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Calcium in PDB 6e2f: Cryo-Em Structure of Human TRPV6 in Complex with Calmodulin

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Human TRPV6 in Complex with Calmodulin (pdb code 6e2f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Cryo-Em Structure of Human TRPV6 in Complex with Calmodulin, PDB code: 6e2f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6e2f

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Calcium binding site 1 out of 6 in the Cryo-Em Structure of Human TRPV6 in Complex with Calmodulin


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 Human TRPV6 in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:0.6
occ:1.00
 OD1 B:ASP542 2.5 0.8 1.0
OD1 D:ASP542 2.6 0.9 1.0
OD1 A:ASP542 2.8 0.9 1.0
CA A:CA902 3.6 0.5 1.0
CG B:ASP542 3.7 0.8 1.0
OD1 C:ASP542 3.8 0.2 1.0
CG D:ASP542 3.8 0.9 1.0
CG A:ASP542 4.0 0.9 1.0
CB B:ASP542 4.4 0.8 1.0
CB D:ASP542 4.5 0.9 1.0
CB A:ASP542 4.5 0.9 1.0
CA B:ASP542 4.6 0.8 1.0
CA A:ASP542 4.6 0.9 1.0
OD2 B:ASP542 4.7 0.8 1.0
CA D:ASP542 4.7 0.9 1.0
OD2 D:ASP542 4.8 0.9 1.0
CG C:ASP542 4.9 0.2 1.0
CA C:ASP542 5.0 0.2 1.0

Calcium binding site 2 out of 6 in 6e2f

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Calcium binding site 2 out of 6 in the Cryo-Em Structure of Human TRPV6 in Complex with Calmodulin


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 Human TRPV6 in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:0.5
occ:1.00
 CA A:CA901 3.6 0.6 1.0
O D:THR539 4.7 0.3 1.0
CG2 A:THR539 4.7 0.2 1.0
O A:THR539 4.7 0.2 1.0
CG2 B:THR539 4.8 0.8 1.0
O C:THR539 4.9 0.2 1.0

Calcium binding site 3 out of 6 in 6e2f

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Calcium binding site 3 out of 6 in the Cryo-Em Structure of Human TRPV6 in Complex with Calmodulin


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 Human TRPV6 in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:0.1
occ:1.00
 OE1 E:GLU31 2.5 0.3 1.0
OD1 E:ASP20 2.5 1.0 1.0
O E:THR26 2.6 0.5 1.0
CG E:ASP20 2.9 1.0 1.0
CG1 E:ILE27 2.9 0.2 1.0
CA E:ASP20 3.0 1.0 1.0
CB E:ASP20 3.1 1.0 1.0
CA E:ILE27 3.3 0.2 1.0
C E:THR26 3.5 0.5 1.0
CB E:ILE27 3.5 0.2 1.0
CD E:GLU31 3.7 0.3 1.0
OD2 E:ASP20 3.8 1.0 1.0
N E:ASP20 3.8 1.0 1.0
N E:ILE27 3.8 0.2 1.0
CG2 E:ILE27 3.9 0.2 1.0
O E:PHE19 4.1 0.1 1.0
C E:ASP20 4.1 1.0 1.0
CD1 E:ILE27 4.1 0.2 1.0
N E:LYS21 4.2 0.4 1.0
C E:PHE19 4.2 0.1 1.0
CB E:GLU31 4.3 0.3 1.0
OE2 E:GLU31 4.4 0.3 1.0
OD1 E:ASP24 4.5 0.4 1.0
CG E:GLU31 4.5 0.3 1.0
CD2 E:PHE19 4.6 0.1 1.0
C E:ILE27 4.6 0.2 1.0
N E:THR28 4.8 0.0 1.0
OD1 E:ASP22 4.8 0.9 1.0
CA E:THR26 4.8 0.5 1.0
N E:THR26 4.9 0.5 1.0

Calcium binding site 4 out of 6 in 6e2f

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Calcium binding site 4 out of 6 in the Cryo-Em Structure of Human TRPV6 in Complex with Calmodulin


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 Human TRPV6 in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:0.8
occ:1.00
 OD1 E:ASN60 2.5 0.5 1.0
OE1 E:GLU67 2.5 0.0 1.0
OD1 E:ASP58 2.6 0.5 1.0
O E:THR62 2.6 0.1 1.0
OD1 E:ASP56 2.7 0.5 1.0
OE2 E:GLU67 2.7 0.0 1.0
ND2 E:ASN60 2.8 0.5 1.0
CD E:GLU67 2.8 0.0 1.0
CG E:ASN60 3.0 0.5 1.0
CG E:ASP58 3.3 0.5 1.0
OD2 E:ASP58 3.4 0.5 1.0
OD1 E:ASP64 3.6 0.3 1.0
C E:THR62 3.7 0.1 1.0
CG E:ASP56 3.7 0.5 1.0
OG1 E:THR62 3.9 0.1 1.0
OD2 E:ASP56 4.1 0.5 1.0
CG E:ASP64 4.2 0.3 1.0
CG E:GLU67 4.2 0.0 1.0
N E:ASP64 4.3 0.3 1.0
CA E:ILE63 4.4 0.5 1.0
CB E:ASN60 4.4 0.5 1.0
N E:ILE63 4.5 0.5 1.0
OD2 E:ASP64 4.5 0.3 1.0
N E:THR62 4.6 0.1 1.0
CA E:THR62 4.6 0.1 1.0
N E:ASN60 4.7 0.5 1.0
N E:ASP58 4.8 0.5 1.0
CB E:ASP58 4.8 0.5 1.0
CB E:THR62 4.8 0.1 1.0
C E:ILE63 4.9 0.5 1.0
N E:ALA57 5.0 0.1 1.0
CD1 E:ILE63 5.0 0.5 1.0
CB E:GLU67 5.0 0.0 1.0
CB E:ASP56 5.0 0.5 1.0

Calcium binding site 5 out of 6 in 6e2f

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Calcium binding site 5 out of 6 in the Cryo-Em Structure of Human TRPV6 in Complex with Calmodulin


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 Human TRPV6 in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:0.9
occ:1.00
 OE2 E:GLU104 2.5 0.8 1.0
OD1 E:ASN97 2.5 1.0 1.0
O E:TYR99 2.5 0.6 1.0
ND2 E:ASN97 2.6 1.0 1.0
OE1 E:GLU104 2.6 0.8 1.0
CD E:GLU104 2.8 0.8 1.0
CG E:ASN97 2.9 1.0 1.0
OD1 E:ASP93 2.9 0.9 1.0
OD1 E:ASP95 3.0 0.8 1.0
C E:TYR99 3.6 0.6 1.0
CG E:ASP95 3.8 0.8 1.0
OD2 E:ASP95 3.8 0.8 1.0
CG E:ASP93 3.9 0.9 1.0
N E:SER101 4.2 0.8 1.0
CA E:ILE100 4.2 0.7 1.0
CG E:GLU104 4.2 0.8 1.0
N E:ILE100 4.3 0.7 1.0
OD2 E:ASP93 4.3 0.9 1.0
CB E:ASN97 4.3 1.0 1.0
CB E:SER101 4.4 0.8 1.0
OG E:SER101 4.5 0.8 1.0
C E:ILE100 4.5 0.7 1.0
N E:TYR99 4.7 0.6 1.0
CA E:TYR99 4.7 0.6 1.0
N E:ASN97 4.8 1.0 1.0
CA E:SER101 4.9 0.8 1.0

Calcium binding site 6 out of 6 in 6e2f

Go back to Calcium Binding Sites List in 6e2f
Calcium binding site 6 out of 6 in the Cryo-Em Structure of Human TRPV6 in Complex with Calmodulin


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 Human TRPV6 in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:0.3
occ:1.00
 OD1 E:ASP131 2.5 0.4 1.0
OD1 E:ASP129 2.5 0.2 1.0
OE2 E:GLU140 2.6 0.7 1.0
O E:GLN135 2.7 0.0 1.0
OD1 E:ASP133 2.8 0.6 1.0
OE1 E:GLU140 2.9 0.7 1.0
CD E:GLU140 2.9 0.7 1.0
OD1 E:ASN137 3.0 0.8 1.0
CG E:ASP131 3.4 0.4 1.0
CG E:ASP133 3.6 0.6 1.0
CG E:ASP129 3.6 0.2 1.0
OD2 E:ASP131 3.6 0.4 1.0
CG E:ASN137 3.7 0.8 1.0
OD2 E:ASP133 3.7 0.6 1.0
C E:GLN135 3.8 0.0 1.0
ND2 E:ASN137 4.1 0.8 1.0
OD2 E:ASP129 4.1 0.2 1.0
N E:ASN137 4.1 0.8 1.0
CG E:GLU140 4.2 0.7 1.0
CA E:VAL136 4.5 0.3 1.0
N E:ASP131 4.6 0.4 1.0
N E:VAL136 4.6 0.3 1.0
C E:VAL136 4.6 0.3 1.0
CB E:ASN137 4.7 0.8 1.0
N E:ILE130 4.7 0.4 1.0
N E:ASP133 4.8 0.6 1.0
CB E:ASP129 4.8 0.2 1.0
CB E:ASP131 4.8 0.4 1.0
N E:GLY132 4.8 0.3 1.0
CA E:ASP129 4.9 0.2 1.0
N E:GLN135 4.9 0.0 1.0
CA E:GLN135 4.9 0.0 1.0
CA E:ASN137 4.9 0.8 1.0
CB E:ASP133 5.0 0.6 1.0
NH2 C:ARG643 5.0 0.9 1.0

Reference:

A.K.Singh, L.L.Mcgoldrick, E.C.Twomey, A.I.Sobolevsky. Mechanism of Calmodulin Inactivation of the Calcium-Selective Trp Channel TRPV6. Sci Adv V. 4 U6088 2018.
ISSN: ESSN 2375-2548
PubMed: 30116787
DOI: 10.1126/SCIADV.AAU6088
Page generated: Mon Jul 15 18:06:39 2024

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