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

The structure of Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Nam Nanobody, PDB code: 6ssp 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)	48.32 / 3.25
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	121.804, 122.354, 128.221, 71.02, 64.19, 61.66
R / Rfree (%)	24.8 / 26.4

The binding sites of Calcium atom in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Nam Nanobody (pdb code 6ssp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Nam Nanobody, PDB code: 6ssp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Nam 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 Nam Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:0.4 occ:1.00 OD1 A:ASP113 2.3 0.2 1.0 OD1 E:ASP158 3.3 0.2 1.0 CG A:ASP113 3.3 0.2 1.0 OD2 E:ASP158 3.7 0.1 1.0 OD2 A:ASP113 3.8 0.1 1.0 CG E:ASP158 3.9 0.6 1.0 OE1 A:GLN31 4.6 91.7 1.0 CB A:ASP113 4.6 87.0 1.0 CA A:ASP113 5.0 84.7 1.0

Calcium binding site 2 out of 8 in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Nam 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 Nam Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:0.2 occ:1.00 OD1 B:ASP113 2.4 87.5 1.0 CG B:ASP113 3.1 86.7 1.0 OD1 A:ASP158 3.3 0.9 1.0 OD2 A:ASP158 3.4 0.6 1.0 OD2 B:ASP113 3.4 94.0 1.0 CG A:ASP158 3.7 0.8 1.0 O A:ASN154 4.2 0.3 1.0 CB B:ASP113 4.3 73.6 1.0 CB A:ASN154 4.6 0.5 1.0 CB A:ILE152 4.7 0.7 1.0 CD1 A:ILE157 4.7 0.2 1.0 C A:ASN154 4.8 0.5 1.0

Calcium binding site 3 out of 8 in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Nam 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 Nam Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:95.1 occ:1.00 OD1 C:ASP113 2.4 94.5 1.0 CG C:ASP113 3.3 93.6 1.0 OD2 C:ASP113 3.4 0.6 1.0 OD1 B:ASP158 3.7 99.6 1.0 OD2 B:ASP158 3.7 0.4 1.0 OD1 B:ASN154 4.1 0.6 1.0 CG B:ASP158 4.1 99.3 1.0 ND2 B:ASN154 4.3 0.7 1.0 CG B:ASN154 4.7 0.2 1.0 CB C:ASP113 4.7 81.8 1.0

Calcium binding site 4 out of 8 in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Nam 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 Nam Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:0.4 occ:1.00 OD1 D:ASP158 2.5 0.3 1.0 OD1 E:ASP113 2.5 1.0 1.0 CG D:ASP158 3.2 0.6 1.0 OD1 D:ASN154 3.2 1.0 1.0 OD2 D:ASP158 3.2 0.8 1.0 CG E:ASP113 3.5 0.8 1.0 OD2 E:ASP113 4.0 0.6 1.0 CG D:ASN154 4.3 0.8 1.0 OE1 E:GLN31 4.3 0.3 1.0 O D:ASN154 4.5 0.3 1.0 CB E:ASP113 4.6 95.8 1.0 ND2 D:ASN154 4.6 0.9 1.0 CB D:ASP158 4.7 0.9 1.0 NE2 E:GLN31 4.9 0.4 1.0 CG2 D:ILE157 4.9 0.9 1.0

Calcium binding site 5 out of 8 in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Nam 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 Nam Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca401 b:0.2 occ:1.00 OD1 F:ASP113 2.3 0.1 1.0 OD1 J:ASP158 3.0 97.5 1.0 CG F:ASP113 3.5 0.0 1.0 OD2 J:ASP158 3.7 0.9 1.0 CG J:ASP158 3.7 98.2 1.0 OE1 F:GLN31 3.8 94.2 1.0 OD2 F:ASP113 4.1 0.4 1.0 CD F:GLN31 4.6 0.6 1.0 CB F:ASP113 4.7 96.3 1.0 NE2 F:GLN31 4.7 94.0 1.0 CA F:ASP113 4.9 93.7 1.0

Calcium binding site 6 out of 8 in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Nam Nanobody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Nam Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca402 b:0.7 occ:1.00 OD1 F:ASP158 2.4 0.9 1.0 OD1 F:ASN154 2.4 0.2 1.0 OD2 F:ASP158 2.8 0.7 1.0 CG F:ASP158 2.9 0.4 1.0 OD1 G:ASP113 3.2 0.7 1.0 CG F:ASN154 3.4 1.0 1.0 ND2 F:ASN154 3.7 0.7 1.0 CB F:ILE152 3.9 0.6 1.0 CG G:ASP113 3.9 1.0 1.0 OD2 G:ASP113 4.2 0.8 1.0 O F:ASN154 4.3 0.8 1.0 CB F:ASP158 4.4 0.7 1.0 CB F:ASN154 4.7 0.2 1.0 CA F:ILE152 4.8 0.7 1.0 C F:ASN154 4.8 0.9 1.0

Calcium binding site 7 out of 8 in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Nam Nanobody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Nam Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca401 b:0.5 occ:1.00 OD1 H:ASP113 2.4 0.7 1.0 OD1 G:ASP158 2.9 0.0 1.0 OD2 G:ASP158 3.3 0.9 1.0 CG H:ASP113 3.3 0.7 1.0 CG G:ASP158 3.5 0.3 1.0 ND2 G:ASN154 3.5 0.4 1.0 OD2 H:ASP113 3.7 0.3 1.0 CG G:ASN154 4.3 0.7 1.0 O G:ASN154 4.4 0.4 1.0 OD1 G:ASN154 4.5 0.6 1.0 CB H:ASP113 4.5 92.6 1.0 OE1 H:GLN31 4.7 96.4 1.0 CB G:ASP158 5.0 0.5 1.0

Calcium binding site 8 out of 8 in the Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Nam Nanobody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Pentameric Ligand-Gated Ion Channel Elic in Complex with A Nam Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca401 b:0.0 occ:1.00 OD1 I:ASP113 2.3 91.8 1.0 ND2 H:ASN154 2.5 0.5 1.0 OD1 H:ASP158 3.0 0.1 1.0 CG I:ASP113 3.1 90.5 1.0 OD1 H:ASN154 3.2 0.7 1.0 CG H:ASN154 3.2 0.9 1.0 OD2 H:ASP158 3.2 0.7 1.0 OD2 I:ASP113 3.4 99.0 1.0 CG H:ASP158 3.5 0.6 1.0 CB I:ASP113 4.4 73.9 1.0 O H:ASN154 4.4 0.9 1.0 NE2 I:GLN31 4.5 76.7 1.0 CB H:ASN154 4.6 0.7 1.0 C H:ASN154 5.0 0.5 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