Ruan,
E.Haley,
I.J.Orozco,
M.Sabat,
R.Myers,
R.Roth,
J.Du,
W.Lu.
Structures of the TRPM5 Channel Elucidate Mechanisms of Activation and Inhibition. Nat.Struct.Mol.Biol. 2021.
ISSN: ESSN 1545-9985
PubMed: 34168372
DOI: 10.1038/S41594-021-00607-4
Page generated: Fri Jul 19 01:59:01 2024
|