Calcium in PDB 9b6i: Cryo-Em Structure of the Avian Great Tit TRPM8 Channel in Complex with the Antagonist Tc-I 2014

The structure of Cryo-Em Structure of the Avian Great Tit TRPM8 Channel in Complex with the Antagonist Tc-I 2014 also contains other interesting chemical elements:

Fluorine

(F)

24 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of the Avian Great Tit TRPM8 Channel in Complex with the Antagonist Tc-I 2014 (pdb code 9b6i). 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 Avian Great Tit TRPM8 Channel in Complex with the Antagonist Tc-I 2014, PDB code: 9b6i:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of the Avian Great Tit TRPM8 Channel in Complex with the Antagonist Tc-I 2014


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 Avian Great Tit TRPM8 Channel in Complex with the Antagonist Tc-I 2014 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1201 b:121.3 occ:1.00 HD22 A:ASN806 2.9 95.8 1.0 OE1 A:GLU792 3.0 114.6 1.0 HD21 A:ASN806 3.1 95.7 1.0 OE2 A:GLU792 3.1 114.1 1.0 ND2 A:ASN806 3.3 99.7 1.0 CD A:GLU792 3.4 115.2 1.0 OD2 A:ASP809 3.9 86.5 1.0 HE2 A:MET795 4.1 124.6 1.0 HG2 A:MET795 4.4 125.5 1.0 HA A:ASN806 4.4 95.0 1.0 HH22 A:ARG848 4.5 53.9 1.0 HE2 A:HIS851 4.5 57.0 1.0 HE3 A:MET795 4.5 124.8 1.0 NH2 A:ARG848 4.6 59.7 1.0 CG A:ASN806 4.6 99.2 1.0 HH21 A:ARG848 4.7 53.7 1.0 HE1 A:TYR800 4.7 123.8 1.0 HD2 A:HIS851 4.8 56.2 1.0 CE A:MET795 4.8 124.5 1.0 HB2 A:MET795 4.9 125.3 1.0 CG A:GLU792 4.9 114.5 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of the Avian Great Tit TRPM8 Channel in Complex with the Antagonist Tc-I 2014


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 Avian Great Tit TRPM8 Channel in Complex with the Antagonist Tc-I 2014 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1201 b:121.3 occ:1.00 HD22 B:ASN806 2.9 95.8 1.0 OE1 B:GLU792 3.0 114.6 1.0 HD21 B:ASN806 3.1 95.7 1.0 OE2 B:GLU792 3.1 114.1 1.0 ND2 B:ASN806 3.3 99.7 1.0 CD B:GLU792 3.4 115.2 1.0 OD2 B:ASP809 3.9 86.5 1.0 HE2 B:MET795 4.1 124.6 1.0 HG2 B:MET795 4.4 125.5 1.0 HA B:ASN806 4.4 95.0 1.0 HH22 B:ARG848 4.5 53.9 1.0 HE2 B:HIS851 4.5 57.0 1.0 HE3 B:MET795 4.5 124.8 1.0 NH2 B:ARG848 4.6 59.7 1.0 CG B:ASN806 4.6 99.2 1.0 HH21 B:ARG848 4.7 53.7 1.0 HE1 B:TYR800 4.7 123.8 1.0 HD2 B:HIS851 4.8 56.2 1.0 CE B:MET795 4.8 124.5 1.0 HB2 B:MET795 4.9 125.3 1.0 CG B:GLU792 4.9 114.5 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of the Avian Great Tit TRPM8 Channel in Complex with the Antagonist Tc-I 2014


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 Avian Great Tit TRPM8 Channel in Complex with the Antagonist Tc-I 2014 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1201 b:121.3 occ:1.00 HD22 D:ASN806 2.9 95.8 1.0 OE1 D:GLU792 3.0 114.6 1.0 HD21 D:ASN806 3.1 95.7 1.0 OE2 D:GLU792 3.1 114.1 1.0 ND2 D:ASN806 3.3 99.7 1.0 CD D:GLU792 3.4 115.2 1.0 OD2 D:ASP809 3.9 86.5 1.0 HE2 D:MET795 4.1 124.6 1.0 HG2 D:MET795 4.4 125.5 1.0 HA D:ASN806 4.4 95.0 1.0 HH22 D:ARG848 4.5 53.9 1.0 HE2 D:HIS851 4.5 57.0 1.0 HE3 D:MET795 4.5 124.8 1.0 NH2 D:ARG848 4.6 59.7 1.0 CG D:ASN806 4.6 99.2 1.0 HH21 D:ARG848 4.7 53.7 1.0 HE1 D:TYR800 4.7 123.8 1.0 HD2 D:HIS851 4.8 56.2 1.0 CE D:MET795 4.8 124.5 1.0 HB2 D:MET795 4.9 125.3 1.0 CG D:GLU792 4.9 114.5 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of the Avian Great Tit TRPM8 Channel in Complex with the Antagonist Tc-I 2014


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 Avian Great Tit TRPM8 Channel in Complex with the Antagonist Tc-I 2014 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1201 b:121.3 occ:1.00 HD22 C:ASN806 2.9 95.8 1.0 OE1 C:GLU792 3.0 114.6 1.0 HD21 C:ASN806 3.1 95.7 1.0 OE2 C:GLU792 3.1 114.1 1.0 ND2 C:ASN806 3.3 99.7 1.0 CD C:GLU792 3.4 115.2 1.0 OD2 C:ASP809 3.9 86.5 1.0 HE2 C:MET795 4.1 124.6 1.0 HG2 C:MET795 4.4 125.5 1.0 HA C:ASN806 4.4 95.0 1.0 HH22 C:ARG848 4.5 53.9 1.0 HE2 C:HIS851 4.5 57.0 1.0 HE3 C:MET795 4.5 124.8 1.0 NH2 C:ARG848 4.6 59.7 1.0 CG C:ASN806 4.6 99.2 1.0 HH21 C:ARG848 4.7 53.7 1.0 HE1 C:TYR800 4.7 123.8 1.0 HD2 C:HIS851 4.8 56.2 1.0 CE C:MET795 4.8 124.5 1.0 HB2 C:MET795 4.9 125.3 1.0 CG C:GLU792 4.9 114.5 1.0

Y.Yin, C.G.Park, F.Zhang, J.G Fedor, S.Feng, Y.Suo, W.Im, S.Y.Lee. Mechanisms of Sensory Adaptation and Inhibition of the Cold and Menthol Receptor TRPM8. Sci Adv V. 10 P2211 2024.
ISSN: ESSN 2375-2548
PubMed: 39093967
DOI: 10.1126/SCIADV.ADP2211