Calcium in PDB 9b8y: Cryo-Em Structure of the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius

Other elements in 9b8y:

The structure of Cryo-Em Structure of the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius also contains other interesting chemical elements:

Vanadium (V) 40 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius (pdb code 9b8y). 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 the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius, PDB code: 9b8y:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 9b8y

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Calcium binding site 1 out of 8 in the Cryo-Em Structure of the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius


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 the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:86.1
occ:1.00
 OE2 A:GLU828 2.1 88.6 1.0
NE2 A:GLN831 2.5 89.5 1.0
OD1 A:ASN865 2.6 89.4 1.0
OD2 A:ASP868 2.6 88.9 1.0
CD A:GLU828 3.0 88.6 1.0
OE1 A:GLU828 3.1 88.6 1.0
CD A:GLN831 3.5 89.5 1.0
OE1 A:GLN831 3.7 89.5 1.0
CG A:ASN865 3.8 89.4 1.0
CG A:ASP868 3.8 88.9 1.0
NH2 A:ARG905 3.9 80.6 1.0
OE2 A:GLU1068 4.1 81.8 1.0
CG A:GLU828 4.4 88.6 1.0
CA A:ASN865 4.4 89.4 1.0
CB A:ASP868 4.6 88.9 1.0
CB A:ASN865 4.6 89.4 1.0
ND2 A:ASN865 4.7 89.4 1.0
N A:ASN865 4.7 89.4 1.0
OD1 A:ASP868 4.7 88.9 1.0
CG A:GLN831 4.8 89.5 1.0
O A:TRP864 4.9 84.9 1.0
CE1 A:TYR859 5.0 93.1 1.0
C A:TRP864 5.0 84.9 1.0

Calcium binding site 2 out of 8 in 9b8y

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Calcium binding site 2 out of 8 in the Cryo-Em Structure of the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius


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 the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2002

b:146.6
occ:1.00
 OE2 A:GLU396 2.2 140.8 1.0
OD2 A:ASP270 2.4 150.3 1.0
O A:ALA392 2.7 145.2 1.0
OD2 A:ASP395 2.7 143.4 1.0
CD A:GLU396 3.1 140.8 1.0
OE1 A:GLU396 3.2 140.8 1.0
CG A:ASP270 3.5 150.3 1.0
CG A:ASP395 3.6 143.4 1.0
OD1 A:ASP395 3.6 143.4 1.0
SG A:CYS385 3.7 148.6 1.0
C A:ALA392 3.9 145.2 1.0
OD1 A:ASP270 4.0 150.3 1.0
CG A:GLU396 4.5 140.8 1.0
CB A:ALA392 4.5 145.2 1.0
CA A:ALA392 4.7 145.2 1.0
CB A:ASP270 4.8 150.3 1.0
N A:TYR393 4.8 142.9 1.0
CA A:TYR393 4.8 142.9 1.0

Calcium binding site 3 out of 8 in 9b8y

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Calcium binding site 3 out of 8 in the Cryo-Em Structure of the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius


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 the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2001

b:86.1
occ:1.00
 OE2 B:GLU828 2.1 88.6 1.0
NE2 B:GLN831 2.5 89.5 1.0
OD1 B:ASN865 2.6 89.4 1.0
OD2 B:ASP868 2.6 88.9 1.0
CD B:GLU828 3.0 88.6 1.0
OE1 B:GLU828 3.1 88.6 1.0
CD B:GLN831 3.5 89.5 1.0
OE1 B:GLN831 3.7 89.5 1.0
CG B:ASN865 3.8 89.4 1.0
CG B:ASP868 3.8 88.9 1.0
NH2 B:ARG905 3.9 80.6 1.0
OE2 B:GLU1068 4.1 81.8 1.0
CG B:GLU828 4.4 88.6 1.0
CA B:ASN865 4.4 89.4 1.0
CB B:ASP868 4.6 88.9 1.0
CB B:ASN865 4.6 89.4 1.0
ND2 B:ASN865 4.7 89.4 1.0
N B:ASN865 4.7 89.4 1.0
OD1 B:ASP868 4.7 88.9 1.0
CG B:GLN831 4.8 89.5 1.0
O B:TRP864 4.9 84.9 1.0
CE1 B:TYR859 5.0 93.1 1.0
C B:TRP864 5.0 84.9 1.0

Calcium binding site 4 out of 8 in 9b8y

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Calcium binding site 4 out of 8 in the Cryo-Em Structure of the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius


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 the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2002

b:146.6
occ:1.00
 OE2 B:GLU396 2.2 140.8 1.0
OD2 B:ASP270 2.4 150.3 1.0
O B:ALA392 2.7 145.2 1.0
OD2 B:ASP395 2.7 143.4 1.0
CD B:GLU396 3.1 140.8 1.0
OE1 B:GLU396 3.2 140.8 1.0
CG B:ASP270 3.5 150.3 1.0
CG B:ASP395 3.6 143.4 1.0
OD1 B:ASP395 3.6 143.4 1.0
SG B:CYS385 3.7 148.6 1.0
C B:ALA392 3.9 145.2 1.0
OD1 B:ASP270 4.0 150.3 1.0
CG B:GLU396 4.5 140.8 1.0
CB B:ALA392 4.5 145.2 1.0
CA B:ALA392 4.7 145.2 1.0
CB B:ASP270 4.8 150.3 1.0
N B:TYR393 4.8 142.9 1.0
CA B:TYR393 4.8 142.9 1.0

Calcium binding site 5 out of 8 in 9b8y

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Calcium binding site 5 out of 8 in the Cryo-Em Structure of the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius


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 the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2001

b:86.1
occ:1.00
 OE2 C:GLU828 2.1 88.6 1.0
NE2 C:GLN831 2.5 89.5 1.0
OD1 C:ASN865 2.6 89.4 1.0
OD2 C:ASP868 2.6 88.9 1.0
CD C:GLU828 3.0 88.6 1.0
OE1 C:GLU828 3.1 88.6 1.0
CD C:GLN831 3.5 89.5 1.0
OE1 C:GLN831 3.7 89.5 1.0
CG C:ASN865 3.8 89.4 1.0
CG C:ASP868 3.8 88.9 1.0
NH2 C:ARG905 3.9 80.6 1.0
OE2 C:GLU1068 4.1 81.8 1.0
CG C:GLU828 4.4 88.6 1.0
CA C:ASN865 4.4 89.4 1.0
CB C:ASP868 4.6 88.9 1.0
CB C:ASN865 4.6 89.4 1.0
ND2 C:ASN865 4.7 89.4 1.0
N C:ASN865 4.7 89.4 1.0
OD1 C:ASP868 4.7 88.9 1.0
CG C:GLN831 4.8 89.5 1.0
O C:TRP864 4.9 84.9 1.0
CE1 C:TYR859 5.0 93.1 1.0
C C:TRP864 5.0 84.9 1.0

Calcium binding site 6 out of 8 in 9b8y

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Calcium binding site 6 out of 8 in the Cryo-Em Structure of the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius


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 the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2002

b:146.6
occ:1.00
 OE2 C:GLU396 2.2 140.8 1.0
OD2 C:ASP270 2.4 150.3 1.0
O C:ALA392 2.7 145.2 1.0
OD2 C:ASP395 2.7 143.4 1.0
CD C:GLU396 3.1 140.8 1.0
OE1 C:GLU396 3.2 140.8 1.0
CG C:ASP270 3.5 150.3 1.0
CG C:ASP395 3.6 143.4 1.0
OD1 C:ASP395 3.6 143.4 1.0
SG C:CYS385 3.7 148.6 1.0
C C:ALA392 3.9 145.2 1.0
OD1 C:ASP270 4.0 150.3 1.0
CG C:GLU396 4.5 140.8 1.0
CB C:ALA392 4.5 145.2 1.0
CA C:ALA392 4.7 145.2 1.0
CB C:ASP270 4.8 150.3 1.0
N C:TYR393 4.8 142.9 1.0
CA C:TYR393 4.8 142.9 1.0

Calcium binding site 7 out of 8 in 9b8y

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Calcium binding site 7 out of 8 in the Cryo-Em Structure of the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius


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 the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2001

b:86.1
occ:1.00
 OE2 D:GLU828 2.1 88.6 1.0
NE2 D:GLN831 2.5 89.5 1.0
OD1 D:ASN865 2.6 89.4 1.0
OD2 D:ASP868 2.6 88.9 1.0
CD D:GLU828 3.0 88.6 1.0
OE1 D:GLU828 3.1 88.6 1.0
CD D:GLN831 3.5 89.5 1.0
OE1 D:GLN831 3.7 89.5 1.0
CG D:ASN865 3.8 89.4 1.0
CG D:ASP868 3.8 88.9 1.0
NH2 D:ARG905 3.9 80.6 1.0
OE2 D:GLU1068 4.1 81.8 1.0
CG D:GLU828 4.4 88.6 1.0
CA D:ASN865 4.4 89.4 1.0
CB D:ASP868 4.6 88.9 1.0
CB D:ASN865 4.6 89.4 1.0
ND2 D:ASN865 4.7 89.4 1.0
N D:ASN865 4.7 89.4 1.0
OD1 D:ASP868 4.7 88.9 1.0
CG D:GLN831 4.8 89.5 1.0
O D:TRP864 4.9 84.9 1.0
CE1 D:TYR859 5.0 93.1 1.0
C D:TRP864 5.0 84.9 1.0

Calcium binding site 8 out of 8 in 9b8y

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Calcium binding site 8 out of 8 in the Cryo-Em Structure of the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius


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 the Human TRPM4 Channel in Complex with Calcium and Decavanadate at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2002

b:146.6
occ:1.00
 OE2 D:GLU396 2.2 140.8 1.0
OD2 D:ASP270 2.4 150.3 1.0
O D:ALA392 2.7 145.2 1.0
OD2 D:ASP395 2.7 143.4 1.0
CD D:GLU396 3.1 140.8 1.0
OE1 D:GLU396 3.2 140.8 1.0
CG D:ASP270 3.5 150.3 1.0
CG D:ASP395 3.6 143.4 1.0
OD1 D:ASP395 3.6 143.4 1.0
SG D:CYS385 3.7 148.6 1.0
C D:ALA392 3.9 145.2 1.0
OD1 D:ASP270 4.0 150.3 1.0
CG D:GLU396 4.5 140.8 1.0
CB D:ALA392 4.5 145.2 1.0
CA D:ALA392 4.7 145.2 1.0
CB D:ASP270 4.8 150.3 1.0
N D:TYR393 4.8 142.9 1.0
CA D:TYR393 4.8 142.9 1.0

Reference:

J.Hu, S.J.Park, T.Walter, I.J.Orozco, G.O'dea, X.Ye, J.Du, W.Lu. Physiological Temperature Drives TRPM4 Ligand Recognition and Gating Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-024-07436-7
Page generated: Fri Jul 19 12:58:33 2024

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