Magnesium in PDB 8sre: Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium and Adp-Ribose, Closed 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, Closed State (pdb code 8sre). 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, Closed State, PDB code: 8sre:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 21 in 8sre

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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, 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 and Adp-Ribose, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1702

b:85.0
occ:1.00
 OD2 A:ASP872 2.7 107.2 1.0
OD1 A:ASN869 2.7 108.2 1.0
OE2 A:GLU850 2.8 114.3 1.0
OE1 A:GLN853 2.8 121.3 1.0
OE1 A:GLU850 3.1 113.9 1.0
CD A:GLU850 3.3 115.9 1.0
CD A:GLN853 3.6 123.7 1.0
NE2 A:GLN853 3.6 126.2 1.0
NH2 A:ARG913 3.7 96.9 1.0
CG A:ASP872 3.8 102.6 1.0
CG A:ASN869 3.9 107.7 1.0
OE2 A:GLU1062 4.4 115.1 1.0
CA A:ASN869 4.5 105.5 1.0
CB A:ASP872 4.5 96.8 1.0
OD1 A:ASP872 4.7 102.5 1.0
CB A:ASN869 4.8 107.8 1.0
CG A:GLU850 4.8 116.1 1.0
N A:ASN869 4.9 106.5 1.0
ND2 A:ASN869 4.9 111.5 1.0
CZ A:ARG913 4.9 92.3 1.0
O A:TRP868 4.9 105.6 1.0
NH1 A:ARG916 4.9 107.0 1.0

Magnesium binding site 2 out of 21 in 8sre

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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, 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 and Adp-Ribose, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1703

b:125.9
occ:1.00
 OE1 A:GLU1114 2.2 135.7 1.0
OE2 A:GLU1114 2.2 136.0 1.0
O A:GLY623 2.2 118.9 1.0
CD A:GLU1114 2.4 137.4 1.0
O A:LEU621 2.6 112.6 1.0
C A:GLY623 3.4 114.6 1.0
C A:LEU621 3.6 107.9 1.0
OG A:SER626 3.9 110.0 1.0
CG A:GLU1114 4.0 134.7 1.0
O A:ILE622 4.0 115.2 1.0
C A:ILE622 4.0 111.6 1.0
O A:TRP620 4.2 103.3 1.0
N A:GLY623 4.2 111.5 1.0
CA A:ASP624 4.3 135.2 1.0
N A:ASP624 4.3 133.1 1.0
CA A:LEU621 4.3 103.0 1.0
CA A:GLY623 4.4 111.3 1.0
N A:ILE622 4.5 110.0 1.0
CA A:ILE622 4.6 112.0 1.0
CB A:GLU1114 4.8 129.8 1.0
CG2 A:THR1117 4.8 118.0 1.0
CA A:GLU1114 4.9 128.9 1.0

Magnesium binding site 3 out of 21 in 8sre

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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, 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 and Adp-Ribose, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1704

b:87.9
occ:1.00
 OE2 A:GLU1390 2.0 87.8 1.0
O A:GLY1370 2.1 88.8 1.0
O A:HOH3203 2.2 99.9 1.0
O1A A:APR1708 2.2 84.6 1.0
O2B A:APR1708 2.2 88.3 1.0
O A:HOH3201 2.4 76.2 1.0
CD A:GLU1390 2.7 88.7 1.0
OE1 A:GLU1390 2.7 92.4 1.0
C A:GLY1370 3.3 74.3 1.0
PB A:APR1708 3.5 85.4 1.0
MG A:MG1705 3.5 66.6 1.0
PA A:APR1708 3.5 101.5 1.0
O3A A:APR1708 3.8 90.2 1.0
N A:GLY1370 3.9 76.8 1.0
CG A:GLU1390 4.1 86.0 1.0
N A:GLY1371 4.2 69.4 1.0
CA A:GLY1370 4.2 66.3 1.0
CA A:GLY1371 4.3 70.8 1.0
O1B A:APR1708 4.3 85.5 1.0
O5' A:APR1708 4.3 94.6 1.0
NH1 A:ARG1360 4.4 78.5 1.0
OE1 A:GLU1386 4.5 100.2 1.0
CD1 A:ILE1358 4.5 69.7 1.0
OD2 A:ASP1460 4.6 108.2 1.0
O2A A:APR1708 4.7 85.6 1.0
O5D A:APR1708 4.7 83.4 1.0
C5D A:APR1708 4.9 83.3 1.0

Magnesium binding site 4 out of 21 in 8sre

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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, 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 and Adp-Ribose, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1705

b:66.6
occ:1.00
 OE1 A:GLU1386 1.9 100.2 1.0
OE2 A:GLU1390 2.2 87.8 1.0
O1A A:APR1708 2.4 84.6 1.0
MG A:MG1706 2.9 76.6 1.0
CD A:GLU1386 2.9 99.7 1.0
CD A:GLU1390 3.0 88.7 1.0
PA A:APR1708 3.4 101.5 1.0
CG A:GLU1390 3.5 86.0 1.0
MG A:MG1704 3.5 87.9 1.0
OE2 A:GLU1386 3.5 103.3 1.0
O A:HOH3201 3.6 76.2 1.0
O2A A:APR1708 3.6 85.6 1.0
OE1 A:GLU1390 3.9 92.4 1.0
OD2 A:ASP1459 4.0 106.8 1.0
O A:GLY1370 4.0 88.8 1.0
O5' A:APR1708 4.1 94.6 1.0
CG A:GLU1386 4.2 87.4 1.0
OE1 A:GLU1389 4.3 104.1 1.0
CB A:GLU1386 4.6 82.0 1.0
CG A:ASP1459 4.6 105.6 1.0
CA A:GLY1371 4.7 70.8 1.0
C A:GLY1370 4.7 74.3 1.0
O3A A:APR1708 4.8 90.2 1.0
CA A:GLU1386 4.9 84.2 1.0
CB A:GLU1390 4.9 75.2 1.0
CB A:ASP1460 4.9 93.5 1.0
O A:GLU1386 5.0 99.6 1.0

Magnesium binding site 5 out of 21 in 8sre

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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, 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 and Adp-Ribose, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1706

b:76.6
occ:1.00
 O2A A:APR1708 2.1 85.6 1.0
OE2 A:GLU1386 2.2 103.3 1.0
MG A:MG1705 2.9 66.6 1.0
OE1 A:GLU1386 2.9 100.2 1.0
CD A:GLU1386 2.9 99.7 1.0
PA A:APR1708 3.1 101.5 1.0
O1A A:APR1708 3.4 84.6 1.0
O5' A:APR1708 3.7 94.6 1.0
O4' A:APR1708 4.0 86.2 1.0
CG A:GLU1386 4.3 87.4 1.0
CA A:GLY1371 4.4 70.8 1.0
O3A A:APR1708 4.5 90.2 1.0
OE1 A:GLU1389 4.6 104.1 1.0
C5' A:APR1708 4.7 86.0 1.0
N A:PHE1372 4.7 64.5 1.0
C4' A:APR1708 4.7 87.7 1.0
OE2 A:GLU1390 4.9 87.8 1.0
C A:GLY1371 5.0 73.2 1.0
O A:PHE1372 5.0 71.8 1.0

Magnesium binding site 6 out of 21 in 8sre

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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, 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 and Adp-Ribose, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1711

b:59.0
occ:1.00
 O D:GLY984 4.0 86.9 1.0
O B:GLY984 4.0 86.9 1.0
O C:GLY984 4.0 86.9 1.0
O A:GLY984 4.0 86.9 1.0
CA B:GLY984 4.0 76.7 1.0
CA D:GLY984 4.0 76.7 1.0
CA C:GLY984 4.0 76.7 1.0
CA A:GLY984 4.1 76.7 1.0
C B:GLY984 4.2 77.6 1.0
C D:GLY984 4.2 77.6 1.0
C C:GLY984 4.2 77.6 1.0
C A:GLY984 4.2 77.6 1.0
O A:TYR983 4.2 80.6 1.0
O B:TYR983 4.3 80.6 1.0
O C:TYR983 4.3 80.6 1.0
O D:TYR983 4.3 80.6 1.0

Magnesium binding site 7 out of 21 in 8sre

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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, 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 and Adp-Ribose, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg6004

b:85.0
occ:1.00
 OD2 D:ASP872 2.7 107.2 1.0
OD1 D:ASN869 2.7 108.2 1.0
OE2 D:GLU850 2.8 114.3 1.0
OE1 D:GLN853 2.8 121.3 1.0
OE1 D:GLU850 3.1 113.9 1.0
CD D:GLU850 3.3 115.9 1.0
CD D:GLN853 3.6 123.7 1.0
NE2 D:GLN853 3.6 126.2 1.0
NH2 D:ARG913 3.7 96.9 1.0
CG D:ASP872 3.8 102.6 1.0
CG D:ASN869 3.9 107.7 1.0
OE2 D:GLU1062 4.4 115.1 1.0
CA D:ASN869 4.5 105.5 1.0
CB D:ASP872 4.5 96.8 1.0
OD1 D:ASP872 4.7 102.5 1.0
CB D:ASN869 4.8 107.8 1.0
CG D:GLU850 4.8 116.1 1.0
N D:ASN869 4.9 106.5 1.0
ND2 D:ASN869 4.9 111.5 1.0
CZ D:ARG913 4.9 92.3 1.0
O D:TRP868 4.9 105.6 1.0
NH1 D:ARG916 4.9 107.0 1.0

Magnesium binding site 8 out of 21 in 8sre

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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, 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 and Adp-Ribose, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg6005

b:125.9
occ:1.00
 OE1 D:GLU1114 2.2 135.7 1.0
OE2 D:GLU1114 2.2 136.0 1.0
O D:GLY623 2.2 118.9 1.0
CD D:GLU1114 2.5 137.4 1.0
O D:LEU621 2.6 112.6 1.0
C D:GLY623 3.4 114.6 1.0
C D:LEU621 3.6 107.9 1.0
OG D:SER626 3.9 110.0 1.0
CG D:GLU1114 4.0 134.7 1.0
O D:ILE622 4.0 115.2 1.0
C D:ILE622 4.0 111.6 1.0
O D:TRP620 4.2 103.3 1.0
N D:GLY623 4.2 111.5 1.0
CA D:ASP624 4.3 135.2 1.0
N D:ASP624 4.3 133.1 1.0
CA D:LEU621 4.3 103.0 1.0
CA D:GLY623 4.4 111.3 1.0
N D:ILE622 4.5 110.0 1.0
CA D:ILE622 4.6 112.0 1.0
CB D:GLU1114 4.8 129.8 1.0
CG2 D:THR1117 4.8 118.0 1.0
CA D:GLU1114 4.9 128.9 1.0

Magnesium binding site 9 out of 21 in 8sre

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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, 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 and Adp-Ribose, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg6006

b:87.9
occ:1.00
 OE2 D:GLU1390 2.0 87.8 1.0
O D:GLY1370 2.1 88.8 1.0
O D:HOH6103 2.2 99.9 1.0
O1A D:APR6010 2.2 84.6 1.0
O2B D:APR6010 2.2 88.3 1.0
O D:HOH6101 2.4 76.2 1.0
CD D:GLU1390 2.7 88.7 1.0
OE1 D:GLU1390 2.7 92.4 1.0
C D:GLY1370 3.3 74.3 1.0
PB D:APR6010 3.5 85.4 1.0
MG D:MG6007 3.5 66.6 1.0
PA D:APR6010 3.5 101.5 1.0
O3A D:APR6010 3.8 90.2 1.0
N D:GLY1370 3.9 76.8 1.0
CG D:GLU1390 4.1 86.0 1.0
N D:GLY1371 4.2 69.4 1.0
CA D:GLY1370 4.2 66.3 1.0
CA D:GLY1371 4.3 70.8 1.0
O1B D:APR6010 4.3 85.5 1.0
O5' D:APR6010 4.3 94.6 1.0
NH1 D:ARG1360 4.4 78.5 1.0
OE1 D:GLU1386 4.5 100.2 1.0
CD1 D:ILE1358 4.5 69.7 1.0
OD2 D:ASP1460 4.6 108.2 1.0
O2A D:APR6010 4.7 85.6 1.0
O5D D:APR6010 4.7 83.4 1.0
C5D D:APR6010 4.9 83.3 1.0

Magnesium binding site 10 out of 21 in 8sre

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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, 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 and Adp-Ribose, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg6007

b:66.6
occ:1.00
 OE1 D:GLU1386 1.9 100.2 1.0
OE2 D:GLU1390 2.2 87.8 1.0
O1A D:APR6010 2.4 84.6 1.0
MG D:MG6008 2.9 76.6 1.0
CD D:GLU1386 2.9 99.7 1.0
CD D:GLU1390 3.0 88.7 1.0
PA D:APR6010 3.4 101.5 1.0
CG D:GLU1390 3.5 86.0 1.0
MG D:MG6006 3.5 87.9 1.0
OE2 D:GLU1386 3.5 103.3 1.0
O D:HOH6101 3.6 76.2 1.0
O2A D:APR6010 3.6 85.6 1.0
OE1 D:GLU1390 3.9 92.4 1.0
OD2 D:ASP1459 4.0 106.8 1.0
O D:GLY1370 4.0 88.8 1.0
O5' D:APR6010 4.1 94.6 1.0
CG D:GLU1386 4.2 87.4 1.0
OE1 D:GLU1389 4.3 104.1 1.0
CB D:GLU1386 4.6 82.0 1.0
CG D:ASP1459 4.6 105.6 1.0
CA D:GLY1371 4.7 70.8 1.0
C D:GLY1370 4.7 74.3 1.0
O3A D:APR6010 4.8 90.2 1.0
CA D:GLU1386 4.9 84.2 1.0
CB D:GLU1390 4.9 75.2 1.0
CB D:ASP1460 4.9 93.5 1.0
O D:GLU1386 5.0 99.6 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 20:00:44 2024

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