Magnesium in PDB 8sr7: Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adenosine Monophosphate, and Ribose-5-Phosphate

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Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adenosine Monophosphate, and Ribose-5-Phosphate (pdb code 8sr7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 17 binding sites of Magnesium where determined in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adenosine Monophosphate, and Ribose-5-Phosphate, PDB code: 8sr7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adenosine Monophosphate, and Ribose-5-Phosphate


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, Adenosine Monophosphate, and Ribose-5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1503 b:73.2 occ:1.00 O A:HOH1603 2.1 74.9 1.0 O A:HOH1610 2.1 74.2 1.0 OE1 A:GLN853 2.3 93.7 1.0 OE1 A:GLU850 2.4 89.2 1.0 OE2 A:GLU850 2.4 85.1 1.0 OD1 A:ASN869 2.6 82.1 1.0 OD2 A:ASP872 2.6 77.4 1.0 CD A:GLU850 2.7 85.1 1.0 CD A:GLN853 3.3 88.9 1.0 CG A:ASP872 3.6 79.3 1.0 NE2 A:GLN853 3.6 86.4 1.0 CG A:ASN869 3.7 80.0 1.0 NH2 A:ARG913 4.0 70.7 1.0 CB A:ASP872 4.2 75.3 1.0 CA A:ASN869 4.2 81.2 1.0 CG A:GLU850 4.2 81.6 1.0 CB A:ASN869 4.4 80.4 1.0 CE2 A:TYR863 4.4 91.6 1.0 OD1 A:ASP872 4.5 79.5 1.0 OH A:TYR863 4.6 95.3 1.0 CG A:GLN853 4.7 84.4 1.0 ND2 A:ASN869 4.7 82.7 1.0 N A:ASN869 4.8 83.3 1.0 O A:TRP868 4.9 79.8 1.0 CZ A:TYR863 4.9 92.1 1.0 CB A:GLN853 5.0 86.6 1.0

Magnesium binding site 2 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adenosine Monophosphate, and Ribose-5-Phosphate


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, Adenosine Monophosphate, and Ribose-5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1504 b:86.4 occ:1.00 O A:GLY623 2.2 78.9 1.0 OE1 A:GLU1114 2.3 95.0 1.0 OE2 A:GLU1114 2.3 96.0 1.0 O A:LEU621 2.5 80.0 1.0 CD A:GLU1114 2.6 96.1 1.0 O A:HOH1609 2.6 86.8 1.0 O A:HOH1608 2.6 83.0 1.0 O A:HOH1606 2.9 79.8 1.0 C A:GLY623 3.4 77.8 1.0 C A:LEU621 3.4 70.7 1.0 O A:ILE622 3.7 79.1 1.0 C A:ILE622 3.9 72.6 1.0 CG A:GLU1114 4.1 87.2 1.0 O A:TRP620 4.1 74.4 1.0 N A:GLY623 4.1 73.8 1.0 CA A:LEU621 4.2 65.6 1.0 OG A:SER626 4.3 78.4 1.0 N A:ASP624 4.3 88.6 1.0 CA A:GLY623 4.3 71.5 1.0 N A:ILE622 4.3 66.7 1.0 CA A:ASP624 4.3 86.9 1.0 CA A:ILE622 4.5 66.7 1.0 CB A:GLU1114 4.7 78.3 1.0 C A:TRP620 5.0 65.5 1.0

Magnesium binding site 3 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adenosine Monophosphate, and Ribose-5-Phosphate


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, Adenosine Monophosphate, and Ribose-5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1505 b:52.1 occ:1.00 O1X A:RP51501 2.1 76.1 1.0 OE1 A:GLU1390 2.1 75.4 1.0 O A:GLY1370 2.3 57.7 1.0 OE2 A:GLU1390 2.3 78.7 1.0 CD A:GLU1390 2.5 72.0 1.0 O A:HOH1601 2.7 51.4 1.0 OD2 A:ASP1460 3.0 90.0 1.0 P' A:RP51501 3.4 90.8 1.0 C A:GLY1370 3.5 44.5 1.0 O5 A:RP51501 3.7 79.3 1.0 CG A:ASP1460 3.8 90.0 1.0 OD1 A:ASP1460 3.9 90.0 1.0 CG A:GLU1390 4.0 67.2 1.0 MG A:MG1506 4.1 69.9 1.0 N A:GLY1370 4.1 42.0 1.0 O3X A:RP51501 4.1 80.6 1.0 CA A:GLY1371 4.3 37.6 1.0 N A:GLY1371 4.4 33.5 1.0 CA A:GLY1370 4.4 39.0 1.0 O2X A:RP51501 4.5 78.3 1.0 NH1 A:ARG1360 4.5 68.9 1.0 OE1 A:GLU1386 4.6 69.0 1.0 CD1 A:ILE1358 4.9 50.6 1.0 CB A:GLU1390 4.9 57.8 1.0 C5 A:RP51501 5.0 73.1 1.0

Magnesium binding site 4 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adenosine Monophosphate, and Ribose-5-Phosphate


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, Adenosine Monophosphate, and Ribose-5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1506 b:69.9 occ:1.00 O A:HOH1601 2.5 51.4 1.0 O3X A:RP51501 2.8 80.6 1.0 C5' A:AMP1502 2.8 87.8 1.0 O4' A:AMP1502 3.2 91.8 1.0 O1X A:RP51501 3.4 76.1 1.0 C4' A:AMP1502 3.4 91.2 1.0 P' A:RP51501 3.7 90.8 1.0 CA A:GLY1371 3.8 37.6 1.0 OE1 A:GLU1386 4.0 69.0 1.0 MG A:MG1505 4.1 52.1 1.0 O5' A:AMP1502 4.1 98.4 1.0 N A:PHE1372 4.1 44.2 1.0 OD2 A:ASP1460 4.4 90.0 1.0 CD A:GLU1386 4.5 67.6 1.0 OE2 A:GLU1390 4.5 78.7 1.0 C1' A:AMP1502 4.5 90.6 1.0 CD2 A:PHE1372 4.5 63.0 1.0 C A:GLY1371 4.5 36.9 1.0 O A:GLY1370 4.5 57.7 1.0 O2X A:RP51501 4.6 78.3 1.0 OE2 A:GLU1386 4.7 66.8 1.0 C3' A:AMP1502 4.9 92.0 1.0 O5 A:RP51501 4.9 79.3 1.0 CG A:ASP1460 5.0 90.0 1.0 N A:GLY1371 5.0 33.5 1.0

Magnesium binding site 5 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adenosine Monophosphate, and Ribose-5-Phosphate


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, Adenosine Monophosphate, and Ribose-5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1510 b:65.5 occ:1.00 O A:GLY984 4.1 62.8 1.0 O D:GLY984 4.1 62.8 1.0 O B:GLY984 4.1 62.8 1.0 O C:GLY984 4.1 62.8 1.0 CA D:GLY984 4.1 47.9 1.0 CA A:GLY984 4.1 47.9 1.0 CA C:GLY984 4.1 47.9 1.0 CA B:GLY984 4.1 47.9 1.0 C A:GLY984 4.2 52.8 1.0 C D:GLY984 4.2 52.8 1.0 C B:GLY984 4.2 52.8 1.0 C C:GLY984 4.2 52.8 1.0 O A:TYR983 4.5 55.5 1.0 O D:TYR983 4.5 55.5 1.0 O C:TYR983 4.5 55.5 1.0 O B:TYR983 4.5 55.5 1.0

Magnesium binding site 6 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adenosine Monophosphate, and Ribose-5-Phosphate


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, Adenosine Monophosphate, and Ribose-5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1503 b:73.2 occ:1.00 O B:HOH1603 2.1 74.9 1.0 O B:HOH1610 2.1 74.2 1.0 OE1 B:GLN853 2.3 93.7 1.0 OE1 B:GLU850 2.4 89.2 1.0 OE2 B:GLU850 2.4 85.1 1.0 OD1 B:ASN869 2.6 82.1 1.0 OD2 B:ASP872 2.6 77.4 1.0 CD B:GLU850 2.7 85.1 1.0 CD B:GLN853 3.3 88.9 1.0 CG B:ASP872 3.6 79.3 1.0 NE2 B:GLN853 3.6 86.4 1.0 CG B:ASN869 3.7 80.0 1.0 NH2 B:ARG913 4.0 70.7 1.0 CB B:ASP872 4.2 75.3 1.0 CA B:ASN869 4.2 81.2 1.0 CG B:GLU850 4.2 81.6 1.0 CB B:ASN869 4.4 80.4 1.0 CE2 B:TYR863 4.4 91.6 1.0 OD1 B:ASP872 4.5 79.5 1.0 OH B:TYR863 4.6 95.3 1.0 CG B:GLN853 4.7 84.4 1.0 ND2 B:ASN869 4.7 82.7 1.0 N B:ASN869 4.8 83.3 1.0 O B:TRP868 4.9 79.8 1.0 CZ B:TYR863 4.9 92.1 1.0 CB B:GLN853 5.0 86.6 1.0

Magnesium binding site 7 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adenosine Monophosphate, and Ribose-5-Phosphate


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, Adenosine Monophosphate, and Ribose-5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1504 b:86.4 occ:1.00 O B:GLY623 2.2 78.9 1.0 OE1 B:GLU1114 2.3 95.0 1.0 OE2 B:GLU1114 2.3 96.0 1.0 O B:LEU621 2.5 80.0 1.0 CD B:GLU1114 2.6 96.1 1.0 O B:HOH1609 2.6 86.8 1.0 O B:HOH1608 2.6 83.0 1.0 O B:HOH1606 2.9 79.8 1.0 C B:GLY623 3.4 77.8 1.0 C B:LEU621 3.4 70.7 1.0 O B:ILE622 3.7 79.1 1.0 C B:ILE622 3.9 72.6 1.0 CG B:GLU1114 4.1 87.2 1.0 O B:TRP620 4.1 74.4 1.0 N B:GLY623 4.1 73.8 1.0 CA B:LEU621 4.2 65.6 1.0 OG B:SER626 4.3 78.4 1.0 N B:ASP624 4.3 88.6 1.0 CA B:GLY623 4.3 71.5 1.0 N B:ILE622 4.3 66.7 1.0 CA B:ASP624 4.3 86.9 1.0 CA B:ILE622 4.5 66.7 1.0 CB B:GLU1114 4.7 78.3 1.0 C B:TRP620 5.0 65.5 1.0

Magnesium binding site 8 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adenosine Monophosphate, and Ribose-5-Phosphate


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, Adenosine Monophosphate, and Ribose-5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1505 b:52.1 occ:1.00 O1X B:RP51501 2.1 76.1 1.0 OE1 B:GLU1390 2.1 75.4 1.0 O B:GLY1370 2.3 57.7 1.0 OE2 B:GLU1390 2.3 78.7 1.0 CD B:GLU1390 2.5 72.0 1.0 O B:HOH1601 2.7 51.4 1.0 OD2 B:ASP1460 3.0 90.0 1.0 P' B:RP51501 3.4 90.8 1.0 C B:GLY1370 3.5 44.5 1.0 O5 B:RP51501 3.7 79.3 1.0 CG B:ASP1460 3.8 90.0 1.0 OD1 B:ASP1460 3.9 90.0 1.0 CG B:GLU1390 4.0 67.2 1.0 MG B:MG1506 4.1 69.9 1.0 N B:GLY1370 4.1 42.0 1.0 O3X B:RP51501 4.1 80.6 1.0 CA B:GLY1371 4.3 37.6 1.0 N B:GLY1371 4.4 33.5 1.0 CA B:GLY1370 4.4 39.0 1.0 O2X B:RP51501 4.5 78.3 1.0 NH1 B:ARG1360 4.5 68.9 1.0 OE1 B:GLU1386 4.6 69.0 1.0 CD1 B:ILE1358 4.9 50.6 1.0 CB B:GLU1390 4.9 57.8 1.0 C5 B:RP51501 5.0 73.1 1.0

Magnesium binding site 9 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adenosine Monophosphate, and Ribose-5-Phosphate


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, Adenosine Monophosphate, and Ribose-5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1506 b:69.9 occ:1.00 O B:HOH1601 2.5 51.4 1.0 O3X B:RP51501 2.8 80.6 1.0 C5' B:AMP1502 2.8 87.8 1.0 O4' B:AMP1502 3.2 91.8 1.0 O1X B:RP51501 3.4 76.1 1.0 C4' B:AMP1502 3.4 91.2 1.0 P' B:RP51501 3.7 90.8 1.0 CA B:GLY1371 3.8 37.6 1.0 OE1 B:GLU1386 4.0 69.0 1.0 MG B:MG1505 4.1 52.1 1.0 O5' B:AMP1502 4.1 98.4 1.0 N B:PHE1372 4.1 44.2 1.0 OD2 B:ASP1460 4.4 90.0 1.0 CD B:GLU1386 4.5 67.6 1.0 OE2 B:GLU1390 4.5 78.7 1.0 C1' B:AMP1502 4.5 90.6 1.0 CD2 B:PHE1372 4.5 63.0 1.0 C B:GLY1371 4.5 36.9 1.0 O B:GLY1370 4.5 57.7 1.0 O2X B:RP51501 4.6 78.3 1.0 OE2 B:GLU1386 4.7 66.8 1.0 C3' B:AMP1502 4.9 92.0 1.0 O5 B:RP51501 4.9 79.3 1.0 CG B:ASP1460 5.0 90.0 1.0 N B:GLY1371 5.0 33.5 1.0

Magnesium binding site 10 out of 17 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, Adenosine Monophosphate, and Ribose-5-Phosphate


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, Adenosine Monophosphate, and Ribose-5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1503 b:73.2 occ:1.00 O C:HOH1603 2.1 74.9 1.0 O C:HOH1610 2.1 74.2 1.0 OE1 C:GLN853 2.3 93.7 1.0 OE1 C:GLU850 2.4 89.2 1.0 OE2 C:GLU850 2.4 85.1 1.0 OD1 C:ASN869 2.6 82.1 1.0 OD2 C:ASP872 2.6 77.4 1.0 CD C:GLU850 2.7 85.1 1.0 CD C:GLN853 3.3 88.9 1.0 CG C:ASP872 3.6 79.3 1.0 NE2 C:GLN853 3.6 86.4 1.0 CG C:ASN869 3.7 80.0 1.0 NH2 C:ARG913 4.0 70.7 1.0 CB C:ASP872 4.2 75.3 1.0 CA C:ASN869 4.2 81.2 1.0 CG C:GLU850 4.2 81.6 1.0 CB C:ASN869 4.4 80.4 1.0 CE2 C:TYR863 4.4 91.6 1.0 OD1 C:ASP872 4.5 79.5 1.0 OH C:TYR863 4.6 95.3 1.0 CG C:GLN853 4.7 84.4 1.0 ND2 C:ASN869 4.7 82.7 1.0 N C:ASN869 4.8 83.3 1.0 O C:TRP868 4.9 79.8 1.0 CZ C:TYR863 4.9 92.1 1.0 CB C:GLN853 5.0 86.6 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.