Calcium in PDB 9b8w: Cryo-Em Structure of the Human TRPM4 in Complex with Calcium at 37 Degrees Celsius

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of the Human TRPM4 in Complex with Calcium at 37 Degrees Celsius (pdb code 9b8w). 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 in Complex with Calcium at 37 Degrees Celsius, PDB code: 9b8w:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 9b8w

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


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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 in Complex with Calcium at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:119.1
occ:1.00
 OE2 A:GLU828 2.3 116.9 1.0
OE1 A:GLN831 2.4 118.7 1.0
OD1 A:ASN865 2.7 121.3 1.0
OD2 A:ASP868 3.1 120.8 1.0
CD A:GLU828 3.1 116.9 1.0
OE1 A:GLU828 3.2 116.9 1.0
CD A:GLN831 3.2 118.7 1.0
NE2 A:GLN831 3.3 118.7 1.0
OE2 A:GLU1068 3.8 112.5 1.0
NH2 A:ARG905 3.9 104.6 1.0
CG A:ASN865 3.9 121.3 1.0
NH1 A:ARG905 4.1 104.6 1.0
CG A:ASP868 4.3 120.8 1.0
CZ A:ARG905 4.5 104.6 1.0
CG A:GLU828 4.6 116.9 1.0
CG A:GLN831 4.6 118.7 1.0
NH2 A:ARG1072 4.7 108.8 1.0
CA A:ASN865 4.7 121.3 1.0
ND2 A:ASN865 4.7 121.3 1.0
CD A:GLU1068 4.8 112.5 1.0
CB A:ASN865 4.9 121.3 1.0
CB A:ASP868 4.9 120.8 1.0
CB A:GLN831 5.0 118.7 1.0

Calcium binding site 2 out of 8 in 9b8w

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Calcium binding site 2 out of 8 in the Cryo-Em Structure of the Human TRPM4 in Complex with Calcium 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 in Complex with Calcium at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2002

b:191.9
occ:1.00
 OD2 A:ASP395 2.4 182.9 1.0
OD2 A:ASP270 2.5 189.0 1.0
OE2 A:GLU396 2.6 177.9 1.0
O A:ALA392 2.7 179.5 1.0
OD1 A:ASP395 2.8 182.9 1.0
CG A:ASP395 2.9 182.9 1.0
SG A:CYS385 3.2 183.8 1.0
OE1 A:GLU396 3.2 177.9 1.0
CD A:GLU396 3.3 177.9 1.0
CG A:ASP270 3.6 189.0 1.0
C A:ALA392 3.9 179.5 1.0
OD1 A:ASP270 4.0 189.0 1.0
CB A:ASP395 4.4 182.9 1.0
CA A:ALA392 4.6 179.5 1.0
CG A:GLU396 4.7 177.9 1.0
CB A:ASP270 4.8 189.0 1.0
N A:TYR393 4.9 176.9 1.0
CB A:CYS385 4.9 183.8 1.0
CB A:ALA392 5.0 179.5 1.0
CA A:TYR393 5.0 176.9 1.0

Calcium binding site 3 out of 8 in 9b8w

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Calcium binding site 3 out of 8 in the Cryo-Em Structure of the Human TRPM4 in Complex with Calcium 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 in Complex with Calcium at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2001

b:119.1
occ:1.00
 OE2 B:GLU828 2.3 116.9 1.0
OE1 B:GLN831 2.4 118.7 1.0
OD1 B:ASN865 2.7 121.3 1.0
OD2 B:ASP868 3.1 120.8 1.0
CD B:GLU828 3.1 116.9 1.0
OE1 B:GLU828 3.2 116.9 1.0
CD B:GLN831 3.2 118.7 1.0
NE2 B:GLN831 3.3 118.7 1.0
OE2 B:GLU1068 3.7 112.5 1.0
NH2 B:ARG905 3.9 104.6 1.0
CG B:ASN865 3.9 121.3 1.0
NH1 B:ARG905 4.1 104.6 1.0
CG B:ASP868 4.3 120.8 1.0
CZ B:ARG905 4.5 104.6 1.0
CG B:GLU828 4.6 116.9 1.0
CG B:GLN831 4.6 118.7 1.0
NH2 B:ARG1072 4.7 108.8 1.0
CA B:ASN865 4.7 121.3 1.0
ND2 B:ASN865 4.7 121.3 1.0
CD B:GLU1068 4.8 112.5 1.0
CB B:ASN865 4.9 121.3 1.0
CB B:ASP868 4.9 120.8 1.0
CB B:GLN831 5.0 118.7 1.0

Calcium binding site 4 out of 8 in 9b8w

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Calcium binding site 4 out of 8 in the Cryo-Em Structure of the Human TRPM4 in Complex with Calcium 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 in Complex with Calcium at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2002

b:191.9
occ:1.00
 OD2 B:ASP395 2.4 182.9 1.0
OD2 B:ASP270 2.5 189.0 1.0
OE2 B:GLU396 2.6 177.9 1.0
O B:ALA392 2.7 179.5 1.0
OD1 B:ASP395 2.8 182.9 1.0
CG B:ASP395 2.9 182.9 1.0
SG B:CYS385 3.2 183.8 1.0
OE1 B:GLU396 3.2 177.9 1.0
CD B:GLU396 3.3 177.9 1.0
CG B:ASP270 3.6 189.0 1.0
C B:ALA392 3.9 179.5 1.0
OD1 B:ASP270 4.0 189.0 1.0
CB B:ASP395 4.4 182.9 1.0
CA B:ALA392 4.6 179.5 1.0
CG B:GLU396 4.7 177.9 1.0
CB B:ASP270 4.8 189.0 1.0
N B:TYR393 4.9 176.9 1.0
CB B:CYS385 4.9 183.8 1.0
CB B:ALA392 5.0 179.5 1.0
CA B:TYR393 5.0 176.9 1.0

Calcium binding site 5 out of 8 in 9b8w

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Calcium binding site 5 out of 8 in the Cryo-Em Structure of the Human TRPM4 in Complex with Calcium 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 in Complex with Calcium at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2001

b:119.1
occ:1.00
 OE2 C:GLU828 2.3 116.9 1.0
OE1 C:GLN831 2.4 118.7 1.0
OD1 C:ASN865 2.7 121.3 1.0
OD2 C:ASP868 3.1 120.8 1.0
CD C:GLU828 3.1 116.9 1.0
OE1 C:GLU828 3.2 116.9 1.0
CD C:GLN831 3.2 118.7 1.0
NE2 C:GLN831 3.3 118.7 1.0
OE2 C:GLU1068 3.8 112.5 1.0
NH2 C:ARG905 3.9 104.6 1.0
CG C:ASN865 3.9 121.3 1.0
NH1 C:ARG905 4.1 104.6 1.0
CG C:ASP868 4.3 120.8 1.0
CZ C:ARG905 4.5 104.6 1.0
CG C:GLU828 4.6 116.9 1.0
CG C:GLN831 4.6 118.7 1.0
NH2 C:ARG1072 4.7 108.8 1.0
CA C:ASN865 4.7 121.3 1.0
ND2 C:ASN865 4.7 121.3 1.0
CD C:GLU1068 4.8 112.5 1.0
CB C:ASN865 4.9 121.3 1.0
CB C:ASP868 4.9 120.8 1.0
CB C:GLN831 5.0 118.7 1.0

Calcium binding site 6 out of 8 in 9b8w

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Calcium binding site 6 out of 8 in the Cryo-Em Structure of the Human TRPM4 in Complex with Calcium 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 in Complex with Calcium at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2002

b:191.9
occ:1.00
 OD2 C:ASP395 2.4 182.9 1.0
OD2 C:ASP270 2.5 189.0 1.0
OE2 C:GLU396 2.6 177.9 1.0
O C:ALA392 2.7 179.5 1.0
OD1 C:ASP395 2.8 182.9 1.0
CG C:ASP395 2.9 182.9 1.0
SG C:CYS385 3.2 183.8 1.0
OE1 C:GLU396 3.2 177.9 1.0
CD C:GLU396 3.3 177.9 1.0
CG C:ASP270 3.6 189.0 1.0
C C:ALA392 3.9 179.5 1.0
OD1 C:ASP270 4.0 189.0 1.0
CB C:ASP395 4.4 182.9 1.0
CA C:ALA392 4.6 179.5 1.0
CG C:GLU396 4.7 177.9 1.0
CB C:ASP270 4.8 189.0 1.0
N C:TYR393 4.9 176.9 1.0
CB C:CYS385 4.9 183.8 1.0
CB C:ALA392 5.0 179.5 1.0
CA C:TYR393 5.0 176.9 1.0

Calcium binding site 7 out of 8 in 9b8w

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Calcium binding site 7 out of 8 in the Cryo-Em Structure of the Human TRPM4 in Complex with Calcium 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 in Complex with Calcium at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2001

b:119.1
occ:1.00
 OE2 D:GLU828 2.3 116.9 1.0
OE1 D:GLN831 2.4 118.7 1.0
OD1 D:ASN865 2.7 121.3 1.0
OD2 D:ASP868 3.1 120.8 1.0
CD D:GLU828 3.1 116.9 1.0
OE1 D:GLU828 3.2 116.9 1.0
CD D:GLN831 3.2 118.7 1.0
NE2 D:GLN831 3.3 118.7 1.0
OE2 D:GLU1068 3.8 112.5 1.0
NH2 D:ARG905 3.9 104.6 1.0
CG D:ASN865 3.9 121.3 1.0
NH1 D:ARG905 4.1 104.6 1.0
CG D:ASP868 4.3 120.8 1.0
CZ D:ARG905 4.5 104.6 1.0
CG D:GLU828 4.6 116.9 1.0
CG D:GLN831 4.6 118.7 1.0
NH2 D:ARG1072 4.7 108.8 1.0
CA D:ASN865 4.7 121.3 1.0
ND2 D:ASN865 4.7 121.3 1.0
CD D:GLU1068 4.8 112.5 1.0
CB D:ASN865 4.9 121.3 1.0
CB D:ASP868 4.9 120.8 1.0
CB D:GLN831 5.0 118.7 1.0

Calcium binding site 8 out of 8 in 9b8w

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Calcium binding site 8 out of 8 in the Cryo-Em Structure of the Human TRPM4 in Complex with Calcium 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 in Complex with Calcium at 37 Degrees Celsius within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2002

b:191.9
occ:1.00
 OD2 D:ASP395 2.4 182.9 1.0
OD2 D:ASP270 2.5 189.0 1.0
OE2 D:GLU396 2.6 177.9 1.0
O D:ALA392 2.7 179.5 1.0
OD1 D:ASP395 2.8 182.9 1.0
CG D:ASP395 2.9 182.9 1.0
SG D:CYS385 3.2 183.8 1.0
OE1 D:GLU396 3.2 177.9 1.0
CD D:GLU396 3.3 177.9 1.0
CG D:ASP270 3.6 189.0 1.0
C D:ALA392 3.9 179.5 1.0
OD1 D:ASP270 4.0 189.0 1.0
CB D:ASP395 4.4 182.9 1.0
CA D:ALA392 4.6 179.5 1.0
CG D:GLU396 4.7 177.9 1.0
CB D:ASP270 4.8 189.0 1.0
N D:TYR393 4.9 176.9 1.0
CB D:CYS385 4.9 183.8 1.0
CB D:ALA392 5.0 179.5 1.0
CA D:TYR393 5.0 176.9 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 12:55:30 2024

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