Calcium in PDB 6d73: Cryo-Em Structure of the Zebrafish TRPM2 Channel in the Presence of CA2+

The binding sites of Calcium atom in the Cryo-Em Structure of the Zebrafish TRPM2 Channel in the Presence of CA2+ (pdb code 6d73). 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 Zebrafish TRPM2 Channel in the Presence of CA2+, PDB code: 6d73:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of the Zebrafish TRPM2 Channel in the Presence of CA2+


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 Zebrafish TRPM2 Channel in the Presence of CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1601 b:95.2 occ:1.00 OE2 B:GLU857 2.5 96.8 1.0 OD1 B:ASN883 2.5 85.2 1.0 OD2 B:ASP886 2.5 77.4 1.0 OE1 B:GLU857 2.6 96.8 1.0 OE1 B:GLN860 2.6 94.1 1.0 CD B:GLU857 2.9 96.8 1.0 CD B:GLN860 3.4 94.1 1.0 NH2 B:ARG925 3.6 67.0 1.0 NE2 B:GLN860 3.6 94.1 1.0 CG B:ASP886 3.6 77.4 1.0 CG B:ASN883 3.7 85.2 1.0 CB B:ASP886 4.1 77.4 1.0 CA B:ASN883 4.2 85.2 1.0 OH B:TYR877 4.3 93.7 1.0 CG B:GLU857 4.4 96.8 1.0 CB B:ASN883 4.5 85.2 1.0 OE2 B:GLU1088 4.5 81.0 1.0 O B:TRP882 4.5 80.2 1.0 N B:ASN883 4.6 85.2 1.0 ND2 B:ASN883 4.7 85.2 1.0 CG B:GLN860 4.7 94.1 1.0 OD1 B:ASP886 4.7 77.4 1.0 C B:TRP882 4.7 80.2 1.0 CZ B:ARG925 4.7 67.0 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of the Zebrafish TRPM2 Channel in the Presence of CA2+


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 Zebrafish TRPM2 Channel in the Presence of CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1601 b:75.3 occ:1.00 OD1 A:ASN883 2.5 74.6 1.0 OE1 A:GLN860 2.5 83.2 1.0 OE2 A:GLU857 2.5 85.9 1.0 NE2 A:GLN860 3.0 83.2 1.0 CD A:GLN860 3.1 83.2 1.0 CD A:GLU857 3.5 85.9 1.0 NH2 A:ARG925 3.5 67.5 1.0 OE1 A:GLU857 3.6 85.9 1.0 CG A:ASN883 3.7 74.6 1.0 ND2 A:ASN883 4.2 74.6 1.0 OD2 A:ASP886 4.6 76.8 1.0 CG A:GLN860 4.6 83.2 1.0 CZ A:ARG925 4.7 67.5 1.0 CG A:GLU857 4.9 85.9 1.0 CB A:ASN883 4.9 74.6 1.0 CA A:ASN883 5.0 74.6 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of the Zebrafish TRPM2 Channel in the Presence of CA2+


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 Zebrafish TRPM2 Channel in the Presence of CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1601 b:75.3 occ:1.00 OD1 C:ASN883 2.5 74.6 1.0 OE1 C:GLN860 2.5 83.2 1.0 OE2 C:GLU857 2.5 85.9 1.0 NE2 C:GLN860 3.0 83.2 1.0 CD C:GLN860 3.1 83.2 1.0 CD C:GLU857 3.5 85.9 1.0 NH2 C:ARG925 3.5 67.5 1.0 OE1 C:GLU857 3.6 85.9 1.0 CG C:ASN883 3.7 74.6 1.0 ND2 C:ASN883 4.2 74.6 1.0 OD2 C:ASP886 4.6 76.8 1.0 CG C:GLN860 4.6 83.2 1.0 CZ C:ARG925 4.7 67.5 1.0 CG C:GLU857 4.9 85.9 1.0 CB C:ASN883 4.9 74.6 1.0 CA C:ASN883 5.0 74.6 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of the Zebrafish TRPM2 Channel in the Presence of CA2+


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 Zebrafish TRPM2 Channel in the Presence of CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1601 b:95.2 occ:1.00 OE2 D:GLU857 2.5 96.8 1.0 OD1 D:ASN883 2.5 85.2 1.0 OD2 D:ASP886 2.5 77.4 1.0 OE1 D:GLU857 2.6 96.8 1.0 OE1 D:GLN860 2.6 94.1 1.0 CD D:GLU857 2.9 96.8 1.0 CD D:GLN860 3.4 94.1 1.0 NH2 D:ARG925 3.6 67.0 1.0 NE2 D:GLN860 3.6 94.1 1.0 CG D:ASP886 3.6 77.4 1.0 CG D:ASN883 3.7 85.2 1.0 CB D:ASP886 4.1 77.4 1.0 CA D:ASN883 4.2 85.2 1.0 OH D:TYR877 4.3 93.7 1.0 CG D:GLU857 4.4 96.8 1.0 CB D:ASN883 4.5 85.2 1.0 OE2 D:GLU1088 4.5 81.0 1.0 O D:TRP882 4.5 80.2 1.0 N D:ASN883 4.6 85.2 1.0 ND2 D:ASN883 4.7 85.2 1.0 CG D:GLN860 4.7 94.1 1.0 OD1 D:ASP886 4.7 77.4 1.0 C D:TRP882 4.7 80.2 1.0 CZ D:ARG925 4.7 67.0 1.0

Y.Yin, M.Wu, A.L.Hsu, W.F.Borschel, M.J.Borgnia, G.C.Lander, S.Y.Lee. Visualizing Structural Transitions of Ligand-Dependent Gating of the TRPM2 Channel. Nat Commun V. 10 3740 2019.
ISSN: ESSN 2041-1723
PubMed: 31431622
DOI: 10.1038/S41467-019-11733-5