Calcium in PDB 5wkv: Structure of An Acid Sensing Ion Channel in A Resting State with Calcium

The structure of Structure of An Acid Sensing Ion Channel in A Resting State with Calcium, PDB code: 5wkv was solved by N.Yoder, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.95 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	109.180, 133.700, 157.650, 90.00, 90.00, 90.00
R / Rfree (%)	28.7 / 29.7

The structure of Structure of An Acid Sensing Ion Channel in A Resting State with Calcium also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Structure of An Acid Sensing Ion Channel in A Resting State with Calcium (pdb code 5wkv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of An Acid Sensing Ion Channel in A Resting State with Calcium, PDB code: 5wkv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of An Acid Sensing Ion Channel in A Resting State with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of An Acid Sensing Ion Channel in A Resting State with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:0.3 occ:1.00 NE2 A:GLN277 2.7 0.5 1.0 OE1 A:GLU412 3.7 0.6 1.0 CD A:GLN277 3.8 0.3 1.0 OE2 A:GLU417 3.8 0.7 1.0 CD A:GLU412 4.4 0.9 1.0 CG A:GLN277 4.5 0.3 1.0 OE2 A:GLU412 4.5 0.3 1.0 NH1 B:ARG370 4.6 0.8 1.0 OE1 A:GLN277 4.6 0.5 1.0 CZ B:ARG370 4.8 0.1 1.0 OE2 A:GLU80 4.9 0.8 1.0 CD A:GLU417 5.0 0.8 1.0

Calcium binding site 2 out of 6 in the Structure of An Acid Sensing Ion Channel in A Resting State with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of An Acid Sensing Ion Channel in A Resting State with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:0.0 occ:1.00 OE2 A:GLU220 3.0 0.7 1.0 OE1 A:GLU220 3.4 0.3 1.0 CD A:GLU220 3.5 0.9 1.0 OE2 B:GLU243 3.8 0.1 1.0 NE2 A:GLN271 4.0 0.4 1.0 OD2 A:ASP408 4.3 0.7 1.0 OE1 B:GLU243 4.6 0.5 1.0 CD B:GLU243 4.7 0.5 1.0 OG1 A:THR215 4.8 0.2 1.0 CG A:GLU220 4.8 0.6 1.0

Calcium binding site 3 out of 6 in the Structure of An Acid Sensing Ion Channel in A Resting State with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of An Acid Sensing Ion Channel in A Resting State with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:0.7 occ:1.00 OE1 C:GLN277 2.5 0.6 1.0 CD C:GLN277 3.6 0.8 1.0 OE2 C:GLU417 3.9 0.9 1.0 OE1 C:GLU412 3.9 0.3 1.0 CG C:GLN277 4.2 0.7 1.0 NE2 C:GLN277 4.6 0.3 1.0 CB C:GLN277 4.8 0.1 1.0 CD C:GLU412 4.9 0.6 1.0 OE2 C:GLU80 5.0 0.1 1.0

Calcium binding site 4 out of 6 in the Structure of An Acid Sensing Ion Channel in A Resting State with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of An Acid Sensing Ion Channel in A Resting State with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca505 b:0.9 occ:1.00 OE2 C:GLU220 3.3 0.4 1.0 OE2 A:GLU243 3.8 0.7 1.0 CD C:GLU220 3.9 0.4 1.0 OE1 C:GLU220 3.9 0.4 1.0 NE2 C:GLN271 4.0 0.7 1.0 OD2 C:ASP408 4.2 0.6 1.0 OE1 A:GLU243 4.6 0.3 1.0 CD A:GLU243 4.6 0.6 1.0 OG1 C:THR215 4.6 0.1 1.0

Calcium binding site 5 out of 6 in the Structure of An Acid Sensing Ion Channel in A Resting State with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of An Acid Sensing Ion Channel in A Resting State with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:0.4 occ:1.00 OE1 B:GLN277 2.9 1.0 1.0 OE1 B:GLU412 3.8 0.1 1.0 CD B:GLN277 3.9 0.4 1.0 OE2 B:GLU417 3.9 0.0 1.0 CG B:GLN277 4.3 0.9 1.0 CB B:GLN277 4.7 0.9 1.0 NH1 C:ARG370 4.7 0.3 1.0 CD B:GLU412 4.8 0.9 1.0 CZ C:ARG370 4.9 0.4 1.0

Calcium binding site 6 out of 6 in the Structure of An Acid Sensing Ion Channel in A Resting State with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of An Acid Sensing Ion Channel in A Resting State with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:0.0 occ:1.00 OE2 B:GLU220 3.3 0.8 1.0 OE1 B:GLU220 3.5 0.7 1.0 CD B:GLU220 3.7 0.7 1.0 OE2 C:GLU243 4.2 0.5 1.0 NE2 B:GLN271 4.4 0.9 1.0 OD2 B:ASP408 4.5 0.1 1.0 OE1 C:GLU243 4.9 0.1 1.0 CD C:GLU243 5.0 0.8 1.0 OG1 B:THR215 5.0 0.7 1.0

N.Yoder, C.Yoshioka, E.Gouaux. Gating Mechanisms of Acid-Sensing Ion Channels. Nature V. 555 397 2018.
ISSN: ESSN 1476-4687
PubMed: 29513651
DOI: 10.1038/NATURE25782