Calcium in PDB 8sra: Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium

Calcium Binding Sites:

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

Calcium binding site 1 out of 8 in 8sra

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3001

b:112.9
occ:1.00
 OE1 A:GLN853 2.5 124.5 1.0
OE2 A:GLU850 2.5 109.4 1.0
OD1 A:ASN869 2.6 119.9 1.0
OE1 A:GLU850 2.7 109.1 1.0
OD2 A:ASP872 2.7 116.7 1.0
CD A:GLU850 2.9 107.6 1.0
CD A:GLN853 3.4 123.8 1.0
NE2 A:GLN853 3.7 124.7 1.0
CG A:ASN869 3.8 119.2 1.0
CG A:ASP872 3.8 114.0 1.0
CA A:ASN869 4.3 113.8 1.0
CB A:ASP872 4.3 110.1 1.0
NH2 A:ARG913 4.4 88.3 1.0
CG A:GLU850 4.4 107.5 1.0
CB A:ASN869 4.5 113.8 1.0
CE1 A:TYR863 4.6 128.8 1.0
OH A:TYR863 4.7 129.4 1.0
ND2 A:ASN869 4.7 123.1 1.0
N A:ASN869 4.8 115.8 1.0
OD1 A:ASP872 4.8 115.6 1.0
CG A:GLN853 4.8 118.7 1.0
O A:TRP868 4.8 106.2 1.0

Calcium binding site 2 out of 8 in 8sra

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3002

b:117.6
occ:1.00
 O A:LEU621 2.1 95.7 1.0
OE2 A:GLU1114 2.4 122.3 1.0
OE1 A:GLU1114 2.5 116.4 1.0
O A:GLY623 2.5 104.9 1.0
CD A:GLU1114 2.8 120.6 1.0
C A:LEU621 3.2 87.2 1.0
CA A:LEU621 3.7 83.4 1.0
C A:GLY623 3.7 102.7 1.0
O A:TRP620 3.7 92.0 1.0
OG A:SER626 3.8 109.0 1.0
CD1 A:LEU621 4.1 90.7 1.0
O A:ILE622 4.2 100.9 1.0
C A:ILE622 4.2 96.3 1.0
CG A:GLU1114 4.3 116.0 1.0
N A:ILE622 4.3 86.4 1.0
N A:GLY623 4.3 101.7 1.0
N A:ASP624 4.6 119.7 1.0
CA A:GLY623 4.6 101.9 1.0
CA A:ASP624 4.6 123.7 1.0
CG A:LEU621 4.6 92.5 1.0
C A:TRP620 4.6 85.4 1.0
N A:LEU621 4.7 85.9 1.0
CA A:ILE622 4.7 90.0 1.0
CG2 A:THR1117 4.7 99.4 1.0
CB A:LEU621 4.7 85.6 1.0
CB A:GLU1114 4.8 108.1 1.0

Calcium binding site 3 out of 8 in 8sra

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3001

b:112.9
occ:1.00
 OE1 B:GLN853 2.5 124.5 1.0
OE2 B:GLU850 2.5 109.4 1.0
OD1 B:ASN869 2.6 119.9 1.0
OE1 B:GLU850 2.7 109.1 1.0
OD2 B:ASP872 2.7 116.7 1.0
CD B:GLU850 2.9 107.6 1.0
CD B:GLN853 3.4 123.8 1.0
NE2 B:GLN853 3.7 124.7 1.0
CG B:ASN869 3.8 119.2 1.0
CG B:ASP872 3.8 114.0 1.0
CA B:ASN869 4.3 113.8 1.0
CB B:ASP872 4.3 110.1 1.0
NH2 B:ARG913 4.4 88.3 1.0
CG B:GLU850 4.4 107.5 1.0
CB B:ASN869 4.5 113.8 1.0
CE1 B:TYR863 4.6 128.8 1.0
OH B:TYR863 4.7 129.4 1.0
ND2 B:ASN869 4.7 123.1 1.0
N B:ASN869 4.8 115.8 1.0
OD1 B:ASP872 4.8 115.6 1.0
CG B:GLN853 4.8 118.7 1.0
O B:TRP868 4.8 106.2 1.0

Calcium binding site 4 out of 8 in 8sra

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3002

b:117.6
occ:1.00
 O B:LEU621 2.1 95.7 1.0
OE2 B:GLU1114 2.4 122.3 1.0
OE1 B:GLU1114 2.5 116.4 1.0
O B:GLY623 2.5 104.9 1.0
CD B:GLU1114 2.8 120.6 1.0
C B:LEU621 3.2 87.2 1.0
CA B:LEU621 3.7 83.4 1.0
C B:GLY623 3.7 102.7 1.0
O B:TRP620 3.7 92.0 1.0
OG B:SER626 3.8 109.0 1.0
CD1 B:LEU621 4.1 90.7 1.0
O B:ILE622 4.2 100.9 1.0
C B:ILE622 4.2 96.3 1.0
CG B:GLU1114 4.3 116.0 1.0
N B:ILE622 4.3 86.4 1.0
N B:GLY623 4.3 101.7 1.0
N B:ASP624 4.6 119.7 1.0
CA B:GLY623 4.6 101.9 1.0
CA B:ASP624 4.6 123.7 1.0
CG B:LEU621 4.6 92.5 1.0
C B:TRP620 4.6 85.4 1.0
N B:LEU621 4.7 85.9 1.0
CA B:ILE622 4.7 90.0 1.0
CG2 B:THR1117 4.7 99.4 1.0
CB B:LEU621 4.7 85.6 1.0
CB B:GLU1114 4.8 108.1 1.0

Calcium binding site 5 out of 8 in 8sra

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca3001

b:112.9
occ:1.00
 OE1 C:GLN853 2.5 124.5 1.0
OE2 C:GLU850 2.5 109.4 1.0
OD1 C:ASN869 2.6 119.9 1.0
OE1 C:GLU850 2.7 109.1 1.0
OD2 C:ASP872 2.7 116.7 1.0
CD C:GLU850 2.9 107.6 1.0
CD C:GLN853 3.4 123.8 1.0
NE2 C:GLN853 3.7 124.7 1.0
CG C:ASN869 3.8 119.2 1.0
CG C:ASP872 3.8 114.0 1.0
CA C:ASN869 4.3 113.8 1.0
CB C:ASP872 4.3 110.1 1.0
NH2 C:ARG913 4.4 88.3 1.0
CG C:GLU850 4.4 107.5 1.0
CB C:ASN869 4.5 113.8 1.0
CE1 C:TYR863 4.6 128.8 1.0
OH C:TYR863 4.7 129.4 1.0
ND2 C:ASN869 4.7 123.1 1.0
N C:ASN869 4.8 115.8 1.0
OD1 C:ASP872 4.8 115.6 1.0
CG C:GLN853 4.8 118.7 1.0
O C:TRP868 4.8 106.2 1.0

Calcium binding site 6 out of 8 in 8sra

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca3002

b:117.6
occ:1.00
 O C:LEU621 2.1 95.7 1.0
OE2 C:GLU1114 2.4 122.3 1.0
OE1 C:GLU1114 2.5 116.4 1.0
O C:GLY623 2.5 104.9 1.0
CD C:GLU1114 2.8 120.6 1.0
C C:LEU621 3.2 87.2 1.0
CA C:LEU621 3.7 83.4 1.0
C C:GLY623 3.7 102.7 1.0
O C:TRP620 3.7 92.0 1.0
OG C:SER626 3.8 109.0 1.0
CD1 C:LEU621 4.1 90.7 1.0
O C:ILE622 4.2 100.9 1.0
C C:ILE622 4.2 96.3 1.0
CG C:GLU1114 4.3 116.0 1.0
N C:ILE622 4.3 86.4 1.0
N C:GLY623 4.3 101.7 1.0
N C:ASP624 4.6 119.7 1.0
CA C:GLY623 4.6 101.9 1.0
CA C:ASP624 4.6 123.7 1.0
CG C:LEU621 4.6 92.5 1.0
C C:TRP620 4.6 85.4 1.0
N C:LEU621 4.7 85.9 1.0
CA C:ILE622 4.7 90.0 1.0
CG2 C:THR1117 4.7 99.4 1.0
CB C:LEU621 4.7 85.6 1.0
CB C:GLU1114 4.8 108.1 1.0

Calcium binding site 7 out of 8 in 8sra

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca6003

b:112.9
occ:1.00
 OE1 D:GLN853 2.5 124.5 1.0
OE2 D:GLU850 2.5 109.4 1.0
OD1 D:ASN869 2.6 119.9 1.0
OE1 D:GLU850 2.7 109.1 1.0
OD2 D:ASP872 2.7 116.7 1.0
CD D:GLU850 2.9 107.6 1.0
CD D:GLN853 3.4 123.8 1.0
NE2 D:GLN853 3.7 124.7 1.0
CG D:ASN869 3.8 119.2 1.0
CG D:ASP872 3.8 114.0 1.0
CA D:ASN869 4.3 113.8 1.0
CB D:ASP872 4.3 110.1 1.0
NH2 D:ARG913 4.4 88.3 1.0
CG D:GLU850 4.4 107.5 1.0
CB D:ASN869 4.5 113.8 1.0
CE1 D:TYR863 4.6 128.8 1.0
OH D:TYR863 4.7 129.4 1.0
ND2 D:ASN869 4.7 123.1 1.0
N D:ASN869 4.8 115.8 1.0
OD1 D:ASP872 4.8 115.6 1.0
CG D:GLN853 4.8 118.7 1.0
O D:TRP868 4.8 106.2 1.0

Calcium binding site 8 out of 8 in 8sra

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cryo-Em Structure of TRPM2 Chanzyme in the Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca6004

b:117.6
occ:1.00
 O D:LEU621 2.1 95.7 1.0
OE2 D:GLU1114 2.4 122.3 1.0
OE1 D:GLU1114 2.5 116.4 1.0
O D:GLY623 2.5 104.9 1.0
CD D:GLU1114 2.8 120.6 1.0
C D:LEU621 3.2 87.2 1.0
CA D:LEU621 3.7 83.4 1.0
C D:GLY623 3.7 102.7 1.0
O D:TRP620 3.7 92.0 1.0
OG D:SER626 3.8 109.0 1.0
CD1 D:LEU621 4.1 90.7 1.0
O D:ILE622 4.2 100.9 1.0
C D:ILE622 4.2 96.3 1.0
CG D:GLU1114 4.3 116.0 1.0
N D:ILE622 4.3 86.4 1.0
N D:GLY623 4.3 101.7 1.0
N D:ASP624 4.6 119.7 1.0
CA D:GLY623 4.6 101.9 1.0
CA D:ASP624 4.6 123.7 1.0
CG D:LEU621 4.6 92.5 1.0
C D:TRP620 4.6 85.4 1.0
N D:LEU621 4.7 85.9 1.0
CA D:ILE622 4.7 90.0 1.0
CG2 D:THR1117 4.7 99.4 1.0
CB D:LEU621 4.7 85.6 1.0
CB D:GLU1114 4.8 108.1 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 Jul 19 11:49:17 2024

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