Magnesium in PDB 8srd: Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium and Adp-Ribose, Open State

Magnesium Binding Sites:

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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 and Adp-Ribose, Open State (pdb code 8srd). 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 and Adp-Ribose, Open State, PDB code: 8srd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 21 in 8srd

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Magnesium binding site 1 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium and Adp-Ribose, Open 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 and Adp-Ribose, Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1702

b:78.5
occ:1.00
 OD1 A:ASN869 2.5 105.9 1.0
OE1 A:GLN853 2.5 123.2 1.0
OD2 A:ASP872 2.6 119.0 1.0
OE2 A:GLU850 3.0 124.3 1.0
OE1 A:GLU850 3.2 124.6 1.0
CD A:GLN853 3.5 119.8 1.0
CD A:GLU850 3.5 123.5 1.0
NE2 A:GLN853 3.7 118.8 1.0
CG A:ASN869 3.8 110.7 1.0
CG A:ASP872 3.8 120.2 1.0
OD1 A:ASP872 4.3 127.2 1.0
NH2 A:ARG913 4.5 97.8 1.0
CA A:ASN869 4.5 108.7 1.0
ND2 A:ASN869 4.6 115.1 1.0
CB A:ASN869 4.7 111.4 1.0
CE1 A:TYR863 4.8 120.5 1.0
CB A:ASP872 4.9 108.9 1.0
N A:ASN869 4.9 109.1 1.0
CG A:GLN853 4.9 116.2 1.0
O A:TRP868 5.0 107.7 1.0
CG A:GLU850 5.0 120.7 1.0

Magnesium binding site 2 out of 21 in 8srd

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Magnesium binding site 2 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium and Adp-Ribose, Open 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 and Adp-Ribose, Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1703

b:134.2
occ:1.00
 OE1 A:GLU1114 2.3 129.8 1.0
OE2 A:GLU1114 2.5 129.6 1.0
CD A:GLU1114 2.7 130.9 1.0
O A:GLY623 2.8 121.4 1.0
O A:LEU621 3.3 107.9 1.0
C A:GLY623 4.0 119.3 1.0
CG A:GLU1114 4.2 125.5 1.0
C A:LEU621 4.2 103.6 1.0
CG2 A:THR1117 4.4 94.5 1.0
O A:TRP620 4.5 93.1 1.0
CA A:ASP624 4.5 126.9 1.0
CA A:LEU621 4.7 100.2 1.0
N A:ASP624 4.7 125.7 1.0
CB A:GLU1114 4.8 119.7 1.0
CB A:THR1117 4.8 96.9 1.0
O A:ILE622 4.8 115.1 1.0
CB A:SER626 4.8 100.0 1.0
CA A:GLU1114 4.9 119.1 1.0
OG1 A:THR1117 5.0 103.4 1.0

Magnesium binding site 3 out of 21 in 8srd

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Magnesium binding site 3 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium and Adp-Ribose, Open 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 and Adp-Ribose, Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1704

b:86.1
occ:1.00
 O2B A:APR1708 2.1 105.5 1.0
OE2 A:GLU1390 2.7 94.9 1.0
O A:GLY1370 2.8 76.8 1.0
OE1 A:GLU1390 2.9 99.7 1.0
CD A:GLU1390 3.1 94.3 1.0
PB A:APR1708 3.4 108.7 1.0
NH1 A:ARG1360 3.7 93.0 1.0
O5D A:APR1708 3.7 101.8 1.0
O1A A:APR1708 3.8 102.3 1.0
CD1 A:ILE1358 3.9 80.7 1.0
C A:GLY1370 4.0 75.1 1.0
N A:GLY1370 4.0 77.2 1.0
O3A A:APR1708 4.4 110.2 1.0
O1B A:APR1708 4.5 93.0 1.0
O3D A:APR1708 4.5 105.0 1.0
OD2 A:ASP1460 4.5 115.3 1.0
CG A:GLU1390 4.5 88.8 1.0
CA A:GLY1370 4.6 77.7 1.0
PA A:APR1708 4.7 109.3 1.0
O A:ILE1368 4.8 86.2 1.0
CZ A:ARG1360 4.8 93.7 1.0
CA A:PRO1369 4.9 59.9 1.0
C A:PRO1369 4.9 71.7 1.0
C5D A:APR1708 4.9 96.9 1.0
O A:ASP1460 4.9 109.2 1.0
C4D A:APR1708 4.9 99.9 1.0

Magnesium binding site 4 out of 21 in 8srd

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Magnesium binding site 4 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium and Adp-Ribose, Open 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 and Adp-Ribose, Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1705

b:67.3
occ:1.00
 OE1 A:GLU1386 2.5 100.7 1.0
MG A:MG1706 2.8 69.9 1.0
OE2 A:GLU1386 3.0 102.1 1.0
O1A A:APR1708 3.0 102.3 1.0
OD2 A:ASP1459 3.1 120.3 1.0
CD A:GLU1386 3.1 103.4 1.0
O2A A:APR1708 3.2 95.3 1.0
OE1 A:GLU1389 3.4 107.0 1.0
PA A:APR1708 3.5 109.3 1.0
O5' A:APR1708 4.0 103.2 1.0
CG A:ASP1459 4.0 114.7 1.0
OE2 A:GLU1390 4.3 94.9 1.0
OD1 A:ASP1459 4.4 111.8 1.0
CG A:GLU1386 4.6 97.8 1.0
CD A:GLU1389 4.6 108.9 1.0
NH1 A:ARG1385 4.8 97.9 1.0

Magnesium binding site 5 out of 21 in 8srd

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Magnesium binding site 5 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium and Adp-Ribose, Open 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 and Adp-Ribose, Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1706

b:69.9
occ:1.00
 OE2 A:GLU1386 2.4 102.1 1.0
MG A:MG1705 2.8 67.3 1.0
O2A A:APR1708 2.8 95.3 1.0
CD A:GLU1386 3.4 103.4 1.0
NH1 A:ARG1385 3.5 97.9 1.0
OE1 A:GLU1386 3.8 100.7 1.0
PA A:APR1708 4.1 109.3 1.0
O A:PHE1372 4.4 85.0 1.0
NH2 A:ARG1385 4.4 101.6 1.0
OD1 A:ASP1374 4.4 120.0 1.0
CZ A:ARG1385 4.5 100.3 1.0
O1A A:APR1708 4.5 102.3 1.0
O4' A:APR1708 4.5 101.1 1.0
CG A:GLU1386 4.6 97.8 1.0
OD2 A:ASP1374 4.6 121.0 1.0
OE1 A:GLU1389 4.7 107.0 1.0
CG A:ASP1374 4.9 120.7 1.0
O5' A:APR1708 4.9 103.2 1.0

Magnesium binding site 6 out of 21 in 8srd

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Magnesium binding site 6 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium and Adp-Ribose, Open 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 and Adp-Ribose, Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1711

b:90.8
occ:1.00
 O C:HOH4003 2.2 79.7 1.0
O C:HOH4002 2.9 96.6 1.0
O A:HOH4002 2.9 96.6 1.0
O B:HOH4002 2.9 96.6 1.0
O D:HOH6102 2.9 96.6 1.0
O B:GLY984 4.2 103.0 1.0
O D:GLY984 4.2 103.0 1.0
O C:GLY984 4.2 103.0 1.0
O A:GLY984 4.2 103.0 1.0
C D:GLY984 4.4 95.6 1.0
C C:GLY984 4.4 95.6 1.0
C B:GLY984 4.4 95.6 1.0
C A:GLY984 4.4 95.6 1.0
CA C:GLY984 4.4 89.8 1.0
CA D:GLY984 4.4 89.8 1.0
CA B:GLY984 4.4 89.8 1.0
CA A:GLY984 4.5 89.8 1.0
O C:TYR983 4.6 89.2 1.0
O B:TYR983 4.6 89.2 1.0
O D:TYR983 4.6 89.2 1.0
O A:TYR983 4.6 89.2 1.0

Magnesium binding site 7 out of 21 in 8srd

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Magnesium binding site 7 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium and Adp-Ribose, Open 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 and Adp-Ribose, Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1702

b:78.5
occ:1.00
 OD1 B:ASN869 2.5 105.9 1.0
OE1 B:GLN853 2.5 123.2 1.0
OD2 B:ASP872 2.6 119.0 1.0
OE2 B:GLU850 3.0 124.3 1.0
OE1 B:GLU850 3.2 124.6 1.0
CD B:GLN853 3.5 119.8 1.0
CD B:GLU850 3.5 123.5 1.0
NE2 B:GLN853 3.7 118.8 1.0
CG B:ASN869 3.8 110.7 1.0
CG B:ASP872 3.8 120.2 1.0
OD1 B:ASP872 4.3 127.2 1.0
NH2 B:ARG913 4.5 97.8 1.0
CA B:ASN869 4.5 108.7 1.0
ND2 B:ASN869 4.6 115.1 1.0
CB B:ASN869 4.7 111.4 1.0
CE1 B:TYR863 4.8 120.5 1.0
CB B:ASP872 4.9 108.9 1.0
N B:ASN869 4.9 109.1 1.0
CG B:GLN853 4.9 116.2 1.0
O B:TRP868 5.0 107.7 1.0
CG B:GLU850 5.0 120.7 1.0

Magnesium binding site 8 out of 21 in 8srd

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Magnesium binding site 8 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium and Adp-Ribose, Open 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 and Adp-Ribose, Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1703

b:134.2
occ:1.00
 OE1 B:GLU1114 2.3 129.8 1.0
OE2 B:GLU1114 2.5 129.6 1.0
CD B:GLU1114 2.7 130.9 1.0
O B:GLY623 2.8 121.4 1.0
O B:LEU621 3.3 107.9 1.0
C B:GLY623 4.0 119.3 1.0
CG B:GLU1114 4.2 125.5 1.0
C B:LEU621 4.2 103.6 1.0
CG2 B:THR1117 4.4 94.5 1.0
O B:TRP620 4.5 93.1 1.0
CA B:ASP624 4.5 126.9 1.0
CA B:LEU621 4.7 100.2 1.0
N B:ASP624 4.7 125.7 1.0
CB B:GLU1114 4.8 119.7 1.0
CB B:THR1117 4.8 96.9 1.0
O B:ILE622 4.8 115.1 1.0
CB B:SER626 4.8 100.0 1.0
CA B:GLU1114 4.9 119.1 1.0
OG1 B:THR1117 5.0 103.4 1.0

Magnesium binding site 9 out of 21 in 8srd

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Magnesium binding site 9 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium and Adp-Ribose, Open 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 and Adp-Ribose, Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1704

b:86.1
occ:1.00
 O2B B:APR1708 2.1 105.5 1.0
OE2 B:GLU1390 2.7 94.9 1.0
O B:GLY1370 2.8 76.8 1.0
OE1 B:GLU1390 2.9 99.7 1.0
CD B:GLU1390 3.1 94.3 1.0
PB B:APR1708 3.4 108.7 1.0
NH1 B:ARG1360 3.7 93.0 1.0
O5D B:APR1708 3.7 101.8 1.0
O1A B:APR1708 3.8 102.3 1.0
CD1 B:ILE1358 3.9 80.7 1.0
C B:GLY1370 4.0 75.1 1.0
N B:GLY1370 4.0 77.2 1.0
O3A B:APR1708 4.4 110.2 1.0
O1B B:APR1708 4.5 93.0 1.0
O3D B:APR1708 4.5 105.0 1.0
OD2 B:ASP1460 4.5 115.3 1.0
CG B:GLU1390 4.5 88.8 1.0
CA B:GLY1370 4.6 77.7 1.0
PA B:APR1708 4.7 109.3 1.0
O B:ILE1368 4.8 86.2 1.0
CZ B:ARG1360 4.8 93.7 1.0
CA B:PRO1369 4.9 59.9 1.0
C B:PRO1369 4.9 71.7 1.0
C5D B:APR1708 4.9 96.9 1.0
O B:ASP1460 4.9 109.2 1.0
C4D B:APR1708 4.9 99.9 1.0

Magnesium binding site 10 out of 21 in 8srd

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Magnesium binding site 10 out of 21 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium and Adp-Ribose, Open 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 and Adp-Ribose, Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1705

b:67.3
occ:1.00
 OE1 B:GLU1386 2.5 100.7 1.0
MG B:MG1706 2.8 69.9 1.0
OE2 B:GLU1386 3.0 102.1 1.0
O1A B:APR1708 3.0 102.3 1.0
OD2 B:ASP1459 3.1 120.3 1.0
CD B:GLU1386 3.1 103.4 1.0
O2A B:APR1708 3.2 95.3 1.0
OE1 B:GLU1389 3.4 107.0 1.0
PA B:APR1708 3.5 109.3 1.0
O5' B:APR1708 4.0 103.2 1.0
CG B:ASP1459 4.0 114.7 1.0
OE2 B:GLU1390 4.3 94.9 1.0
OD1 B:ASP1459 4.4 111.8 1.0
CG B:GLU1386 4.6 97.8 1.0
CD B:GLU1389 4.6 108.9 1.0
NH1 B:ARG1385 4.8 97.9 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 20:00:14 2024

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