Magnesium in PDB 8sri: Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State

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Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State (pdb code 8sri). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State, PDB code: 8sri:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in the Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1702 b:53.6 occ:1.00 OE1 A:GLN853 2.4 103.2 1.0 OD1 A:ASN869 2.8 78.7 1.0 OD2 A:ASP872 2.9 89.1 1.0 OE2 A:GLU850 2.9 79.6 1.0 CD A:GLN853 3.1 98.3 1.0 NE2 A:GLN853 3.1 99.0 1.0 OE1 A:GLU850 3.2 80.2 1.0 CD A:GLU850 3.5 79.8 1.0 NH2 A:ARG913 3.7 83.3 1.0 CG A:ASN869 4.0 83.5 1.0 CG A:ASP872 4.0 88.9 1.0 CG A:GLN853 4.5 90.4 1.0 OE2 A:GLU1062 4.5 106.0 1.0 CA A:ASN869 4.7 82.1 1.0 CB A:ASP872 4.7 84.6 1.0 CE1 A:TYR863 4.8 103.6 1.0 CB A:ASN869 4.9 82.5 1.0 ND2 A:ASN869 4.9 93.1 1.0 OD1 A:ASP872 4.9 89.9 1.0 CG A:GLU850 5.0 82.3 1.0 CZ A:ARG913 5.0 75.5 1.0

Magnesium binding site 2 out of 16 in the Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1703 b:190.0 occ:1.00 O2B A:APR1707 2.1 195.4 1.0 OE2 A:GLU1390 2.1 168.0 1.0 O A:GLY1370 2.4 173.3 1.0 OE1 A:GLU1390 2.5 167.1 1.0 CD A:GLU1390 2.6 166.0 1.0 O1A A:APR1707 3.0 196.6 1.0 OD2 A:ASP1460 3.1 158.5 1.0 PB A:APR1707 3.4 194.4 1.0 C A:GLY1370 3.5 171.3 1.0 N A:GLY1370 3.7 170.9 1.0 MG A:MG1704 3.8 184.2 1.0 O5D A:APR1707 3.9 194.7 1.0 CG A:GLU1390 4.1 164.1 1.0 CG A:ASP1460 4.1 159.8 1.0 PA A:APR1707 4.2 196.7 1.0 CA A:GLY1370 4.2 170.8 1.0 O3A A:APR1707 4.2 195.0 1.0 CD1 A:ILE1358 4.2 111.3 1.0 OD1 A:ASP1460 4.4 160.3 1.0 OE1 A:GLU1386 4.5 183.8 1.0 N A:GLY1371 4.6 187.1 1.0 O1B A:APR1707 4.6 194.5 1.0 NH1 A:ARG1360 4.6 138.3 1.0 C A:PRO1369 4.7 133.5 1.0 CA A:PRO1369 4.8 131.7 1.0 CA A:GLY1371 4.8 188.0 1.0 O3D A:APR1707 4.8 195.8 1.0 CB A:GLU1390 5.0 162.3 1.0

Magnesium binding site 3 out of 16 in the Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1704 b:184.2 occ:1.00 MG A:MG1705 2.1 187.6 1.0 O1A A:APR1707 2.1 196.6 1.0 OD1 A:ASP1460 2.2 160.3 1.0 OE2 A:GLU1390 2.3 168.0 1.0 OE1 A:GLU1386 2.3 183.8 1.0 O5' A:APR1707 3.0 196.0 1.0 PA A:APR1707 3.1 196.7 1.0 CG A:ASP1460 3.2 159.8 1.0 CD A:GLU1390 3.3 166.0 1.0 CD A:GLU1386 3.4 182.6 1.0 OD2 A:ASP1460 3.4 158.5 1.0 CG A:GLU1390 3.7 164.1 1.0 MG A:MG1703 3.8 190.0 1.0 OE2 A:GLU1386 3.9 181.7 1.0 O2A A:APR1707 4.2 196.2 1.0 C5' A:APR1707 4.2 196.0 1.0 O2B A:APR1707 4.2 195.4 1.0 O3A A:APR1707 4.3 195.0 1.0 OE1 A:GLU1390 4.4 167.1 1.0 O A:GLY1370 4.5 173.3 1.0 CB A:ASP1460 4.5 159.4 1.0 CG A:GLU1386 4.6 181.3 1.0 PB A:APR1707 4.9 194.4 1.0

Magnesium binding site 4 out of 16 in the Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1705 b:187.6 occ:1.00 MG A:MG1704 2.1 184.2 1.0 O5' A:APR1707 2.3 196.0 1.0 O1A A:APR1707 2.4 196.6 1.0 PA A:APR1707 2.5 196.7 1.0 OE1 A:GLU1386 2.8 183.8 1.0 O2A A:APR1707 2.8 196.2 1.0 OE2 A:GLU1386 2.9 181.7 1.0 CD A:GLU1386 3.1 182.6 1.0 C5' A:APR1707 3.7 196.0 1.0 OD1 A:ASP1460 3.9 160.3 1.0 O4' A:APR1707 4.0 197.6 1.0 O3A A:APR1707 4.1 195.0 1.0 OE2 A:GLU1390 4.1 168.0 1.0 C4' A:APR1707 4.2 196.4 1.0 CG A:GLU1386 4.4 181.3 1.0 CA A:GLY1371 4.8 188.0 1.0 CG A:ASP1460 4.9 159.8 1.0

Magnesium binding site 5 out of 16 in the Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1702 b:53.6 occ:1.00 OE1 B:GLN853 2.4 103.2 1.0 OD1 B:ASN869 2.8 78.7 1.0 OD2 B:ASP872 2.9 89.1 1.0 OE2 B:GLU850 2.9 79.6 1.0 CD B:GLN853 3.1 98.3 1.0 NE2 B:GLN853 3.1 99.0 1.0 OE1 B:GLU850 3.2 80.2 1.0 CD B:GLU850 3.5 79.8 1.0 NH2 B:ARG913 3.7 83.3 1.0 CG B:ASN869 4.0 83.5 1.0 CG B:ASP872 4.0 88.9 1.0 CG B:GLN853 4.5 90.4 1.0 OE2 B:GLU1062 4.5 106.0 1.0 CA B:ASN869 4.7 82.1 1.0 CB B:ASP872 4.7 84.6 1.0 CE1 B:TYR863 4.8 103.6 1.0 CB B:ASN869 4.9 82.5 1.0 ND2 B:ASN869 4.9 93.1 1.0 OD1 B:ASP872 4.9 89.9 1.0 CG B:GLU850 5.0 82.3 1.0 CZ B:ARG913 5.0 75.5 1.0

Magnesium binding site 6 out of 16 in the Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1703 b:190.0 occ:1.00 O2B B:APR1706 2.1 195.4 1.0 OE2 B:GLU1390 2.1 168.0 1.0 O B:GLY1370 2.4 173.3 1.0 OE1 B:GLU1390 2.5 167.1 1.0 CD B:GLU1390 2.6 166.0 1.0 O1A B:APR1706 3.0 196.6 1.0 OD2 B:ASP1460 3.1 158.5 1.0 PB B:APR1706 3.4 194.4 1.0 C B:GLY1370 3.5 171.3 1.0 N B:GLY1370 3.7 170.9 1.0 MG B:MG1704 3.8 184.2 1.0 O5D B:APR1706 3.9 194.7 1.0 CG B:GLU1390 4.1 164.1 1.0 CG B:ASP1460 4.1 159.8 1.0 PA B:APR1706 4.2 196.7 1.0 CA B:GLY1370 4.2 170.8 1.0 O3A B:APR1706 4.2 195.0 1.0 CD1 B:ILE1358 4.2 111.3 1.0 OD1 B:ASP1460 4.4 160.3 1.0 OE1 B:GLU1386 4.5 183.8 1.0 N B:GLY1371 4.6 187.1 1.0 O1B B:APR1706 4.6 194.5 1.0 NH1 B:ARG1360 4.6 138.3 1.0 C B:PRO1369 4.7 133.5 1.0 CA B:PRO1369 4.8 131.7 1.0 CA B:GLY1371 4.8 188.0 1.0 O3D B:APR1706 4.8 195.8 1.0 CB B:GLU1390 5.0 162.3 1.0

Magnesium binding site 7 out of 16 in the Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1704 b:184.2 occ:1.00 MG B:MG1705 2.1 187.6 1.0 O1A B:APR1706 2.1 196.6 1.0 OD1 B:ASP1460 2.2 160.3 1.0 OE2 B:GLU1390 2.3 168.0 1.0 OE1 B:GLU1386 2.3 183.8 1.0 O5' B:APR1706 3.0 196.0 1.0 PA B:APR1706 3.1 196.7 1.0 CG B:ASP1460 3.2 159.8 1.0 CD B:GLU1390 3.3 166.0 1.0 CD B:GLU1386 3.4 182.6 1.0 OD2 B:ASP1460 3.4 158.5 1.0 CG B:GLU1390 3.7 164.1 1.0 MG B:MG1703 3.8 190.0 1.0 OE2 B:GLU1386 3.9 181.7 1.0 O2A B:APR1706 4.2 196.2 1.0 C5' B:APR1706 4.2 196.0 1.0 O2B B:APR1706 4.2 195.4 1.0 O3A B:APR1706 4.3 195.0 1.0 OE1 B:GLU1390 4.4 167.1 1.0 O B:GLY1370 4.5 173.3 1.0 CB B:ASP1460 4.5 159.4 1.0 CG B:GLU1386 4.6 181.3 1.0 PB B:APR1706 4.9 194.4 1.0

Magnesium binding site 8 out of 16 in the Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1705 b:187.6 occ:1.00 MG B:MG1704 2.1 184.2 1.0 O5' B:APR1706 2.3 196.0 1.0 O1A B:APR1706 2.4 196.6 1.0 PA B:APR1706 2.5 196.7 1.0 OE1 B:GLU1386 2.8 183.8 1.0 O2A B:APR1706 2.8 196.2 1.0 OE2 B:GLU1386 2.9 181.7 1.0 CD B:GLU1386 3.1 182.6 1.0 C5' B:APR1706 3.7 196.0 1.0 OD1 B:ASP1460 3.9 160.3 1.0 O4' B:APR1706 4.0 197.6 1.0 O3A B:APR1706 4.1 195.0 1.0 OE2 B:GLU1390 4.1 168.0 1.0 C4' B:APR1706 4.2 196.4 1.0 CG B:GLU1386 4.4 181.3 1.0 CA B:GLY1371 4.8 188.0 1.0 CG B:ASP1460 4.9 159.8 1.0

Magnesium binding site 9 out of 16 in the Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1702 b:53.6 occ:1.00 OE1 C:GLN853 2.4 103.2 1.0 OD1 C:ASN869 2.8 78.7 1.0 OD2 C:ASP872 2.9 89.1 1.0 OE2 C:GLU850 2.9 79.6 1.0 CD C:GLN853 3.1 98.3 1.0 NE2 C:GLN853 3.1 99.0 1.0 OE1 C:GLU850 3.2 80.2 1.0 CD C:GLU850 3.5 79.8 1.0 NH2 C:ARG913 3.7 83.3 1.0 CG C:ASN869 4.0 83.5 1.0 CG C:ASP872 4.0 88.9 1.0 CG C:GLN853 4.5 90.4 1.0 OE2 C:GLU1062 4.5 106.0 1.0 CA C:ASN869 4.7 82.1 1.0 CB C:ASP872 4.7 84.6 1.0 CE1 C:TYR863 4.8 103.6 1.0 CB C:ASN869 4.9 82.5 1.0 ND2 C:ASN869 4.9 93.1 1.0 OD1 C:ASP872 4.9 89.9 1.0 CG C:GLU850 5.0 82.3 1.0 CZ C:ARG913 5.0 75.5 1.0

Magnesium binding site 10 out of 16 in the Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of TRPM2 Chanzyme (E1114A) in the Presence of Magnesium and Adp-Ribose, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1703 b:190.0 occ:1.00 O2B C:APR1707 2.1 195.4 1.0 OE2 C:GLU1390 2.1 168.0 1.0 O C:GLY1370 2.4 173.3 1.0 OE1 C:GLU1390 2.5 167.1 1.0 CD C:GLU1390 2.6 166.0 1.0 O1A C:APR1707 3.0 196.6 1.0 OD2 C:ASP1460 3.1 158.5 1.0 PB C:APR1707 3.4 194.4 1.0 C C:GLY1370 3.5 171.3 1.0 N C:GLY1370 3.7 170.9 1.0 MG C:MG1704 3.8 184.2 1.0 O5D C:APR1707 3.9 194.7 1.0 CG C:GLU1390 4.1 164.1 1.0 CG C:ASP1460 4.1 159.8 1.0 PA C:APR1707 4.2 196.7 1.0 CA C:GLY1370 4.2 170.8 1.0 O3A C:APR1707 4.2 195.0 1.0 CD1 C:ILE1358 4.2 111.3 1.0 OD1 C:ASP1460 4.4 160.3 1.0 OE1 C:GLU1386 4.5 183.8 1.0 N C:GLY1371 4.6 187.1 1.0 O1B C:APR1707 4.6 194.5 1.0 NH1 C:ARG1360 4.6 138.3 1.0 C C:PRO1369 4.7 133.5 1.0 CA C:PRO1369 4.8 131.7 1.0 CA C:GLY1371 4.8 188.0 1.0 O3D C:APR1707 4.8 195.8 1.0 CB C:GLU1390 5.0 162.3 1.0

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