Calcium in PDB 6o20: Cryo-Em Structure of TRPV5 with Calmodulin Bound

The binding sites of Calcium atom in the Cryo-Em Structure of TRPV5 with Calmodulin Bound (pdb code 6o20). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of TRPV5 with Calmodulin Bound, PDB code: 6o20:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of TRPV5 with Calmodulin Bound


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 TRPV5 with Calmodulin Bound within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca201 b:0.2 occ:1.00 OD1 F:ASP129 2.5 0.5 1.0 OD1 F:ASP131 2.5 0.5 1.0 OD1 F:ASP133 2.6 0.7 1.0 O F:GLN135 2.6 0.9 1.0 OD2 F:ASP131 3.0 0.5 1.0 CG F:ASP131 3.1 0.5 1.0 OD2 F:ASP133 3.2 0.7 1.0 CG F:ASP133 3.3 0.7 1.0 N F:ASN137 3.4 0.6 1.0 CG F:ASP129 3.6 0.5 1.0 C F:GLN135 3.8 0.9 1.0 CB F:ASN137 3.9 0.6 1.0 C F:VAL136 3.9 0.5 1.0 CA F:VAL136 4.0 0.5 1.0 OD2 F:ASP129 4.1 0.5 1.0 CA F:ASN137 4.2 0.6 1.0 N F:VAL136 4.4 0.5 1.0 CB F:ASP131 4.6 0.5 1.0 CB F:ASP133 4.7 0.7 1.0 O F:VAL136 4.8 0.5 1.0 N F:ASP133 4.8 0.7 1.0 CB F:ASP129 4.8 0.5 1.0 N F:ASP131 4.9 0.5 1.0 N F:GLN135 4.9 0.9 1.0 CA F:GLN135 4.9 0.9 1.0 CA F:ASP129 4.9 0.5 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of TRPV5 with Calmodulin Bound


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 TRPV5 with Calmodulin Bound within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca202 b:95.8 occ:1.00 O F:TYR99 2.5 0.2 1.0 OD1 F:ASP95 2.5 99.3 1.0 OE1 F:GLU104 2.6 0.3 1.0 OD2 F:ASP95 2.6 99.3 1.0 OD1 F:ASP93 2.6 0.1 1.0 CG F:ASP95 2.9 99.3 1.0 OD1 F:ASN97 3.0 98.2 1.0 CG F:ASP93 3.5 0.1 1.0 C F:TYR99 3.5 0.2 1.0 O F:ILE100 3.6 0.9 1.0 OD2 F:ASP93 3.6 0.1 1.0 CD F:GLU104 3.6 0.3 1.0 C F:ILE100 3.7 0.9 1.0 CB F:SER101 3.8 0.5 1.0 CG F:ASN97 3.9 98.2 1.0 ND2 F:ASN97 4.0 98.2 1.0 N F:SER101 4.1 0.5 1.0 CA F:ILE100 4.2 0.9 1.0 OE2 F:GLU104 4.2 0.3 1.0 N F:ILE100 4.2 0.9 1.0 CB F:ASP95 4.3 99.3 1.0 CA F:SER101 4.6 0.5 1.0 CA F:TYR99 4.6 0.2 1.0 CG F:GLU104 4.7 0.3 1.0 N F:TYR99 4.8 0.2 1.0 CB F:ASP93 4.8 0.1 1.0 CB F:TYR99 4.8 0.2 1.0 N F:ASP95 4.9 99.3 1.0 OG F:SER101 5.0 0.5 1.0 CB F:GLU104 5.0 0.3 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of TRPV5 with Calmodulin Bound


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 TRPV5 with Calmodulin Bound within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca203 b:0.3 occ:1.00 O F:GLY25 2.5 0.4 1.0 O F:THR26 2.5 0.3 1.0 OE2 F:GLU31 2.5 0.7 1.0 OE1 F:GLU31 2.6 0.7 1.0 CD F:GLU31 2.9 0.7 1.0 OD2 F:ASP20 3.4 0.5 1.0 C F:GLY25 3.4 0.4 1.0 C F:THR26 3.6 0.3 1.0 O F:ASP22 3.8 0.1 1.0 N F:THR26 4.1 0.3 1.0 CB F:THR28 4.1 0.3 1.0 CA F:THR26 4.3 0.3 1.0 CG F:ASP20 4.3 0.5 1.0 CA F:GLY23 4.3 0.1 1.0 CG F:GLU31 4.4 0.7 1.0 CA F:GLY25 4.5 0.4 1.0 N F:THR28 4.5 0.3 1.0 OD1 F:ASP20 4.5 0.5 1.0 C F:GLY23 4.6 0.1 1.0 N F:GLY25 4.6 0.4 1.0 N F:ILE27 4.6 0.6 1.0 C F:ILE27 4.7 0.6 1.0 C F:ASP22 4.8 0.1 1.0 CA F:ILE27 4.8 0.6 1.0 N F:ASP24 4.9 0.2 1.0 CA F:THR28 4.9 0.3 1.0 O F:GLY23 5.0 0.1 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of TRPV5 with Calmodulin Bound


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 TRPV5 with Calmodulin Bound within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca204 b:0.9 occ:1.00 OE1 F:GLU67 2.5 0.8 1.0 O F:THR62 2.5 0.1 1.0 OD1 F:ASP58 2.6 0.4 1.0 OD1 F:ASN60 3.0 0.6 1.0 OD2 F:ASP56 3.2 0.5 1.0 OD2 F:ASP64 3.4 1.0 1.0 OD1 F:ASP56 3.6 0.5 1.0 CD F:GLU67 3.7 0.8 1.0 CG F:ASP58 3.7 0.4 1.0 C F:THR62 3.7 0.1 1.0 CG F:ASP56 3.8 0.5 1.0 CA F:ILE63 4.0 0.2 1.0 CG F:ASN60 4.0 0.6 1.0 OD2 F:ASP58 4.0 0.4 1.0 O F:ASN60 4.1 0.6 1.0 CG F:ASP64 4.2 1.0 1.0 N F:ASP64 4.3 1.0 1.0 OE2 F:GLU67 4.3 0.8 1.0 N F:ILE63 4.3 0.2 1.0 OG1 F:THR62 4.3 0.1 1.0 O F:GLY59 4.4 0.4 1.0 C F:ILE63 4.5 0.2 1.0 ND2 F:ASN60 4.6 0.6 1.0 CG F:GLU67 4.7 0.8 1.0 CB F:ASP64 4.9 1.0 1.0 CA F:THR62 4.9 0.1 1.0 OD1 F:ASP64 4.9 1.0 1.0 C F:ASN60 4.9 0.6 1.0 O F:ASP58 4.9 0.4 1.0 CG2 F:ILE63 5.0 0.2 1.0 CB F:ASP58 5.0 0.4 1.0

S.Dang, M.K.Van Goor, D.Asarnow, Y.Wang, D.Julius, Y.Cheng, J.Van Der Wijst. Structural Insight Into TRPV5 Channel Function and Modulation. Proc.Natl.Acad.Sci.Usa V. 116 8869 2019.
ISSN: ESSN 1091-6490
PubMed: 30975749
DOI: 10.1073/PNAS.1820323116