Calcium in PDB 6nr3: Cryo-Em Structure of the TRPM8 Ion Channel in Complex with High Occupancy Icilin, Pi(4,5)P2, and Calcium

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of the TRPM8 Ion Channel in Complex with High Occupancy Icilin, Pi(4,5)P2, and Calcium (pdb code 6nr3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of the TRPM8 Ion Channel in Complex with High Occupancy Icilin, Pi(4,5)P2, and Calcium, PDB code: 6nr3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6nr3

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Calcium binding site 1 out of 4 in the Cryo-Em Structure of the TRPM8 Ion Channel in Complex with High Occupancy Icilin, Pi(4,5)P2, and Calcium


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 TRPM8 Ion Channel in Complex with High Occupancy Icilin, Pi(4,5)P2, and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1203

b:30.0
occ:1.00
OE1 A:GLN785 2.5 0.6 1.0
OD1 A:ASN799 2.6 0.3 1.0
NE2 A:GLN785 2.6 0.6 1.0
CD A:GLN785 2.9 0.6 1.0
OD2 A:ASP802 3.2 0.0 1.0
OE1 A:GLU782 3.2 0.5 1.0
O06 A:KX71201 3.5 20.0 1.0
CG A:ASN799 3.8 0.3 1.0
OE2 A:GLU782 3.8 0.5 1.0
CD A:GLU782 3.9 0.5 1.0
H041 A:KX71201 4.0 20.0 1.0
CG A:ASP802 4.3 0.0 1.0
CG A:GLN785 4.3 0.6 1.0
C05 A:KX71201 4.4 20.0 1.0
ND2 A:ASN799 4.5 0.3 1.0
N04 A:KX71201 4.6 20.0 1.0
CA A:ASN799 4.6 0.3 1.0
OE2 A:GLU1003 4.7 30.0 1.0
CE1 A:TYR793 4.7 0.9 1.0
NH1 A:ARG841 4.8 90.6 1.0
NH2 A:ARG841 4.8 90.6 1.0
CB A:ASN799 4.8 0.3 1.0
OD1 A:ASP802 4.9 0.0 1.0

Calcium binding site 2 out of 4 in 6nr3

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Calcium binding site 2 out of 4 in the Cryo-Em Structure of the TRPM8 Ion Channel in Complex with High Occupancy Icilin, Pi(4,5)P2, and Calcium


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 TRPM8 Ion Channel in Complex with High Occupancy Icilin, Pi(4,5)P2, and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1203

b:30.0
occ:1.00
OE1 B:GLN785 2.5 0.6 1.0
OD1 B:ASN799 2.6 0.3 1.0
NE2 B:GLN785 2.6 0.6 1.0
CD B:GLN785 2.9 0.6 1.0
OD2 B:ASP802 3.2 0.0 1.0
OE1 B:GLU782 3.2 0.5 1.0
O06 B:KX71201 3.5 20.0 1.0
CG B:ASN799 3.8 0.3 1.0
OE2 B:GLU782 3.8 0.5 1.0
CD B:GLU782 3.9 0.5 1.0
H041 B:KX71201 4.0 20.0 1.0
CG B:ASP802 4.3 0.0 1.0
CG B:GLN785 4.3 0.6 1.0
C05 B:KX71201 4.4 20.0 1.0
ND2 B:ASN799 4.5 0.3 1.0
N04 B:KX71201 4.6 20.0 1.0
CA B:ASN799 4.6 0.3 1.0
OE2 B:GLU1003 4.7 30.0 1.0
CE1 B:TYR793 4.7 0.9 1.0
NH1 B:ARG841 4.8 90.6 1.0
NH2 B:ARG841 4.8 90.6 1.0
CB B:ASN799 4.8 0.3 1.0
OD1 B:ASP802 4.9 0.0 1.0

Calcium binding site 3 out of 4 in 6nr3

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Calcium binding site 3 out of 4 in the Cryo-Em Structure of the TRPM8 Ion Channel in Complex with High Occupancy Icilin, Pi(4,5)P2, and Calcium


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 TRPM8 Ion Channel in Complex with High Occupancy Icilin, Pi(4,5)P2, and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1203

b:30.0
occ:1.00
OE1 C:GLN785 2.5 0.6 1.0
OD1 C:ASN799 2.6 0.3 1.0
NE2 C:GLN785 2.6 0.6 1.0
CD C:GLN785 2.9 0.6 1.0
OD2 C:ASP802 3.2 0.0 1.0
OE1 C:GLU782 3.2 0.5 1.0
O06 C:KX71201 3.5 20.0 1.0
CG C:ASN799 3.8 0.3 1.0
OE2 C:GLU782 3.8 0.5 1.0
CD C:GLU782 3.9 0.5 1.0
H041 C:KX71201 4.0 20.0 1.0
CG C:ASP802 4.3 0.0 1.0
CG C:GLN785 4.3 0.6 1.0
C05 C:KX71201 4.4 20.0 1.0
ND2 C:ASN799 4.5 0.3 1.0
N04 C:KX71201 4.6 20.0 1.0
CA C:ASN799 4.6 0.3 1.0
OE2 C:GLU1003 4.7 30.0 1.0
CE1 C:TYR793 4.7 0.9 1.0
NH1 C:ARG841 4.8 90.6 1.0
NH2 C:ARG841 4.8 90.6 1.0
CB C:ASN799 4.8 0.3 1.0
OD1 C:ASP802 4.9 0.0 1.0

Calcium binding site 4 out of 4 in 6nr3

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Calcium binding site 4 out of 4 in the Cryo-Em Structure of the TRPM8 Ion Channel in Complex with High Occupancy Icilin, Pi(4,5)P2, and Calcium


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 TRPM8 Ion Channel in Complex with High Occupancy Icilin, Pi(4,5)P2, and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1203

b:30.0
occ:1.00
OE1 D:GLN785 2.5 0.6 1.0
OD1 D:ASN799 2.6 0.3 1.0
NE2 D:GLN785 2.6 0.6 1.0
CD D:GLN785 2.9 0.6 1.0
OD2 D:ASP802 3.2 0.0 1.0
OE1 D:GLU782 3.2 0.5 1.0
O06 D:KX71201 3.5 20.0 1.0
CG D:ASN799 3.8 0.3 1.0
OE2 D:GLU782 3.8 0.5 1.0
CD D:GLU782 3.9 0.5 1.0
H041 D:KX71201 4.0 20.0 1.0
CG D:ASP802 4.3 0.0 1.0
CG D:GLN785 4.3 0.6 1.0
C05 D:KX71201 4.4 20.0 1.0
ND2 D:ASN799 4.5 0.3 1.0
N04 D:KX71201 4.6 20.0 1.0
CA D:ASN799 4.6 0.3 1.0
OE2 D:GLU1003 4.7 30.0 1.0
CE1 D:TYR793 4.7 0.9 1.0
NH1 D:ARG841 4.8 90.6 1.0
NH2 D:ARG841 4.8 90.6 1.0
CB D:ASN799 4.8 0.3 1.0
OD1 D:ASP802 4.9 0.0 1.0

Reference:

Y.Yin, S.C.Le, A.L.Hsu, M.J.Borgnia, H.Yang, S.Y.Lee. Structural Basis of Cooling Agent and Lipid Sensing By the Cold-Activated TRPM8 Channel. Science V. 363 2019.
ISSN: ESSN 1095-9203
PubMed: 30733385
DOI: 10.1126/SCIENCE.AAV9334
Page generated: Sat Dec 12 07:23:05 2020

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