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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

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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

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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 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 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 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

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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

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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

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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

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