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

Magnesium Binding Sites:

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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 8srg). 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 in the Presence of Magnesium, Adenosine Monophosphate, and Ribose-5-Phosphate, PDB code: 8srg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 8srg

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Magnesium binding site 1 out of 16 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:155.8
occ:1.00
 OD1 A:ASN869 2.3 180.9 1.0
OE1 A:GLN853 2.5 187.9 1.0
OE1 A:GLU850 2.8 202.8 1.0
OE2 A:GLU850 3.0 201.2 1.0
OD2 A:ASP872 3.1 210.6 1.0
CD A:GLU850 3.3 201.1 1.0
CD A:GLN853 3.6 187.6 1.0
CG A:ASN869 3.6 182.4 1.0
NE2 A:GLN853 4.0 188.3 1.0
CG A:ASP872 4.2 208.3 1.0
NH2 A:ARG913 4.2 143.2 1.0
OE2 A:GLU1062 4.3 173.9 1.0
ND2 A:ASN869 4.4 182.9 1.0
CA A:ASN869 4.5 185.6 1.0
CB A:ASN869 4.6 184.3 1.0
OD1 A:ASP872 4.6 208.9 1.0
CE1 A:TYR863 4.7 174.4 1.0
CG A:GLU850 4.8 201.0 1.0
N A:ASN869 4.8 187.7 1.0
CG A:GLN853 4.9 185.7 1.0

Magnesium binding site 2 out of 16 in 8srg

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Magnesium binding site 2 out of 16 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:196.3
occ:1.00
 O A:GLY623 2.1 176.0 1.0
OE1 A:GLU1114 2.2 206.0 1.0
O A:LEU621 2.3 155.7 1.0
OE2 A:GLU1114 2.7 210.6 1.0
CD A:GLU1114 2.7 207.5 1.0
C A:LEU621 3.3 153.9 1.0
C A:GLY623 3.3 174.0 1.0
O A:ILE622 3.5 149.5 1.0
C A:ILE622 3.7 152.7 1.0
N A:GLY623 3.9 172.9 1.0
CG A:GLU1114 4.1 205.1 1.0
O A:TRP620 4.1 151.1 1.0
CA A:LEU621 4.2 151.8 1.0
N A:ILE622 4.2 155.5 1.0
CA A:GLY623 4.2 171.8 1.0
CA A:ILE622 4.3 152.2 1.0
N A:ASP624 4.3 188.2 1.0
CA A:ASP624 4.4 189.5 1.0
OG A:SER626 4.6 170.7 1.0
CD1 A:LEU621 4.9 153.1 1.0
C A:TRP620 5.0 152.0 1.0

Magnesium binding site 3 out of 16 in 8srg

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Magnesium binding site 3 out of 16 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:294.2
occ:1.00
 O A:GLY1370 2.1 322.0 1.0
OE2 A:GLU1390 2.1 283.8 1.0
O1X A:RP51501 2.1 348.6 1.0
OE1 A:GLU1390 2.5 286.2 1.0
CD A:GLU1390 2.6 284.4 1.0
P' A:RP51501 3.2 349.8 1.0
O5 A:RP51501 3.3 349.8 1.0
C A:GLY1370 3.3 321.4 1.0
N A:GLY1370 3.5 321.6 1.0
MG A:MG1506 3.6 255.6 1.0
CA A:GLY1370 4.0 321.8 1.0
CG A:GLU1390 4.1 283.6 1.0
NH1 A:ARG1360 4.2 272.1 1.0
O3X A:RP51501 4.2 349.6 1.0
O2X A:RP51501 4.3 350.2 1.0
N A:GLY1371 4.4 327.4 1.0
OD2 A:ASP1460 4.4 284.2 1.0
CD1 A:ILE1358 4.4 261.1 1.0
OD1 A:ASP1460 4.5 283.0 1.0
CA A:GLY1371 4.6 326.9 1.0
C5 A:RP51501 4.6 350.2 1.0
C A:PRO1369 4.6 305.7 1.0
CA A:PRO1369 4.8 304.6 1.0
CG A:ASP1460 4.8 283.5 1.0
CB A:GLU1390 5.0 284.9 1.0
O A:ILE1368 5.0 279.4 1.0

Magnesium binding site 4 out of 16 in 8srg

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Magnesium binding site 4 out of 16 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:255.6
occ:1.00
 O1X A:RP51501 2.4 348.6 1.0
OD2 A:ASP1460 2.7 284.2 1.0
OE2 A:GLU1390 2.8 283.8 1.0
C5' A:AMP1502 3.3 330.6 1.0
O3X A:RP51501 3.3 349.6 1.0
P' A:RP51501 3.4 349.8 1.0
CG A:ASP1460 3.6 283.5 1.0
MG A:MG1505 3.6 294.2 1.0
OD1 A:ASP1460 3.8 283.0 1.0
CD A:GLU1390 4.1 284.4 1.0
O A:GLY1370 4.1 322.0 1.0
C4' A:AMP1502 4.1 329.4 1.0
O2X A:RP51501 4.2 350.2 1.0
O4' A:AMP1502 4.2 328.9 1.0
O5' A:AMP1502 4.4 332.6 1.0
CA A:GLY1371 4.6 326.9 1.0
O1P A:AMP1502 4.6 330.7 1.0
O3P A:AMP1502 4.6 329.9 1.0
O5 A:RP51501 4.8 349.8 1.0
CG A:GLU1390 4.8 283.6 1.0
P A:AMP1502 4.9 332.9 1.0
OE1 A:GLU1390 5.0 286.2 1.0
CB A:ASP1460 5.0 283.3 1.0

Magnesium binding site 5 out of 16 in 8srg

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Magnesium binding site 5 out of 16 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
B:Mg1503

b:155.8
occ:1.00
 OD1 B:ASN869 2.3 180.9 1.0
OE1 B:GLN853 2.5 187.9 1.0
OE1 B:GLU850 2.8 202.8 1.0
OE2 B:GLU850 3.0 201.2 1.0
OD2 B:ASP872 3.1 210.6 1.0
CD B:GLU850 3.3 201.1 1.0
CD B:GLN853 3.6 187.6 1.0
CG B:ASN869 3.6 182.4 1.0
NE2 B:GLN853 4.0 188.3 1.0
CG B:ASP872 4.2 208.3 1.0
NH2 B:ARG913 4.2 143.2 1.0
OE2 B:GLU1062 4.3 173.9 1.0
ND2 B:ASN869 4.4 182.9 1.0
CA B:ASN869 4.5 185.6 1.0
CB B:ASN869 4.6 184.3 1.0
OD1 B:ASP872 4.6 208.9 1.0
CE1 B:TYR863 4.7 174.4 1.0
CG B:GLU850 4.8 201.0 1.0
N B:ASN869 4.8 187.7 1.0
CG B:GLN853 4.9 185.7 1.0

Magnesium binding site 6 out of 16 in 8srg

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Magnesium binding site 6 out of 16 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:Mg1504

b:196.3
occ:1.00
 O B:GLY623 2.1 176.0 1.0
OE1 B:GLU1114 2.2 206.0 1.0
O B:LEU621 2.3 155.7 1.0
OE2 B:GLU1114 2.7 210.6 1.0
CD B:GLU1114 2.7 207.5 1.0
C B:LEU621 3.3 153.9 1.0
C B:GLY623 3.3 174.0 1.0
O B:ILE622 3.5 149.5 1.0
C B:ILE622 3.7 152.7 1.0
N B:GLY623 3.9 172.9 1.0
CG B:GLU1114 4.1 205.1 1.0
O B:TRP620 4.1 151.1 1.0
CA B:LEU621 4.2 151.8 1.0
N B:ILE622 4.2 155.5 1.0
CA B:GLY623 4.2 171.8 1.0
CA B:ILE622 4.3 152.2 1.0
N B:ASP624 4.3 188.2 1.0
CA B:ASP624 4.4 189.5 1.0
OG B:SER626 4.6 170.7 1.0
CD1 B:LEU621 4.9 153.1 1.0
C B:TRP620 5.0 152.0 1.0

Magnesium binding site 7 out of 16 in 8srg

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Magnesium binding site 7 out of 16 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:Mg1505

b:294.2
occ:1.00
 O B:GLY1370 2.1 322.0 1.0
OE2 B:GLU1390 2.1 283.8 1.0
O1X B:RP51501 2.1 348.6 1.0
OE1 B:GLU1390 2.5 286.2 1.0
CD B:GLU1390 2.6 284.4 1.0
P' B:RP51501 3.2 349.8 1.0
O5 B:RP51501 3.3 349.8 1.0
C B:GLY1370 3.3 321.4 1.0
N B:GLY1370 3.5 321.6 1.0
MG B:MG1506 3.6 255.6 1.0
CA B:GLY1370 4.0 321.8 1.0
CG B:GLU1390 4.1 283.6 1.0
NH1 B:ARG1360 4.2 272.1 1.0
O3X B:RP51501 4.2 349.6 1.0
O2X B:RP51501 4.3 350.2 1.0
N B:GLY1371 4.4 327.4 1.0
OD2 B:ASP1460 4.4 284.2 1.0
CD1 B:ILE1358 4.4 261.1 1.0
OD1 B:ASP1460 4.5 283.0 1.0
CA B:GLY1371 4.6 326.9 1.0
C5 B:RP51501 4.6 350.2 1.0
C B:PRO1369 4.6 305.7 1.0
CA B:PRO1369 4.8 304.6 1.0
CG B:ASP1460 4.8 283.5 1.0
CB B:GLU1390 5.0 284.9 1.0
O B:ILE1368 5.0 279.4 1.0

Magnesium binding site 8 out of 16 in 8srg

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Magnesium binding site 8 out of 16 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:Mg1506

b:255.6
occ:1.00
 O1X B:RP51501 2.4 348.6 1.0
OD2 B:ASP1460 2.7 284.2 1.0
OE2 B:GLU1390 2.8 283.8 1.0
C5' B:AMP1502 3.3 330.6 1.0
O3X B:RP51501 3.3 349.6 1.0
P' B:RP51501 3.4 349.8 1.0
CG B:ASP1460 3.6 283.5 1.0
MG B:MG1505 3.6 294.2 1.0
OD1 B:ASP1460 3.8 283.0 1.0
CD B:GLU1390 4.1 284.4 1.0
O B:GLY1370 4.1 322.0 1.0
C4' B:AMP1502 4.1 329.4 1.0
O2X B:RP51501 4.2 350.2 1.0
O4' B:AMP1502 4.2 328.9 1.0
O5' B:AMP1502 4.4 332.6 1.0
CA B:GLY1371 4.6 326.9 1.0
O1P B:AMP1502 4.6 330.7 1.0
O3P B:AMP1502 4.6 329.9 1.0
O5 B:RP51501 4.8 349.8 1.0
CG B:GLU1390 4.8 283.6 1.0
P B:AMP1502 4.9 332.9 1.0
OE1 B:GLU1390 5.0 286.2 1.0
CB B:ASP1460 5.0 283.3 1.0

Magnesium binding site 9 out of 16 in 8srg

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Magnesium binding site 9 out of 16 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
C:Mg1503

b:155.8
occ:1.00
 OD1 C:ASN869 2.3 180.9 1.0
OE1 C:GLN853 2.5 187.9 1.0
OE1 C:GLU850 2.8 202.8 1.0
OE2 C:GLU850 3.0 201.2 1.0
OD2 C:ASP872 3.1 210.6 1.0
CD C:GLU850 3.3 201.1 1.0
CD C:GLN853 3.6 187.6 1.0
CG C:ASN869 3.6 182.4 1.0
NE2 C:GLN853 4.0 188.3 1.0
CG C:ASP872 4.2 208.3 1.0
NH2 C:ARG913 4.2 143.2 1.0
OE2 C:GLU1062 4.3 173.9 1.0
ND2 C:ASN869 4.4 182.9 1.0
CA C:ASN869 4.5 185.6 1.0
CB C:ASN869 4.6 184.3 1.0
OD1 C:ASP872 4.6 208.9 1.0
CE1 C:TYR863 4.7 174.4 1.0
CG C:GLU850 4.8 201.0 1.0
N C:ASN869 4.8 187.7 1.0
CG C:GLN853 4.9 185.7 1.0

Magnesium binding site 10 out of 16 in 8srg

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Magnesium binding site 10 out of 16 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:Mg1504

b:196.3
occ:1.00
 O C:GLY623 2.1 176.0 1.0
OE1 C:GLU1114 2.2 206.0 1.0
O C:LEU621 2.3 155.7 1.0
OE2 C:GLU1114 2.7 210.6 1.0
CD C:GLU1114 2.7 207.5 1.0
C C:LEU621 3.3 153.9 1.0
C C:GLY623 3.3 174.0 1.0
O C:ILE622 3.5 149.5 1.0
C C:ILE622 3.7 152.7 1.0
N C:GLY623 3.9 172.9 1.0
CG C:GLU1114 4.1 205.1 1.0
O C:TRP620 4.1 151.1 1.0
CA C:LEU621 4.2 151.8 1.0
N C:ILE622 4.2 155.5 1.0
CA C:GLY623 4.2 171.8 1.0
CA C:ILE622 4.3 152.2 1.0
N C:ASP624 4.3 188.2 1.0
CA C:ASP624 4.4 189.5 1.0
OG C:SER626 4.6 170.7 1.0
CD1 C:LEU621 4.9 153.1 1.0
C C:TRP620 5.0 152.0 1.0

Reference:

Y.Huang, W.Lu, J.Du. Coupling Enzymatic Activity and Gating in An Ancient Trpm Chanzyme and Its Molecular Evolution To Be Published.
Page generated: Fri Oct 4 20:00:53 2024

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