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Calcium in PDB 7mbv: Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 5 Mm Calcium and 0.5 Mm Ndna

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 5 Mm Calcium and 0.5 Mm Ndna (pdb code 7mbv). 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 5 Mm Calcium and 0.5 Mm Ndna, PDB code: 7mbv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 7mbv

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Calcium binding site 1 out of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 5 Mm Calcium and 0.5 Mm Ndna


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 5 Mm Calcium and 0.5 Mm Ndna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1502

b:24.8
occ:1.00
OE2 A:GLU768 2.5 21.6 1.0
OD1 A:ASN794 2.5 15.4 1.0
OD2 A:ASP797 2.9 15.2 1.0
CD A:GLU768 3.2 21.6 1.0
OE1 A:GLU768 3.3 21.6 1.0
CG A:ASN794 3.7 15.4 1.0
CG A:ASP797 4.1 15.2 1.0
ND2 A:ASN794 4.5 15.4 1.0
CG A:GLU768 4.6 21.6 1.0
CA A:ASN794 4.6 15.4 1.0
CB A:ASN794 4.7 15.4 1.0
CE1 A:TYR788 4.7 19.7 1.0
N A:ASN794 4.9 15.4 1.0
OD1 A:ASP797 4.9 15.2 1.0
OH A:TYR788 5.0 19.7 1.0
CB A:ASP797 5.0 15.2 1.0

Calcium binding site 2 out of 8 in 7mbv

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Calcium binding site 2 out of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 5 Mm Calcium and 0.5 Mm Ndna


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 5 Mm Calcium and 0.5 Mm Ndna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1503

b:34.5
occ:1.00
OE1 A:GLU212 2.4 47.6 1.0
OE2 A:GLU337 2.5 32.0 1.0
O A:ASP333 2.7 41.3 1.0
SG A:CYS324 2.8 38.9 1.0
OE1 A:GLU337 3.0 32.0 1.0
CD A:GLU337 3.1 32.0 1.0
OD1 A:ASP336 3.2 36.5 1.0
CD A:GLU212 3.6 47.6 1.0
CB A:CYS324 3.7 38.9 1.0
C A:ASP333 3.7 41.3 1.0
CG A:ASP336 4.1 36.5 1.0
OE2 A:GLU212 4.1 47.6 1.0
OD2 A:ASP336 4.2 36.5 1.0
CB A:ASP333 4.3 41.3 1.0
CA A:ASP333 4.4 41.3 1.0
CG A:GLU337 4.6 32.0 1.0
N A:PHE334 4.7 37.3 1.0
CG A:GLU212 4.8 47.6 1.0
CG A:ASP333 4.9 41.3 1.0
CA A:PHE334 4.9 37.3 1.0
CA A:CYS324 4.9 38.9 1.0

Calcium binding site 3 out of 8 in 7mbv

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Calcium binding site 3 out of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 5 Mm Calcium and 0.5 Mm Ndna


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 5 Mm Calcium and 0.5 Mm Ndna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1502

b:24.8
occ:1.00
OE2 B:GLU768 2.5 21.6 1.0
OD1 B:ASN794 2.5 15.4 1.0
OD2 B:ASP797 2.9 15.2 1.0
CD B:GLU768 3.2 21.6 1.0
OE1 B:GLU768 3.3 21.6 1.0
CG B:ASN794 3.7 15.4 1.0
CG B:ASP797 4.1 15.2 1.0
ND2 B:ASN794 4.5 15.4 1.0
CG B:GLU768 4.6 21.6 1.0
CA B:ASN794 4.6 15.4 1.0
CB B:ASN794 4.7 15.4 1.0
CE1 B:TYR788 4.7 19.7 1.0
N B:ASN794 4.9 15.4 1.0
OD1 B:ASP797 4.9 15.2 1.0
OH B:TYR788 5.0 19.7 1.0
CB B:ASP797 5.0 15.2 1.0

Calcium binding site 4 out of 8 in 7mbv

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Calcium binding site 4 out of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 5 Mm Calcium and 0.5 Mm Ndna


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 5 Mm Calcium and 0.5 Mm Ndna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1503

b:34.5
occ:1.00
OE1 B:GLU212 2.4 47.6 1.0
OE2 B:GLU337 2.5 32.0 1.0
O B:ASP333 2.7 41.3 1.0
SG B:CYS324 2.8 38.9 1.0
OE1 B:GLU337 3.0 32.0 1.0
CD B:GLU337 3.1 32.0 1.0
OD1 B:ASP336 3.2 36.5 1.0
CD B:GLU212 3.6 47.6 1.0
CB B:CYS324 3.7 38.9 1.0
C B:ASP333 3.7 41.3 1.0
CG B:ASP336 4.1 36.5 1.0
OE2 B:GLU212 4.1 47.6 1.0
OD2 B:ASP336 4.2 36.5 1.0
CB B:ASP333 4.3 41.3 1.0
CA B:ASP333 4.4 41.3 1.0
CG B:GLU337 4.6 32.0 1.0
N B:PHE334 4.7 37.3 1.0
CG B:GLU212 4.8 47.6 1.0
CG B:ASP333 4.9 41.3 1.0
CA B:PHE334 4.9 37.3 1.0
CA B:CYS324 4.9 38.9 1.0

Calcium binding site 5 out of 8 in 7mbv

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Calcium binding site 5 out of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 5 Mm Calcium and 0.5 Mm Ndna


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 5 Mm Calcium and 0.5 Mm Ndna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1502

b:24.8
occ:1.00
OE2 C:GLU768 2.5 21.6 1.0
OD1 C:ASN794 2.5 15.4 1.0
OD2 C:ASP797 2.9 15.2 1.0
CD C:GLU768 3.2 21.6 1.0
OE1 C:GLU768 3.3 21.6 1.0
CG C:ASN794 3.7 15.4 1.0
CG C:ASP797 4.1 15.2 1.0
ND2 C:ASN794 4.5 15.4 1.0
CG C:GLU768 4.6 21.6 1.0
CA C:ASN794 4.6 15.4 1.0
CB C:ASN794 4.7 15.4 1.0
CE1 C:TYR788 4.7 19.7 1.0
N C:ASN794 4.9 15.4 1.0
OD1 C:ASP797 4.9 15.2 1.0
OH C:TYR788 5.0 19.7 1.0
CB C:ASP797 5.0 15.2 1.0

Calcium binding site 6 out of 8 in 7mbv

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Calcium binding site 6 out of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 5 Mm Calcium and 0.5 Mm Ndna


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 5 Mm Calcium and 0.5 Mm Ndna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1503

b:34.5
occ:1.00
OE1 C:GLU212 2.4 47.6 1.0
OE2 C:GLU337 2.5 32.0 1.0
O C:ASP333 2.7 41.3 1.0
SG C:CYS324 2.8 38.9 1.0
OE1 C:GLU337 3.0 32.0 1.0
CD C:GLU337 3.1 32.0 1.0
OD1 C:ASP336 3.2 36.5 1.0
CD C:GLU212 3.6 47.6 1.0
CB C:CYS324 3.7 38.9 1.0
C C:ASP333 3.7 41.3 1.0
CG C:ASP336 4.1 36.5 1.0
OE2 C:GLU212 4.1 47.6 1.0
OD2 C:ASP336 4.2 36.5 1.0
CB C:ASP333 4.3 41.3 1.0
CA C:ASP333 4.4 41.3 1.0
CG C:GLU337 4.6 32.0 1.0
N C:PHE334 4.7 37.3 1.0
CG C:GLU212 4.8 47.6 1.0
CG C:ASP333 4.9 41.3 1.0
CA C:PHE334 4.9 37.3 1.0
CA C:CYS324 4.9 38.9 1.0

Calcium binding site 7 out of 8 in 7mbv

Go back to Calcium Binding Sites List in 7mbv
Calcium binding site 7 out of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 5 Mm Calcium and 0.5 Mm Ndna


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 5 Mm Calcium and 0.5 Mm Ndna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca3003

b:24.8
occ:1.00
OE2 D:GLU768 2.5 21.6 1.0
OD1 D:ASN794 2.5 15.4 1.0
OD2 D:ASP797 2.9 15.2 1.0
CD D:GLU768 3.2 21.6 1.0
OE1 D:GLU768 3.3 21.6 1.0
CG D:ASN794 3.7 15.4 1.0
CG D:ASP797 4.1 15.2 1.0
ND2 D:ASN794 4.5 15.4 1.0
CG D:GLU768 4.6 21.6 1.0
CA D:ASN794 4.6 15.4 1.0
CB D:ASN794 4.7 15.4 1.0
CE1 D:TYR788 4.7 19.7 1.0
N D:ASN794 4.9 15.4 1.0
OD1 D:ASP797 4.9 15.2 1.0
OH D:TYR788 5.0 19.7 1.0
CB D:ASP797 5.0 15.2 1.0

Calcium binding site 8 out of 8 in 7mbv

Go back to Calcium Binding Sites List in 7mbv
Calcium binding site 8 out of 8 in the Cryo-Em Structure of Zebrafish TRPM5 in the Presence of 5 Mm Calcium and 0.5 Mm Ndna


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 5 Mm Calcium and 0.5 Mm Ndna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca3004

b:34.5
occ:1.00
OE1 D:GLU212 2.4 47.6 1.0
OE2 D:GLU337 2.5 32.0 1.0
O D:ASP333 2.7 41.3 1.0
SG D:CYS324 2.8 38.9 1.0
OE1 D:GLU337 3.0 32.0 1.0
CD D:GLU337 3.1 32.0 1.0
OD1 D:ASP336 3.2 36.5 1.0
CD D:GLU212 3.6 47.6 1.0
CB D:CYS324 3.7 38.9 1.0
C D:ASP333 3.7 41.3 1.0
CG D:ASP336 4.1 36.5 1.0
OE2 D:GLU212 4.1 47.6 1.0
OD2 D:ASP336 4.2 36.5 1.0
CB D:ASP333 4.3 41.3 1.0
CA D:ASP333 4.4 41.3 1.0
CG D:GLU337 4.6 32.0 1.0
N D:PHE334 4.7 37.3 1.0
CG D:GLU212 4.8 47.6 1.0
CG D:ASP333 4.9 41.3 1.0
CA D:PHE334 4.9 37.3 1.0
CA D:CYS324 4.9 38.9 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 01:59:09 2024

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