Calcium in PDB 8src: Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose

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Binding sites:

The binding sites of Calcium atom in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose (pdb code 8src). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 17 binding sites of Calcium where determined in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose, PDB code: 8src:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose


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 TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1702 b:138.8 occ:1.00 OE1 A:GLN853 2.5 148.5 1.0 OD2 A:ASP872 2.5 135.5 1.0 OD1 A:ASN869 2.6 128.2 1.0 OE2 A:GLU850 2.8 141.7 1.0 OE1 A:GLU850 3.0 141.9 1.0 CD A:GLU850 3.3 140.3 1.0 CD A:GLN853 3.5 146.8 1.0 CG A:ASP872 3.6 131.7 1.0 CG A:ASN869 3.8 128.1 1.0 NE2 A:GLN853 3.8 146.3 1.0 NH2 A:ARG913 3.8 103.3 1.0 OD1 A:ASP872 4.4 131.3 1.0 CB A:ASP872 4.5 128.1 1.0 OE2 A:GLU1062 4.5 126.7 1.0 CA A:ASN869 4.5 125.1 1.0 CB A:ASN869 4.7 125.2 1.0 ND2 A:ASN869 4.7 130.6 1.0 CG A:GLU850 4.8 138.4 1.0 N A:ASN869 4.8 129.6 1.0 CE1 A:TYR863 4.8 145.5 1.0 CG A:GLN853 4.9 143.8 1.0 O A:TRP868 4.9 107.1 1.0 CZ A:ARG913 5.0 97.1 1.0

Calcium binding site 2 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose


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 TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1703 b:152.1 occ:1.00 O A:LEU621 2.2 107.5 1.0 OE1 A:GLU1114 2.4 143.0 1.0 O A:GLY623 2.5 118.3 1.0 O A:ILE622 3.1 105.8 1.0 OE2 A:GLU1114 3.1 138.1 1.0 CD A:GLU1114 3.1 140.5 1.0 C A:ILE622 3.4 103.5 1.0 C A:LEU621 3.4 99.9 1.0 C A:GLY623 3.5 116.7 1.0 N A:GLY623 3.9 114.9 1.0 CA A:ILE622 4.0 102.7 1.0 N A:ILE622 4.2 103.3 1.0 CA A:GLY623 4.2 112.2 1.0 CA A:LEU621 4.4 94.6 1.0 CG A:GLU1114 4.5 135.2 1.0 N A:ASP624 4.6 132.2 1.0 O A:TRP620 4.6 89.9 1.0 CD1 A:LEU621 4.6 107.4 1.0 CA A:ASP624 4.8 133.8 1.0

Calcium binding site 3 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose


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 TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1704 b:149.1 occ:1.00 OE2 A:GLU1390 2.3 158.4 1.0 O2B A:APR1707 2.3 142.0 1.0 O A:GLY1370 2.7 131.4 1.0 O1A A:APR1707 2.7 140.0 1.0 CD A:GLU1390 3.0 158.8 1.0 OD2 A:ASP1460 3.1 149.1 1.0 OE1 A:GLU1390 3.1 160.7 1.0 PB A:APR1707 3.3 149.9 1.0 O5D A:APR1707 3.4 146.6 1.0 O3A A:APR1707 3.6 137.2 1.0 PA A:APR1707 3.7 138.8 1.0 CA A:CA1705 3.8 163.3 1.0 C A:GLY1370 4.0 128.6 1.0 CG A:ASP1460 4.1 149.1 1.0 NH1 A:ARG1360 4.2 123.0 1.0 OD1 A:ASP1460 4.2 150.3 1.0 N A:GLY1370 4.4 127.5 1.0 CG A:GLU1390 4.4 155.4 1.0 O5' A:APR1707 4.5 136.6 1.0 O1B A:APR1707 4.7 143.2 1.0 CD1 A:ILE1358 4.8 120.8 1.0 OE1 A:GLU1386 4.8 167.3 1.0 C5D A:APR1707 4.8 139.4 1.0 CA A:GLY1370 4.8 128.7 1.0 CA A:GLY1371 4.9 132.6 1.0 N A:GLY1371 4.9 131.3 1.0

Calcium binding site 4 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose


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 TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1705 b:163.3 occ:1.00 O1A A:APR1707 2.1 140.0 1.0 OE1 A:GLU1386 2.3 167.3 1.0 OE2 A:GLU1390 2.4 158.4 1.0 OD1 A:ASP1460 2.9 150.3 1.0 PA A:APR1707 3.4 138.8 1.0 CD A:GLU1386 3.4 166.9 1.0 CD A:GLU1390 3.4 158.8 1.0 O2A A:APR1707 3.7 138.0 1.0 CG A:ASP1460 3.8 149.1 1.0 CA A:CA1704 3.8 149.1 1.0 OE2 A:GLU1386 3.8 164.5 1.0 CG A:GLU1390 3.8 155.4 1.0 OD2 A:ASP1460 4.0 149.1 1.0 O5' A:APR1707 4.3 136.6 1.0 OE1 A:GLU1390 4.5 160.7 1.0 O3A A:APR1707 4.5 137.2 1.0 OE1 A:GLU1389 4.6 171.9 1.0 CG A:GLU1386 4.6 167.0 1.0 O A:GLY1370 4.7 131.4 1.0 O2B A:APR1707 4.8 142.0 1.0

Calcium binding site 5 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose


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 TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1710 b:130.8 occ:1.00 CA A:GLY984 4.1 79.4 1.0 CA D:GLY984 4.1 79.4 1.0 CA C:GLY984 4.1 79.4 1.0 CA B:GLY984 4.2 79.4 1.0 O A:GLY984 4.3 86.7 1.0 O D:GLY984 4.4 86.7 1.0 O C:GLY984 4.4 86.7 1.0 O B:GLY984 4.4 86.7 1.0 O A:TYR983 4.4 77.2 1.0 O D:TYR983 4.4 77.2 1.0 O C:TYR983 4.4 77.2 1.0 O B:TYR983 4.4 77.2 1.0 C A:GLY984 4.4 80.0 1.0 C D:GLY984 4.5 80.0 1.0 C C:GLY984 4.5 80.0 1.0 C B:GLY984 4.5 80.0 1.0

Calcium binding site 6 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose


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 TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1702 b:138.8 occ:1.00 OE1 B:GLN853 2.5 148.5 1.0 OD2 B:ASP872 2.5 135.5 1.0 OD1 B:ASN869 2.6 128.2 1.0 OE2 B:GLU850 2.8 141.7 1.0 OE1 B:GLU850 3.0 141.9 1.0 CD B:GLU850 3.3 140.3 1.0 CD B:GLN853 3.5 146.8 1.0 CG B:ASP872 3.6 131.7 1.0 CG B:ASN869 3.8 128.1 1.0 NE2 B:GLN853 3.8 146.3 1.0 NH2 B:ARG913 3.8 103.3 1.0 OD1 B:ASP872 4.4 131.3 1.0 CB B:ASP872 4.5 128.1 1.0 OE2 B:GLU1062 4.5 126.7 1.0 CA B:ASN869 4.5 125.1 1.0 CB B:ASN869 4.7 125.2 1.0 ND2 B:ASN869 4.7 130.6 1.0 CG B:GLU850 4.8 138.4 1.0 N B:ASN869 4.8 129.6 1.0 CE1 B:TYR863 4.8 145.5 1.0 CG B:GLN853 4.9 143.8 1.0 O B:TRP868 4.9 107.1 1.0 CZ B:ARG913 5.0 97.1 1.0

Calcium binding site 7 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose


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 TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1703 b:152.1 occ:1.00 O B:LEU621 2.2 107.5 1.0 OE1 B:GLU1114 2.4 143.0 1.0 O B:GLY623 2.5 118.3 1.0 O B:ILE622 3.1 105.8 1.0 OE2 B:GLU1114 3.1 138.1 1.0 CD B:GLU1114 3.1 140.5 1.0 C B:ILE622 3.4 103.5 1.0 C B:LEU621 3.4 99.9 1.0 C B:GLY623 3.5 116.7 1.0 N B:GLY623 3.9 114.9 1.0 CA B:ILE622 4.0 102.7 1.0 N B:ILE622 4.2 103.3 1.0 CA B:GLY623 4.2 112.2 1.0 CA B:LEU621 4.4 94.6 1.0 CG B:GLU1114 4.5 135.2 1.0 N B:ASP624 4.6 132.2 1.0 O B:TRP620 4.6 89.9 1.0 CD1 B:LEU621 4.6 107.4 1.0 CA B:ASP624 4.8 133.8 1.0

Calcium binding site 8 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose


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 TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1704 b:149.1 occ:1.00 OE2 B:GLU1390 2.3 158.4 1.0 O2B B:APR1707 2.3 142.0 1.0 O B:GLY1370 2.7 131.4 1.0 O1A B:APR1707 2.7 140.0 1.0 CD B:GLU1390 3.0 158.8 1.0 OD2 B:ASP1460 3.1 149.1 1.0 OE1 B:GLU1390 3.1 160.7 1.0 PB B:APR1707 3.3 149.9 1.0 O5D B:APR1707 3.4 146.6 1.0 O3A B:APR1707 3.6 137.2 1.0 PA B:APR1707 3.7 138.8 1.0 CA B:CA1705 3.8 163.3 1.0 C B:GLY1370 4.0 128.6 1.0 CG B:ASP1460 4.1 149.1 1.0 NH1 B:ARG1360 4.2 123.0 1.0 OD1 B:ASP1460 4.2 150.3 1.0 N B:GLY1370 4.4 127.5 1.0 CG B:GLU1390 4.4 155.4 1.0 O5' B:APR1707 4.5 136.6 1.0 O1B B:APR1707 4.7 143.2 1.0 CD1 B:ILE1358 4.8 120.8 1.0 OE1 B:GLU1386 4.8 167.3 1.0 C5D B:APR1707 4.8 139.4 1.0 CA B:GLY1370 4.8 128.7 1.0 CA B:GLY1371 4.9 132.6 1.0 N B:GLY1371 4.9 131.3 1.0

Calcium binding site 9 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1705 b:163.3 occ:1.00 O1A B:APR1707 2.1 140.0 1.0 OE1 B:GLU1386 2.3 167.3 1.0 OE2 B:GLU1390 2.4 158.4 1.0 OD1 B:ASP1460 2.9 150.3 1.0 PA B:APR1707 3.4 138.8 1.0 CD B:GLU1386 3.4 166.9 1.0 CD B:GLU1390 3.4 158.8 1.0 O2A B:APR1707 3.7 138.0 1.0 CG B:ASP1460 3.8 149.1 1.0 CA B:CA1704 3.8 149.1 1.0 OE2 B:GLU1386 3.8 164.5 1.0 CG B:GLU1390 3.8 155.4 1.0 OD2 B:ASP1460 4.0 149.1 1.0 O5' B:APR1707 4.3 136.6 1.0 OE1 B:GLU1390 4.5 160.7 1.0 O3A B:APR1707 4.5 137.2 1.0 OE1 B:GLU1389 4.6 171.9 1.0 CG B:GLU1386 4.6 167.0 1.0 O B:GLY1370 4.7 131.4 1.0 O2B B:APR1707 4.8 142.0 1.0

Calcium binding site 10 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1702 b:138.8 occ:1.00 OE1 C:GLN853 2.5 148.5 1.0 OD2 C:ASP872 2.5 135.5 1.0 OD1 C:ASN869 2.6 128.2 1.0 OE2 C:GLU850 2.8 141.7 1.0 OE1 C:GLU850 3.0 141.9 1.0 CD C:GLU850 3.3 140.3 1.0 CD C:GLN853 3.5 146.8 1.0 CG C:ASP872 3.6 131.7 1.0 CG C:ASN869 3.8 128.1 1.0 NE2 C:GLN853 3.8 146.3 1.0 NH2 C:ARG913 3.8 103.3 1.0 OD1 C:ASP872 4.4 131.3 1.0 CB C:ASP872 4.5 128.1 1.0 OE2 C:GLU1062 4.5 126.7 1.0 CA C:ASN869 4.5 125.1 1.0 CB C:ASN869 4.7 125.2 1.0 ND2 C:ASN869 4.7 130.6 1.0 CG C:GLU850 4.8 138.4 1.0 N C:ASN869 4.8 129.6 1.0 CE1 C:TYR863 4.8 145.5 1.0 CG C:GLN853 4.9 143.8 1.0 O C:TRP868 4.9 107.1 1.0 CZ C:ARG913 5.0 97.1 1.0

Y.Huang, S.Kumar, W.Lu, J.Du. Coupling Enzymatic Activity and Gating in An Ancient Trpm Chanzyme and Its Molecular Evolution To Be Published.