Calcium in PDB 6ssi: Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Pam Nanobody

The structure of Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Pam Nanobody, PDB code: 6ssi was solved by C.Ulens, M.Brams, G.L.Evans, R.Spurny, C.Govaerts, E.Pardon, J.Steyaert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.06 / 2.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.604, 146.563, 140.242, 90.00, 111.39, 90.00
R / Rfree (%)	23 / 24.6

The binding sites of Calcium atom in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Pam Nanobody (pdb code 6ssi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Pam Nanobody, PDB code: 6ssi:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Pam Nanobody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Pam Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:0.2 occ:1.00 OD2 A:ASP158 2.4 0.2 1.0 OE2 A:GLU155 2.5 0.9 1.0 O A:ASP153 2.6 0.1 1.0 OD1 A:ASP158 2.6 0.5 1.0 CG A:ASP158 2.8 0.8 1.0 CD A:GLU155 3.5 0.9 1.0 C A:ASP153 3.8 99.6 1.0 CG A:GLU155 4.1 0.1 1.0 OD1 E:ASP113 4.1 86.3 1.0 CB A:GLU155 4.2 99.7 1.0 N A:ASP153 4.3 93.0 1.0 CB A:ASP158 4.3 90.3 1.0 N A:GLU155 4.3 98.3 1.0 OE1 A:GLU155 4.4 0.8 1.0 CA A:ASP153 4.5 93.7 1.0 CG E:ASP113 4.8 83.8 1.0 N A:ASN154 4.8 96.7 1.0 OD2 E:ASP113 4.8 93.8 1.0 CA A:GLU155 4.9 98.3 1.0 CB A:ASP153 4.9 95.9 1.0 CA A:ASN154 5.0 96.5 1.0 C A:ASN154 5.0 0.0 1.0

Calcium binding site 2 out of 5 in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Pam Nanobody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Pam Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca405 b:0.6 occ:1.00 OD2 B:ASP158 2.5 0.8 1.0 O B:ASP153 2.6 0.2 1.0 CG B:ASP158 3.2 95.0 1.0 OD1 B:ASP158 3.2 95.1 1.0 OE2 B:GLU155 3.4 0.5 1.0 C B:ASP153 3.8 0.0 1.0 OD1 A:ASP113 3.8 83.1 1.0 CD B:GLU155 4.0 0.2 1.0 N B:ASP153 4.2 95.2 1.0 CA B:ASP153 4.5 96.0 1.0 CG B:GLU155 4.5 0.5 1.0 CB B:GLU155 4.5 0.1 1.0 CB B:ASP158 4.7 87.4 1.0 CG A:ASP113 4.7 80.6 1.0 OE1 B:GLU155 4.7 0.6 1.0 N B:GLU155 4.8 99.6 1.0 N B:ASN154 4.8 99.3 1.0 CB B:ASP153 4.8 98.1 1.0 OD2 A:ASP113 5.0 91.1 1.0

Calcium binding site 3 out of 5 in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Pam Nanobody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Pam Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca405 b:0.9 occ:1.00 OD2 C:ASP158 2.3 0.5 1.0 O C:ASP153 2.5 0.2 1.0 OD1 C:ASP158 2.6 96.4 1.0 OE1 C:GLU155 2.6 0.8 1.0 CG C:ASP158 2.7 94.6 1.0 CD C:GLU155 3.7 0.4 1.0 C C:ASP153 3.8 0.1 1.0 OD1 B:ASP113 4.1 80.1 1.0 CB C:ASP158 4.2 83.9 1.0 CG C:GLU155 4.3 0.2 1.0 CB C:GLU155 4.3 98.7 1.0 N C:GLU155 4.4 97.0 1.0 N C:ASP153 4.6 95.4 1.0 OE2 C:GLU155 4.6 1.0 1.0 CA C:ASP153 4.7 95.8 1.0 N C:ASN154 4.7 97.7 1.0 CA C:ASN154 4.8 97.0 1.0 C C:ASN154 4.8 0.0 1.0 CD1 C:ILE157 4.9 96.9 1.0 CG1 C:ILE157 4.9 95.6 1.0 CG B:ASP113 4.9 77.3 1.0 CA C:GLU155 5.0 97.3 1.0

Calcium binding site 4 out of 5 in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Pam Nanobody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Pam Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca405 b:0.7 occ:1.00 OD2 D:ASP158 2.3 0.0 1.0 OE1 D:GLU155 2.4 0.9 1.0 O D:ASP153 2.4 0.4 1.0 OD1 D:ASP158 2.7 0.8 1.0 CG D:ASP158 2.8 0.6 1.0 CD D:GLU155 3.5 0.9 1.0 C D:ASP153 3.7 0.9 1.0 CB D:ASP158 4.2 91.6 1.0 N D:ASP153 4.2 98.8 1.0 O D:HOH512 4.2 64.6 1.0 CG D:GLU155 4.3 0.8 1.0 CB D:GLU155 4.4 0.9 1.0 CA D:ASP153 4.4 0.7 1.0 OE2 D:GLU155 4.4 0.9 1.0 N D:GLU155 4.5 0.9 1.0 OD1 C:ASP113 4.6 89.5 1.0 N D:ASN154 4.7 1.0 1.0 C D:ASN154 4.8 0.5 1.0 CA D:ASN154 4.8 0.7 1.0 CB D:ASP153 4.8 0.6 1.0

Calcium binding site 5 out of 5 in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Pam Nanobody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Pam Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca406 b:0.8 occ:1.00 OE1 E:GLU155 2.5 0.3 1.0 OD2 E:ASP158 2.5 0.5 1.0 OD1 E:ASP158 2.6 93.7 1.0 OD1 D:ASP113 2.7 82.4 1.0 CG E:ASP158 2.9 93.2 1.0 O E:ASP153 3.5 0.4 1.0 CD E:GLU155 3.7 0.1 1.0 CG D:ASP113 3.7 81.0 1.0 OD2 D:ASP113 4.2 91.3 1.0 OE2 E:GLU155 4.4 0.6 1.0 CB E:ASP158 4.4 84.1 1.0 CD1 E:ILE157 4.6 96.6 1.0 CB E:GLU155 4.7 0.7 1.0 CG E:GLU155 4.7 0.8 1.0 C E:ASP153 4.8 0.3 1.0 CB D:ASP113 4.9 63.0 1.0 CG1 E:ILE157 4.9 94.8 1.0

M.Brams, C.Govaerts, K.Kambara, K.L.Price, R.Spurny, A.Gharpure, E.Pardon, G.L.Evans, D.Bertrand, S.C.Lummis, R.E.Hibbs, J.Steyaert, C.Ulens. Modulation of the Erwinia Ligand-Gated Ion Channel (Elic) and the 5-HT3 Receptor Via A Common Vestibule Site. Elife V. 9 2020.
ISSN: ESSN 2050-084X
PubMed: 31990273
DOI: 10.7554/ELIFE.51511