Calcium in PDB 8srk: Cryo-Em Structure of TRPM2 Chanzyme (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of TRPM2 Chanzyme (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose (pdb code 8srk). 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 (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose, PDB code: 8srk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 8srk

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Calcium binding site 1 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose


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 (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1702

b:73.9
occ:1.00
 OD1 A:ASN869 2.6 127.0 1.0
OD2 A:ASP872 3.5 130.4 1.0
CG A:ASN869 3.8 127.0 1.0
NH2 A:ARG913 4.1 114.0 1.0
CG A:ASP872 4.5 130.4 1.0
ND2 A:ASN869 4.5 127.0 1.0
CB A:GLN853 4.5 129.7 1.0
CB A:ASN869 4.9 127.0 1.0

Calcium binding site 2 out of 8 in 8srk

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Calcium binding site 2 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose


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 (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1703

b:115.8
occ:1.00
 O A:GLY623 2.6 124.2 1.0
O A:LEU621 2.6 126.9 1.0
C A:GLY623 3.7 124.2 1.0
C A:LEU621 3.8 126.9 1.0
C A:ILE622 4.1 122.7 1.0
O A:ILE622 4.3 122.7 1.0
N A:GLY623 4.3 124.2 1.0
CA A:ILE622 4.4 122.7 1.0
N A:ASP624 4.5 133.0 1.0
CA A:GLY623 4.6 124.2 1.0
CA A:ASP624 4.6 133.0 1.0
N A:ILE622 4.6 122.7 1.0
CB A:GLU1114 4.6 116.5 1.0
CA A:LEU621 4.8 126.9 1.0
O A:TRP620 4.8 117.4 1.0
CG2 A:THR1117 4.9 120.0 1.0
CA A:GLU1114 4.9 116.5 1.0

Calcium binding site 3 out of 8 in 8srk

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Calcium binding site 3 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose


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 (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1702

b:73.9
occ:1.00
 OD1 B:ASN869 2.6 127.0 1.0
OD2 B:ASP872 3.5 130.4 1.0
CG B:ASN869 3.8 127.0 1.0
NH2 B:ARG913 4.1 114.0 1.0
CG B:ASP872 4.5 130.4 1.0
ND2 B:ASN869 4.5 127.0 1.0
CB B:GLN853 4.5 129.7 1.0
CB B:ASN869 4.9 127.0 1.0

Calcium binding site 4 out of 8 in 8srk

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Calcium binding site 4 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose


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 (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1703

b:115.8
occ:1.00
 O B:GLY623 2.6 124.2 1.0
O B:LEU621 2.6 126.9 1.0
C B:GLY623 3.7 124.2 1.0
C B:LEU621 3.8 126.9 1.0
C B:ILE622 4.1 122.7 1.0
O B:ILE622 4.3 122.7 1.0
N B:GLY623 4.3 124.2 1.0
CA B:ILE622 4.4 122.7 1.0
N B:ASP624 4.5 133.0 1.0
CA B:GLY623 4.6 124.2 1.0
CA B:ASP624 4.6 133.0 1.0
N B:ILE622 4.6 122.7 1.0
CB B:GLU1114 4.6 116.5 1.0
CA B:LEU621 4.8 126.9 1.0
O B:TRP620 4.8 117.4 1.0
CG2 B:THR1117 4.9 120.0 1.0
CA B:GLU1114 4.9 116.5 1.0

Calcium binding site 5 out of 8 in 8srk

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Calcium binding site 5 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose


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 (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1702

b:73.9
occ:1.00
 OD1 C:ASN869 2.6 127.0 1.0
OD2 C:ASP872 3.5 130.4 1.0
CG C:ASN869 3.8 127.0 1.0
NH2 C:ARG913 4.1 114.0 1.0
CG C:ASP872 4.5 130.4 1.0
ND2 C:ASN869 4.5 127.0 1.0
CB C:GLN853 4.5 129.7 1.0
CB C:ASN869 4.9 127.0 1.0

Calcium binding site 6 out of 8 in 8srk

Go back to Calcium Binding Sites List in 8srk
Calcium binding site 6 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose


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 (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1703

b:115.8
occ:1.00
 O C:GLY623 2.6 124.2 1.0
O C:LEU621 2.6 126.9 1.0
C C:GLY623 3.7 124.2 1.0
C C:LEU621 3.8 126.9 1.0
C C:ILE622 4.1 122.7 1.0
O C:ILE622 4.3 122.7 1.0
N C:GLY623 4.3 124.2 1.0
CA C:ILE622 4.4 122.7 1.0
N C:ASP624 4.5 133.0 1.0
CA C:GLY623 4.6 124.2 1.0
CA C:ASP624 4.6 133.0 1.0
N C:ILE622 4.6 122.7 1.0
CB C:GLU1114 4.6 116.5 1.0
CA C:LEU621 4.8 126.9 1.0
O C:TRP620 4.8 117.4 1.0
CG2 C:THR1117 4.9 120.0 1.0
CA C:GLU1114 4.9 116.5 1.0

Calcium binding site 7 out of 8 in 8srk

Go back to Calcium Binding Sites List in 8srk
Calcium binding site 7 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose


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 (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca6004

b:73.9
occ:1.00
 OD1 D:ASN869 2.6 127.0 1.0
OD2 D:ASP872 3.5 130.4 1.0
CG D:ASN869 3.8 127.0 1.0
NH2 D:ARG913 4.1 114.0 1.0
CG D:ASP872 4.5 130.4 1.0
ND2 D:ASN869 4.5 127.0 1.0
CB D:GLN853 4.5 129.7 1.0
CB D:ASN869 4.9 127.0 1.0

Calcium binding site 8 out of 8 in 8srk

Go back to Calcium Binding Sites List in 8srk
Calcium binding site 8 out of 8 in the Cryo-Em Structure of TRPM2 Chanzyme (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose


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 (Without NUDT9-H Domain) in the Presence of Ca and Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca6005

b:115.8
occ:1.00
 O D:GLY623 2.6 124.2 1.0
O D:LEU621 2.6 126.9 1.0
C D:GLY623 3.7 124.2 1.0
C D:LEU621 3.8 126.9 1.0
C D:ILE622 4.1 122.7 1.0
O D:ILE622 4.3 122.7 1.0
N D:GLY623 4.3 124.2 1.0
CA D:ILE622 4.4 122.7 1.0
N D:ASP624 4.5 133.0 1.0
CA D:GLY623 4.6 124.2 1.0
CA D:ASP624 4.6 133.0 1.0
N D:ILE622 4.6 122.7 1.0
CB D:GLU1114 4.6 116.5 1.0
CA D:LEU621 4.8 126.9 1.0
O D:TRP620 4.8 117.4 1.0
CG2 D:THR1117 4.9 120.0 1.0
CA D:GLU1114 4.9 116.5 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 Jul 19 11:50:25 2024

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