Magnesium in PDB 8srf: Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, Closed State

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, Closed State (pdb code 8srf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 21 binding sites of Magnesium where determined in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, Closed State, PDB code: 8srf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, 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 in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1504 b:81.2 occ:1.00 OE1 A:GLN853 2.2 111.3 1.0 OD1 A:ASN869 2.6 98.4 1.0 OD2 A:ASP872 2.7 98.0 1.0 OE2 A:GLU850 2.9 103.6 1.0 OE1 A:GLU850 3.2 105.7 1.0 CD A:GLN853 3.3 115.7 1.0 CD A:GLU850 3.4 104.7 1.0 NH2 A:ARG913 3.7 90.0 1.0 CG A:ASN869 3.8 96.1 1.0 CG A:ASP872 3.8 95.4 1.0 NE2 A:GLN853 3.9 119.0 1.0 OE2 A:GLU1062 4.3 113.5 1.0 CA A:ASN869 4.4 93.5 1.0 CG A:GLN853 4.5 115.5 1.0 CB A:ASP872 4.5 87.6 1.0 CB A:ASN869 4.7 93.7 1.0 OD1 A:ASP872 4.7 97.8 1.0 ND2 A:ASN869 4.8 101.1 1.0 N A:ASN869 4.8 97.3 1.0 O A:TRP868 4.9 96.3 1.0 CZ A:ARG913 4.9 84.2 1.0 CG A:GLU850 4.9 104.2 1.0

Magnesium binding site 2 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, 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 in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1505 b:111.4 occ:1.00 OE1 A:GLU1114 2.1 131.3 1.0 O A:GLY623 2.2 111.0 1.0 O A:LEU621 2.5 99.8 1.0 OE2 A:GLU1114 2.7 131.9 1.0 CD A:GLU1114 2.8 131.7 1.0 C A:GLY623 3.3 108.4 1.0 O A:ILE622 3.5 107.2 1.0 C A:LEU621 3.5 95.0 1.0 C A:ILE622 3.6 103.9 1.0 N A:GLY623 3.9 104.8 1.0 CA A:GLY623 4.2 103.9 1.0 CG A:GLU1114 4.2 129.2 1.0 CA A:ILE622 4.3 103.6 1.0 N A:ILE622 4.3 101.7 1.0 OG A:SER626 4.3 105.4 1.0 O A:TRP620 4.3 97.7 1.0 N A:ASP624 4.3 126.0 1.0 CA A:ASP624 4.4 126.5 1.0 CA A:LEU621 4.4 90.1 1.0 CB A:GLU1114 4.9 125.4 1.0

Magnesium binding site 3 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, 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 in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1506 b:70.8 occ:1.00 OE2 A:GLU1390 2.1 92.2 1.0 O1X A:RP51501 2.1 94.9 1.0 O2P A:AMP1502 2.1 89.2 1.0 OD2 A:ASP1460 2.3 108.3 1.0 O A:GLY1370 2.8 77.3 1.0 MG A:MG1507 2.9 81.2 1.0 CD A:GLU1390 3.0 91.0 1.0 CG A:ASP1460 3.1 107.7 1.0 P' A:RP51501 3.2 103.3 1.0 OD1 A:ASP1460 3.3 110.5 1.0 OE1 A:GLU1390 3.4 92.0 1.0 O3X A:RP51501 3.5 88.2 1.0 P A:AMP1502 3.6 111.7 1.0 O5 A:RP51501 3.9 96.7 1.0 C A:GLY1370 4.0 71.9 1.0 O1P A:AMP1502 4.0 96.3 1.0 O5' A:AMP1502 4.2 99.5 1.0 OE1 A:GLU1386 4.3 99.1 1.0 CG A:GLU1390 4.3 87.8 1.0 CA A:GLY1371 4.3 73.7 1.0 C5' A:AMP1502 4.5 94.2 1.0 O2X A:RP51501 4.5 95.6 1.0 CB A:ASP1460 4.6 101.8 1.0 NH1 A:ARG1360 4.6 86.2 1.0 N A:GLY1371 4.7 72.4 1.0 O3P A:AMP1502 4.7 103.0 1.0 N A:GLY1370 4.9 76.3 1.0

Magnesium binding site 4 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, 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 in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1507 b:81.2 occ:1.00 OE2 A:GLU1390 2.1 92.2 1.0 O1P A:AMP1502 2.1 96.3 1.0 OE1 A:GLU1386 2.1 99.1 1.0 O2P A:AMP1502 2.2 89.2 1.0 OD1 A:ASP1460 2.4 110.5 1.0 P A:AMP1502 2.6 111.7 1.0 MG A:MG1506 2.9 70.8 1.0 CD A:GLU1390 3.2 91.0 1.0 CD A:GLU1386 3.3 100.8 1.0 CG A:ASP1460 3.3 107.7 1.0 O3P A:AMP1502 3.4 103.0 1.0 OD2 A:ASP1460 3.5 108.3 1.0 CG A:GLU1390 3.6 87.8 1.0 OD2 A:ASP1459 3.7 112.6 1.0 OE2 A:GLU1386 3.9 101.0 1.0 O5' A:AMP1502 3.9 99.5 1.0 O A:GLY1370 4.3 77.3 1.0 OE1 A:GLU1390 4.3 92.0 1.0 C5' A:AMP1502 4.4 94.2 1.0 MG A:MG1508 4.4 77.4 1.0 CG A:GLU1386 4.4 92.9 1.0 OE1 A:GLU1389 4.6 108.9 1.0 CG A:ASP1459 4.7 110.5 1.0 CB A:ASP1460 4.7 101.8 1.0 O1X A:RP51501 4.9 94.9 1.0 CA A:GLY1371 4.9 73.7 1.0 CB A:GLU1386 4.9 87.5 1.0

Magnesium binding site 5 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, 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 in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1508 b:77.4 occ:1.00 O3P A:AMP1502 2.1 103.0 1.0 OE2 A:GLU1386 2.5 101.0 1.0 O1P A:AMP1502 3.3 96.3 1.0 P A:AMP1502 3.3 111.7 1.0 NH1 A:ARG1385 3.3 89.6 1.0 CD A:GLU1386 3.5 100.8 1.0 OE1 A:GLU1386 3.9 99.1 1.0 O5' A:AMP1502 4.2 99.5 1.0 CZ A:ARG1385 4.3 92.7 1.0 OD1 A:ASP1374 4.4 108.8 1.0 OD2 A:ASP1374 4.4 108.3 1.0 MG A:MG1507 4.4 81.2 1.0 O A:PHE1372 4.4 70.9 1.0 NH2 A:ARG1385 4.4 92.5 1.0 O4' A:AMP1502 4.4 101.1 1.0 O2P A:AMP1502 4.5 89.2 1.0 OE1 A:GLU1389 4.6 108.9 1.0 CG A:GLU1386 4.7 92.9 1.0 CG A:ASP1374 4.7 106.7 1.0 C8 A:AMP1502 4.8 94.0 1.0

Magnesium binding site 6 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, 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 in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1512 b:58.0 occ:1.00 O A:GLY984 3.9 80.4 1.0 O D:GLY984 3.9 80.4 1.0 O B:GLY984 3.9 80.4 1.0 O C:GLY984 3.9 80.4 1.0 C A:GLY984 4.1 69.7 1.0 C D:GLY984 4.1 69.7 1.0 C B:GLY984 4.1 69.7 1.0 C C:GLY984 4.1 69.7 1.0 CA A:GLY984 4.1 71.9 1.0 CA D:GLY984 4.1 71.9 1.0 CA B:GLY984 4.1 71.9 1.0 CA C:GLY984 4.1 71.9 1.0 O D:TYR983 4.4 69.5 1.0 O A:TYR983 4.4 69.5 1.0 O B:TYR983 4.4 69.5 1.0 O C:TYR983 4.4 69.5 1.0 N A:GLU985 4.9 58.6 1.0 N D:GLU985 4.9 58.6 1.0 N B:GLU985 4.9 58.6 1.0 N C:GLU985 4.9 58.6 1.0

Magnesium binding site 7 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, 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 in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1504 b:81.2 occ:1.00 OE1 B:GLN853 2.2 111.3 1.0 OD1 B:ASN869 2.6 98.4 1.0 OD2 B:ASP872 2.7 98.0 1.0 OE2 B:GLU850 2.9 103.6 1.0 OE1 B:GLU850 3.2 105.7 1.0 CD B:GLN853 3.3 115.7 1.0 CD B:GLU850 3.4 104.7 1.0 NH2 B:ARG913 3.7 90.0 1.0 CG B:ASN869 3.8 96.1 1.0 CG B:ASP872 3.8 95.4 1.0 NE2 B:GLN853 3.9 119.0 1.0 OE2 B:GLU1062 4.3 113.5 1.0 CA B:ASN869 4.4 93.5 1.0 CG B:GLN853 4.5 115.5 1.0 CB B:ASP872 4.5 87.6 1.0 CB B:ASN869 4.7 93.7 1.0 OD1 B:ASP872 4.7 97.8 1.0 ND2 B:ASN869 4.8 101.1 1.0 N B:ASN869 4.8 97.3 1.0 O B:TRP868 4.9 96.3 1.0 CZ B:ARG913 4.9 84.2 1.0 CG B:GLU850 4.9 104.2 1.0

Magnesium binding site 8 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, 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 in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1505 b:111.4 occ:1.00 OE1 B:GLU1114 2.1 131.3 1.0 O B:GLY623 2.2 111.0 1.0 O B:LEU621 2.5 99.8 1.0 OE2 B:GLU1114 2.7 131.9 1.0 CD B:GLU1114 2.8 131.7 1.0 C B:GLY623 3.3 108.4 1.0 O B:ILE622 3.5 107.2 1.0 C B:LEU621 3.5 95.0 1.0 C B:ILE622 3.6 103.9 1.0 N B:GLY623 3.9 104.8 1.0 CA B:GLY623 4.2 103.9 1.0 CG B:GLU1114 4.2 129.2 1.0 CA B:ILE622 4.3 103.6 1.0 N B:ILE622 4.3 101.7 1.0 OG B:SER626 4.3 105.4 1.0 O B:TRP620 4.3 97.7 1.0 N B:ASP624 4.3 126.0 1.0 CA B:ASP624 4.4 126.5 1.0 CA B:LEU621 4.4 90.1 1.0 CB B:GLU1114 4.9 125.4 1.0

Magnesium binding site 9 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, 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 in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1506 b:70.8 occ:1.00 OE2 B:GLU1390 2.1 92.2 1.0 O1X B:RP51501 2.1 94.9 1.0 O2P B:AMP1502 2.1 89.2 1.0 OD2 B:ASP1460 2.3 108.3 1.0 O B:GLY1370 2.8 77.3 1.0 MG B:MG1507 2.9 81.2 1.0 CD B:GLU1390 3.0 91.0 1.0 CG B:ASP1460 3.1 107.7 1.0 P' B:RP51501 3.2 103.3 1.0 OD1 B:ASP1460 3.3 110.5 1.0 OE1 B:GLU1390 3.4 92.0 1.0 O3X B:RP51501 3.5 88.2 1.0 P B:AMP1502 3.6 111.7 1.0 O5 B:RP51501 3.9 96.7 1.0 C B:GLY1370 4.0 71.9 1.0 O1P B:AMP1502 4.0 96.3 1.0 O5' B:AMP1502 4.2 99.5 1.0 OE1 B:GLU1386 4.3 99.1 1.0 CG B:GLU1390 4.3 87.8 1.0 CA B:GLY1371 4.3 73.7 1.0 C5' B:AMP1502 4.5 94.2 1.0 O2X B:RP51501 4.5 95.6 1.0 CB B:ASP1460 4.6 101.8 1.0 NH1 B:ARG1360 4.6 86.2 1.0 N B:GLY1371 4.7 72.4 1.0 O3P B:AMP1502 4.7 103.0 1.0 N B:GLY1370 4.9 76.3 1.0

Magnesium binding site 10 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, 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 in the Presence of Magnesium, Adp- Ribose, Adenosine Monophosphate, and Ribose-5-Phosphate, Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1507 b:81.2 occ:1.00 OE2 B:GLU1390 2.1 92.2 1.0 O1P B:AMP1502 2.1 96.3 1.0 OE1 B:GLU1386 2.1 99.1 1.0 O2P B:AMP1502 2.2 89.2 1.0 OD1 B:ASP1460 2.4 110.5 1.0 P B:AMP1502 2.6 111.7 1.0 MG B:MG1506 2.9 70.8 1.0 CD B:GLU1390 3.2 91.0 1.0 CD B:GLU1386 3.3 100.8 1.0 CG B:ASP1460 3.3 107.7 1.0 O3P B:AMP1502 3.4 103.0 1.0 OD2 B:ASP1460 3.5 108.3 1.0 CG B:GLU1390 3.6 87.8 1.0 OD2 B:ASP1459 3.7 112.6 1.0 OE2 B:GLU1386 3.9 101.0 1.0 O5' B:AMP1502 3.9 99.5 1.0 O B:GLY1370 4.3 77.3 1.0 OE1 B:GLU1390 4.3 92.0 1.0 C5' B:AMP1502 4.4 94.2 1.0 MG B:MG1508 4.4 77.4 1.0 CG B:GLU1386 4.4 92.9 1.0 OE1 B:GLU1389 4.6 108.9 1.0 CG B:ASP1459 4.7 110.5 1.0 CB B:ASP1460 4.7 101.8 1.0 O1X B:RP51501 4.9 94.9 1.0 CA B:GLY1371 4.9 73.7 1.0 CB B:GLU1386 4.9 87.5 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.