Calcium in PDB 6wu5: Human Calcium and Integrin Binding Protein 3

The structure of Human Calcium and Integrin Binding Protein 3, PDB code: 6wu5 was solved by G.Dionne, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.32 / 1.88
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	61.752, 61.752, 180.969, 90, 90, 120
R / Rfree (%)	17.8 / 20.6

The structure of Human Calcium and Integrin Binding Protein 3 also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Calcium atom in the Human Calcium and Integrin Binding Protein 3 (pdb code 6wu5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Human Calcium and Integrin Binding Protein 3, PDB code: 6wu5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human Calcium and Integrin Binding Protein 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Calcium and Integrin Binding Protein 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:52.4 occ:1.00 OD1 A:ASN118 2.1 75.3 1.0 O A:TYR122 2.3 45.0 1.0 OD1 A:ASP116 2.4 44.7 1.0 OD2 A:ASP127 2.4 51.6 1.0 O A:HOH346 2.4 58.2 1.0 OD1 A:ASP120 2.4 51.7 1.0 CG A:ASN118 3.1 69.0 1.0 HD21 A:ASN118 3.2 74.1 1.0 CG A:ASP120 3.3 55.1 1.0 H A:ASP120 3.4 52.4 1.0 H A:ASN118 3.4 59.9 1.0 H A:TYR122 3.5 48.4 1.0 C A:TYR122 3.5 40.5 1.0 ND2 A:ASN118 3.5 74.1 1.0 CG A:ASP116 3.5 47.7 1.0 HA A:ASP116 3.5 43.6 1.0 CG A:ASP127 3.6 48.5 1.0 H A:CYS124 3.7 46.7 1.0 OD2 A:ASP120 3.8 61.3 1.0 HA A:ILE123 3.8 38.8 1.0 HB2 A:TYR122 3.9 44.0 1.0 N A:ASN118 4.1 59.9 1.0 CA A:ASP116 4.1 43.6 1.0 H A:ASN119 4.1 59.7 1.0 H A:PHE117 4.2 45.9 1.0 OD1 A:ASP127 4.2 52.7 1.0 N A:TYR122 4.2 48.4 1.0 N A:ASP120 4.2 52.4 1.0 CB A:ASP116 4.2 46.5 1.0 C A:ASP116 4.3 50.0 1.0 CA A:TYR122 4.3 45.5 1.0 HD22 A:ASN118 4.3 74.1 1.0 CB A:ASN118 4.3 62.3 1.0 N A:PHE117 4.3 45.9 1.0 HB2 A:ASP116 4.4 46.5 1.0 N A:CYS124 4.4 46.7 1.0 N A:ILE123 4.4 39.4 1.0 OD2 A:ASP116 4.4 41.6 1.0 HB3 A:CYS124 4.4 57.1 1.0 N A:ASN119 4.4 59.7 1.0 CA A:ILE123 4.5 38.8 1.0 CB A:ASP120 4.5 61.1 1.0 CA A:ASN118 4.5 67.3 1.0 CB A:TYR122 4.6 44.0 1.0 O A:HOH304 4.6 61.0 1.0 C A:ASN118 4.6 65.9 1.0 HB2 A:ASP127 4.6 44.4 1.0 HB3 A:ASP120 4.7 61.1 1.0 CB A:ASP127 4.7 44.4 1.0 H A:ASP121 4.7 48.1 1.0 CA A:ASP120 4.8 65.3 1.0 HB3 A:ASN118 4.8 62.3 1.0 SG A:CYS124 4.8 55.1 1.0 O A:ASP116 4.8 42.2 1.0 HB3 A:TYR122 4.9 44.0 1.0 HB3 A:ASP127 4.9 44.4 1.0 C A:ILE123 4.9 45.1 1.0 N A:ASP121 4.9 48.1 1.0 C A:ASP120 5.0 58.3 1.0 HB2 A:ASN118 5.0 62.3 1.0

Calcium binding site 2 out of 2 in the Human Calcium and Integrin Binding Protein 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Calcium and Integrin Binding Protein 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:54.0 occ:1.00 OD1 B:ASN118 2.3 76.3 1.0 O B:TYR122 2.3 46.3 1.0 OD2 B:ASP127 2.3 49.6 1.0 OD1 B:ASP120 2.4 62.9 1.0 OD1 B:ASP116 2.4 44.8 1.0 O B:HOH371 2.5 50.9 1.0 CG B:ASP120 3.2 63.3 1.0 CG B:ASN118 3.3 64.9 1.0 HD21 B:ASN118 3.4 66.9 1.0 CG B:ASP127 3.5 44.2 1.0 C B:TYR122 3.5 46.0 1.0 H B:ASP120 3.5 60.4 1.0 H B:ASN118 3.5 60.4 1.0 CG B:ASP116 3.5 52.9 1.0 HA B:ASP116 3.6 44.7 1.0 H B:TYR122 3.6 47.5 1.0 OD2 B:ASP120 3.6 65.1 1.0 H B:CYS124 3.6 48.9 1.0 HA B:ILE123 3.7 42.2 1.0 ND2 B:ASN118 3.8 66.9 1.0 OD1 B:ASP127 4.0 48.5 1.0 H B:PHE117 4.2 44.5 1.0 CA B:ASP116 4.2 44.7 1.0 HB2 B:TYR122 4.2 48.9 1.0 O B:HOH330 4.2 61.8 1.0 N B:TYR122 4.3 47.5 1.0 CB B:ASP116 4.3 40.9 1.0 N B:ASP120 4.3 60.4 1.0 N B:ASN118 4.3 60.4 1.0 C B:ASP116 4.3 45.3 1.0 N B:CYS124 4.4 48.9 1.0 CB B:ASP120 4.4 64.6 1.0 N B:ILE123 4.4 43.9 1.0 HB2 B:ASP116 4.4 40.9 1.0 OD2 B:ASP116 4.4 49.3 1.0 N B:PHE117 4.4 44.5 1.0 CA B:ILE123 4.4 42.2 1.0 CA B:TYR122 4.4 49.4 1.0 HB3 B:CYS124 4.5 50.8 1.0 HB3 B:ASP120 4.5 64.6 1.0 H B:ASN119 4.5 57.8 1.0 HB2 B:ASP127 4.6 39.8 1.0 CB B:ASN118 4.6 57.6 1.0 SG B:CYS124 4.6 53.0 1.0 CB B:ASP127 4.6 39.8 1.0 HD22 B:ASN118 4.6 66.9 1.0 H B:ASP121 4.7 49.7 1.0 CA B:ASP120 4.7 68.1 1.0 N B:ASN119 4.8 57.8 1.0 CB B:TYR122 4.8 48.9 1.0 CA B:ASN118 4.9 59.8 1.0 HG B:CYS124 4.9 53.0 1.0 C B:ILE123 4.9 44.0 1.0 HB3 B:ASP127 4.9 39.8 1.0 C B:ASP120 4.9 65.8 1.0 N B:ASP121 4.9 49.7 1.0 C B:ASN118 4.9 63.0 1.0 O B:ASP116 4.9 47.9 1.0

X.Liang, X.Qiu, G.Dionne, C.Cunningham, M.L.Pucak, G.Peng, Y.Kim, A.Lauer, L.Shapiro, U.Mueller. CIB2 and CIB3 Are Auxiliary Subunits of the Mechanotransduction Channel of Hair Cells Neuron 2021.
ISSN: ISSN 0896-6273
DOI: 10.1016/J.NEURON.2021.05.007