Magnesium in PDB 8sr9: Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium (pdb code 8sr9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium, PDB code: 8sr9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8sr9

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Magnesium binding site 1 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:112.9
occ:1.00
 OD1 A:ASN869 2.7 135.2 1.0
OE1 A:GLN853 3.0 138.8 1.0
OD2 A:ASP872 3.5 138.2 1.0
OE2 A:GLU850 3.5 125.1 1.0
OE1 A:GLU850 3.7 128.5 1.0
CG A:ASN869 3.9 133.4 1.0
CD A:GLN853 3.9 138.4 1.0
CD A:GLU850 4.0 126.2 1.0
NE2 A:GLN853 4.2 138.2 1.0
NH2 A:ARG916 4.6 120.5 1.0
CG A:ASP872 4.6 136.0 1.0
ND2 A:ASN869 4.6 132.5 1.0
CA A:ASN869 4.9 127.5 1.0
NH2 A:ARG913 4.9 104.3 1.0
CB A:ASN869 5.0 129.5 1.0

Magnesium binding site 2 out of 8 in 8sr9

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Magnesium binding site 2 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:125.1
occ:1.00
 O A:LEU621 1.9 100.8 1.0
O A:TRP620 2.2 105.7 1.0
C A:LEU621 2.4 98.9 1.0
CA A:LEU621 2.5 96.5 1.0
O A:GLY623 2.7 123.7 1.0
C A:TRP620 3.1 99.2 1.0
N A:LEU621 3.2 96.6 1.0
N A:ILE622 3.5 97.5 1.0
C A:GLY623 3.7 120.2 1.0
OG A:SER626 3.7 110.6 1.0
CD1 A:LEU621 3.7 105.1 1.0
N A:GLY623 3.8 117.5 1.0
CB A:LEU621 3.9 100.1 1.0
C A:ILE622 4.0 100.3 1.0
OE1 A:GLU1114 4.1 131.7 1.0
CG A:LEU621 4.2 107.0 1.0
CA A:ILE622 4.3 96.8 1.0
CA A:GLY623 4.3 117.6 1.0
O A:ILE622 4.4 100.6 1.0
OE2 A:GLU1114 4.4 129.3 1.0
CA A:TRP620 4.5 98.2 1.0
N A:ASP624 4.7 132.0 1.0
CD A:GLU1114 4.7 133.0 1.0
CB A:SER626 4.8 105.6 1.0
CA A:ASP624 4.9 132.8 1.0
CD2 A:TRP620 5.0 100.5 1.0

Magnesium binding site 3 out of 8 in 8sr9

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Magnesium binding site 3 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:112.9
occ:1.00
 OD1 B:ASN869 2.7 135.2 1.0
OE1 B:GLN853 3.0 138.8 1.0
OD2 B:ASP872 3.5 138.2 1.0
OE2 B:GLU850 3.5 125.1 1.0
OE1 B:GLU850 3.7 128.5 1.0
CG B:ASN869 3.9 133.4 1.0
CD B:GLN853 3.9 138.4 1.0
CD B:GLU850 4.0 126.2 1.0
NE2 B:GLN853 4.2 138.2 1.0
NH2 B:ARG916 4.6 120.5 1.0
CG B:ASP872 4.6 136.0 1.0
ND2 B:ASN869 4.6 132.5 1.0
CA B:ASN869 4.9 127.5 1.0
NH2 B:ARG913 4.9 104.3 1.0
CB B:ASN869 5.0 129.5 1.0

Magnesium binding site 4 out of 8 in 8sr9

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Magnesium binding site 4 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:125.1
occ:1.00
 O B:LEU621 1.9 100.8 1.0
O B:TRP620 2.2 105.7 1.0
C B:LEU621 2.4 98.9 1.0
CA B:LEU621 2.5 96.5 1.0
O B:GLY623 2.7 123.7 1.0
C B:TRP620 3.1 99.2 1.0
N B:LEU621 3.2 96.6 1.0
N B:ILE622 3.5 97.5 1.0
C B:GLY623 3.7 120.2 1.0
OG B:SER626 3.7 110.6 1.0
CD1 B:LEU621 3.7 105.1 1.0
N B:GLY623 3.8 117.5 1.0
CB B:LEU621 3.9 100.1 1.0
C B:ILE622 4.0 100.3 1.0
OE1 B:GLU1114 4.1 131.7 1.0
CG B:LEU621 4.2 107.0 1.0
CA B:ILE622 4.3 96.8 1.0
CA B:GLY623 4.3 117.6 1.0
O B:ILE622 4.4 100.6 1.0
OE2 B:GLU1114 4.4 129.3 1.0
CA B:TRP620 4.5 98.2 1.0
N B:ASP624 4.7 132.0 1.0
CD B:GLU1114 4.7 133.0 1.0
CB B:SER626 4.8 105.6 1.0
CA B:ASP624 4.9 132.8 1.0
CD2 B:TRP620 5.0 100.5 1.0

Magnesium binding site 5 out of 8 in 8sr9

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Magnesium binding site 5 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:112.9
occ:1.00
 OD1 C:ASN869 2.7 135.2 1.0
OE1 C:GLN853 3.0 138.8 1.0
OD2 C:ASP872 3.5 138.2 1.0
OE2 C:GLU850 3.5 125.1 1.0
OE1 C:GLU850 3.7 128.5 1.0
CG C:ASN869 3.9 133.4 1.0
CD C:GLN853 3.9 138.4 1.0
CD C:GLU850 4.0 126.2 1.0
NE2 C:GLN853 4.2 138.2 1.0
NH2 C:ARG916 4.6 120.5 1.0
CG C:ASP872 4.6 136.0 1.0
ND2 C:ASN869 4.6 132.5 1.0
CA C:ASN869 4.9 127.5 1.0
NH2 C:ARG913 4.9 104.3 1.0
CB C:ASN869 5.0 129.5 1.0

Magnesium binding site 6 out of 8 in 8sr9

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Magnesium binding site 6 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:125.1
occ:1.00
 O C:LEU621 1.9 100.8 1.0
O C:TRP620 2.2 105.7 1.0
C C:LEU621 2.4 98.9 1.0
CA C:LEU621 2.5 96.5 1.0
O C:GLY623 2.7 123.7 1.0
C C:TRP620 3.1 99.2 1.0
N C:LEU621 3.2 96.6 1.0
N C:ILE622 3.5 97.5 1.0
C C:GLY623 3.7 120.2 1.0
OG C:SER626 3.7 110.6 1.0
CD1 C:LEU621 3.7 105.1 1.0
N C:GLY623 3.8 117.5 1.0
CB C:LEU621 3.9 100.1 1.0
C C:ILE622 4.0 100.3 1.0
OE1 C:GLU1114 4.1 131.7 1.0
CG C:LEU621 4.2 107.0 1.0
CA C:ILE622 4.3 96.8 1.0
CA C:GLY623 4.3 117.6 1.0
O C:ILE622 4.4 100.6 1.0
OE2 C:GLU1114 4.4 129.3 1.0
CA C:TRP620 4.5 98.2 1.0
N C:ASP624 4.7 132.0 1.0
CD C:GLU1114 4.7 133.0 1.0
CB C:SER626 4.8 105.6 1.0
CA C:ASP624 4.9 132.8 1.0
CD2 C:TRP620 5.0 100.5 1.0

Magnesium binding site 7 out of 8 in 8sr9

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Magnesium binding site 7 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg6003

b:112.9
occ:1.00
 OD1 D:ASN869 2.7 135.2 1.0
OE1 D:GLN853 3.0 138.8 1.0
OD2 D:ASP872 3.5 138.2 1.0
OE2 D:GLU850 3.5 125.1 1.0
OE1 D:GLU850 3.7 128.5 1.0
CG D:ASN869 3.9 133.4 1.0
CD D:GLN853 3.9 138.4 1.0
CD D:GLU850 4.0 126.2 1.0
NE2 D:GLN853 4.2 138.2 1.0
NH2 D:ARG916 4.6 120.5 1.0
CG D:ASP872 4.6 136.0 1.0
ND2 D:ASN869 4.6 132.5 1.0
CA D:ASN869 4.9 127.5 1.0
NH2 D:ARG913 4.9 104.3 1.0
CB D:ASN869 5.0 129.5 1.0

Magnesium binding site 8 out of 8 in 8sr9

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Magnesium binding site 8 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Magnesium


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg6004

b:125.1
occ:1.00
 O D:LEU621 1.9 100.8 1.0
O D:TRP620 2.2 105.7 1.0
C D:LEU621 2.4 98.9 1.0
CA D:LEU621 2.5 96.5 1.0
O D:GLY623 2.7 123.7 1.0
C D:TRP620 3.1 99.2 1.0
N D:LEU621 3.2 96.6 1.0
N D:ILE622 3.5 97.5 1.0
C D:GLY623 3.7 120.2 1.0
OG D:SER626 3.7 110.6 1.0
CD1 D:LEU621 3.7 105.1 1.0
N D:GLY623 3.8 117.5 1.0
CB D:LEU621 3.9 100.1 1.0
C D:ILE622 4.0 100.3 1.0
OE1 D:GLU1114 4.1 131.7 1.0
CG D:LEU621 4.2 107.0 1.0
CA D:ILE622 4.3 96.8 1.0
CA D:GLY623 4.3 117.6 1.0
O D:ILE622 4.4 100.6 1.0
OE2 D:GLU1114 4.4 129.3 1.0
CA D:TRP620 4.5 98.2 1.0
N D:ASP624 4.7 132.0 1.0
CD D:GLU1114 4.7 133.0 1.0
CB D:SER626 4.8 105.6 1.0
CA D:ASP624 4.9 132.8 1.0
CD2 D:TRP620 5.0 100.5 1.0

Reference:

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.
Page generated: Fri Oct 4 20:00:13 2024

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