Calcium in PDB 8z3f: Complex Structure of CIB2 and TMC1 CR1

The structure of Complex Structure of CIB2 and TMC1 CR1, PDB code: 8z3f was solved by S.Wu, L.Lin, Q.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.52 / 1.74
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.177, 36.225, 63.496, 90, 98.87, 90
R / Rfree (%)	17.7 / 20

The binding sites of Calcium atom in the Complex Structure of CIB2 and TMC1 CR1 (pdb code 8z3f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Complex Structure of CIB2 and TMC1 CR1, PDB code: 8z3f:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Complex Structure of CIB2 and TMC1 CR1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex Structure of CIB2 and TMC1 CR1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:18.8 occ:1.00 OD1 A:ASN118 2.1 21.1 1.0 OD2 A:ASP127 2.2 20.6 1.0 O A:PHE122 2.2 19.6 1.0 OD1 A:ASP116 2.3 15.2 1.0 OD2 A:ASP120 2.3 20.4 1.0 O A:HOH369 2.4 27.9 1.0 CG A:ASP127 3.2 17.9 1.0 CG A:ASP120 3.3 26.8 1.0 CG A:ASN118 3.3 25.5 1.0 CG A:ASP116 3.4 15.8 1.0 C A:PHE122 3.4 14.8 1.0 OD1 A:ASP127 3.6 18.1 1.0 OD1 A:ASP120 3.8 26.1 1.0 ND2 A:ASN118 3.9 30.9 1.0 OD2 A:ASP116 4.1 16.9 1.0 N A:ASP120 4.1 17.4 1.0 N A:PHE122 4.1 14.7 1.0 N A:ILE123 4.3 13.9 1.0 CA A:PHE122 4.3 16.5 1.0 CA A:ASP116 4.3 11.6 1.0 CA A:ILE123 4.3 15.9 1.0 CB A:ASP116 4.3 14.6 1.0 N A:ASN118 4.3 19.7 1.0 N A:CYS124 4.4 15.9 1.0 CB A:ASP120 4.4 22.6 1.0 N A:THR119 4.4 16.4 1.0 SG A:CYS124 4.5 28.2 1.0 CB A:ASP127 4.5 14.3 1.0 C A:ASP116 4.5 15.3 1.0 CB A:ASN118 4.5 16.9 1.0 C A:ASN118 4.5 22.9 1.0 N A:ASN121 4.6 13.7 1.0 CA A:ASP120 4.7 14.5 1.0 CA A:ASN118 4.7 17.9 1.0 CB A:PHE122 4.7 17.0 1.0 N A:PHE117 4.7 13.2 1.0 C A:ILE123 4.8 15.6 1.0 C A:ASP120 4.8 20.2 1.0

Calcium binding site 2 out of 3 in the Complex Structure of CIB2 and TMC1 CR1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex Structure of CIB2 and TMC1 CR1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:40.8 occ:1.00 O A:LYS163 2.3 24.4 1.0 OD2 A:ASP168 2.4 24.2 1.0 OD1 A:ASP157 2.4 45.0 1.0 O A:HOH446 2.5 40.2 1.0 OD1 A:ASP161 2.6 49.2 1.0 CG A:ASP161 3.5 57.8 1.0 C A:LYS163 3.5 21.2 1.0 CG A:ASP157 3.6 38.8 1.0 CG A:ASP168 3.6 23.6 1.0 OD2 A:ASP159 3.7 64.8 1.0 CB A:ASP159 3.8 55.9 1.0 OD2 A:ASP161 3.8 56.9 1.0 N A:GLY165 4.0 16.2 1.0 CA A:LEU164 4.1 20.1 1.0 CG A:ASP159 4.1 72.0 1.0 N A:ASP159 4.2 65.9 1.0 OD1 A:ASP168 4.2 27.8 1.0 N A:LEU164 4.2 19.1 1.0 CA A:ASP157 4.3 42.9 1.0 OD2 A:ASP157 4.4 36.9 1.0 CB A:ASP157 4.4 31.2 1.0 N A:ASP161 4.4 53.6 1.0 N A:GLY160 4.4 52.7 1.0 N A:LYS163 4.5 27.9 1.0 CA A:ASP159 4.5 57.5 1.0 C A:LEU164 4.5 16.2 1.0 N A:LEU158 4.6 43.3 1.0 C A:ASP157 4.6 49.7 1.0 O A:HOH403 4.6 22.7 1.0 CB A:ASP168 4.6 21.2 1.0 CA A:LYS163 4.7 30.2 1.0 CB A:ASP161 4.7 51.3 1.0 CG A:LYS163 4.9 32.3 1.0 C A:ASP159 5.0 65.6 1.0 CD2 A:LEU164 5.0 37.8 1.0

Calcium binding site 3 out of 3 in the Complex Structure of CIB2 and TMC1 CR1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex Structure of CIB2 and TMC1 CR1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:85.7 occ:1.00 N A:ASP143 2.8 17.4 1.0 O A:HOH502 3.1 40.3 1.0 CG A:ASP143 3.1 26.6 1.0 CB A:ASP143 3.1 23.4 1.0 OD1 A:ASN141 3.2 22.9 1.0 OD2 A:ASP143 3.3 28.0 1.0 CG A:ASN141 3.3 26.9 1.0 CA A:ASP143 3.5 16.4 1.0 N A:GLU142 3.6 20.2 1.0 ND2 A:ASN141 3.6 29.9 1.0 OD1 A:ASP143 3.7 27.2 1.0 CB A:GLU142 3.7 27.0 1.0 C A:GLU142 3.7 20.2 1.0 CA A:GLU142 3.9 23.3 1.0 CB A:ASN141 4.1 22.7 1.0 C A:ASN141 4.3 19.9 1.0 O A:HOH389 4.3 33.2 1.0 C A:ASP143 4.6 12.8 1.0 N A:GLU144 4.6 14.2 1.0 CG A:GLU142 4.8 26.7 1.0 CA A:ASN141 4.8 20.9 1.0 O A:GLU142 4.9 16.9 1.0 O A:ASN141 4.9 16.0 1.0 OE1 A:GLU142 5.0 39.2 1.0

S.Wu, L.Lin, Q.Hu, X.Yao, H.Wang, S.Liu, Q.Liu, Y.Xi, Y.Lin, J.Gong, R.Hu, W.Zhan, Y.Luo, G.He, Z.Liu, W.Xiong, Q.Wang, Z.Xu, F.Bai, Q.Lu. Mechano-Electrical Transduction Components TMC1-CIB2 Undergo A Ca 2+ -Induced Conformational Change Linked to Hearing Loss. Dev.Cell 2025.
ISSN: ISSN 1534-5807
PubMed: 39889697
DOI: 10.1016/J.DEVCEL.2025.01.004