Chlorine in PDB 8jgj: Cryo-Em Structure of Mclc-3 with Atp

The binding sites of Chlorine atom in the Cryo-Em Structure of Mclc-3 with Atp (pdb code 8jgj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Cryo-Em Structure of Mclc-3 with Atp, PDB code: 8jgj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Cryo-Em Structure of Mclc-3 with Atp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cryo-Em Structure of Mclc-3 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl902 b:10.4 occ:1.00 HG13 A:ILE528 2.8 13.8 1.0 HB2 A:SER453 2.9 20.6 1.0 HG11 A:VAL273 3.1 11.8 1.0 HA2 A:GLY280 3.3 9.9 1.0 HG2 A:LYS281 3.3 12.5 1.0 H A:LYS281 3.3 12.5 1.0 HG21 A:ILE528 3.4 13.8 1.0 OE2 A:GLU282 3.6 14.1 1.0 CG1 A:ILE528 3.8 13.8 1.0 HG3 A:LYS281 3.8 12.5 1.0 CB A:SER453 3.8 20.6 1.0 CG1 A:VAL273 3.9 11.8 1.0 HG12 A:VAL273 3.9 11.8 1.0 CG A:LYS281 4.0 12.5 1.0 HA3 A:GLY280 4.1 9.9 1.0 CA A:GLY280 4.1 9.9 1.0 HB3 A:SER453 4.1 20.6 1.0 N A:LYS281 4.1 12.5 1.0 H A:SER453 4.1 20.6 1.0 HZ2 A:LYS281 4.1 12.5 1.0 HE3 A:LYS281 4.2 12.5 1.0 HD11 A:ILE528 4.2 13.8 1.0 HG12 A:ILE528 4.2 13.8 1.0 CG2 A:ILE528 4.3 13.8 1.0 HD22 A:ASN451 4.3 21.0 1.0 HG13 A:VAL273 4.3 11.8 1.0 HG22 A:VAL273 4.3 11.8 1.0 HG A:SER453 4.3 20.6 1.0 HG2 A:GLU282 4.4 14.1 1.0 HB A:ILE528 4.4 13.8 1.0 CB A:ILE528 4.4 13.8 1.0 CD1 A:ILE528 4.5 13.8 1.0 OG A:SER453 4.6 20.6 1.0 HG21 A:VAL273 4.6 11.8 1.0 C A:GLY280 4.6 9.9 1.0 HD12 A:ILE528 4.6 13.8 1.0 N A:SER453 4.6 20.6 1.0 HB A:THR452 4.6 16.6 1.0 CD A:GLU282 4.7 14.1 1.0 O A:LEU279 4.7 9.5 1.0 HG22 A:ILE528 4.7 13.8 1.0 CA A:SER453 4.8 20.6 1.0 CG2 A:VAL273 4.8 11.8 1.0 CE A:LYS281 4.8 12.5 1.0 HG23 A:ILE528 4.9 13.8 1.0 NZ A:LYS281 4.9 12.5 1.0 CD A:LYS281 5.0 12.5 1.0 CB A:VAL273 5.0 11.8 1.0 HA A:SER453 5.0 20.6 1.0 CG A:GLU282 5.0 14.1 1.0

Chlorine binding site 2 out of 6 in the Cryo-Em Structure of Mclc-3 with Atp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cryo-Em Structure of Mclc-3 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl903 b:22.0 occ:1.00 HA3 A:GLY238 3.1 9.3 1.0 HA2 A:GLY519 3.2 12.5 1.0 HA2 A:GLY238 3.5 9.3 1.0 CA A:GLY238 3.7 9.3 1.0 HA3 A:GLY519 3.9 12.5 1.0 H A:SER239 4.0 9.1 1.0 CA A:GLY519 4.0 12.5 1.0 ND1 A:HIS633 4.4 9.1 1.0 N A:SER239 4.6 9.1 1.0 CE1 A:HIS633 4.6 9.1 1.0 HD22 A:ASN637 4.6 11.2 1.0 N A:GLY238 4.7 9.3 1.0 C A:GLY238 4.7 9.3 1.0 O A:PHE518 4.8 9.3 1.0 N A:GLY519 4.8 12.5 1.0 H A:ILE520 4.9 11.5 1.0 H A:GLY240 4.9 10.2 1.0

Chlorine binding site 3 out of 6 in the Cryo-Em Structure of Mclc-3 with Atp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cryo-Em Structure of Mclc-3 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl904 b:9.8 occ:1.00 OG A:SER239 2.4 9.1 1.0 HG A:SER239 2.5 9.1 1.0 OH A:TYR630 2.6 11.8 1.0 H A:LEU526 2.6 10.7 1.0 HD12 A:ILE241 2.7 11.6 1.0 HB2 A:SER239 2.9 9.1 1.0 HE1 A:TYR630 2.9 11.8 1.0 CB A:SER239 3.1 9.1 1.0 HA3 A:GLY283 3.1 10.9 1.0 HH A:TYR630 3.2 11.8 1.0 CZ A:TYR630 3.4 11.8 1.0 HB3 A:LEU526 3.4 10.7 1.0 CE1 A:TYR630 3.4 11.8 1.0 HB3 A:SER239 3.4 9.1 1.0 N A:LEU526 3.4 10.7 1.0 HA2 A:GLY525 3.5 8.7 1.0 CD1 A:ILE241 3.6 11.6 1.0 HD11 A:ILE241 3.7 11.6 1.0 HB2 A:LEU526 3.8 10.7 1.0 HA2 A:GLY283 3.9 10.9 1.0 CA A:GLY283 3.9 10.9 1.0 HZ A:PHE518 3.9 9.3 1.0 CB A:LEU526 4.0 10.7 1.0 HB A:ILE241 4.0 11.6 1.0 H A:PHE527 4.1 12.8 1.0 CA A:GLY525 4.2 8.7 1.0 HD13 A:ILE241 4.2 11.6 1.0 HE1 A:PHE518 4.2 9.3 1.0 CA A:LEU526 4.2 10.7 1.0 HA3 A:GLY525 4.3 8.7 1.0 C A:GLY525 4.3 8.7 1.0 HG13 A:ILE241 4.3 11.6 1.0 HD3 A:PRO284 4.4 9.8 1.0 CG1 A:ILE241 4.4 11.6 1.0 CA A:SER239 4.5 9.1 1.0 CZ A:PHE518 4.5 9.3 1.0 C A:GLY283 4.6 10.9 1.0 N A:PHE527 4.6 12.8 1.0 CE2 A:PHE527 4.6 12.8 1.0 HA A:SER239 4.6 9.1 1.0 CE2 A:TYR630 4.6 11.8 1.0 CD2 A:PHE527 4.6 12.8 1.0 CE1 A:PHE518 4.7 9.3 1.0 CD1 A:TYR630 4.7 11.8 1.0 HE2 A:PHE527 4.7 12.8 1.0 CB A:ILE241 4.7 11.6 1.0 HD2 A:PHE527 4.7 12.8 1.0 C A:LEU526 4.7 10.7 1.0 H A:ILE241 4.8 11.6 1.0 HE2 A:TYR630 4.9 11.8 1.0 O A:GLY283 5.0 10.9 1.0 HD3 A:PRO242 5.0 10.5 1.0 H A:GLY283 5.0 10.9 1.0 CZ A:PHE527 5.0 12.8 1.0

Chlorine binding site 4 out of 6 in the Cryo-Em Structure of Mclc-3 with Atp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cryo-Em Structure of Mclc-3 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl902 b:9.5 occ:1.00 HG13 B:ILE528 2.8 13.6 1.0 HB2 B:SER453 3.0 20.2 1.0 HG11 B:VAL273 3.0 11.5 1.0 HA2 B:GLY280 3.3 9.8 1.0 HG21 B:ILE528 3.3 13.6 1.0 H B:LYS281 3.3 12.1 1.0 HG2 B:LYS281 3.3 12.1 1.0 CG1 B:ILE528 3.8 13.6 1.0 OE2 B:GLU282 3.8 13.7 1.0 HG3 B:LYS281 3.8 12.1 1.0 CG1 B:VAL273 3.9 11.5 1.0 HG12 B:VAL273 3.9 11.5 1.0 CB B:SER453 3.9 20.2 1.0 HA3 B:GLY280 4.0 9.8 1.0 CG B:LYS281 4.0 12.1 1.0 CA B:GLY280 4.0 9.8 1.0 N B:LYS281 4.1 12.1 1.0 HB3 B:SER453 4.1 20.2 1.0 H B:SER453 4.1 20.2 1.0 CG2 B:ILE528 4.2 13.6 1.0 HE3 B:LYS281 4.2 12.1 1.0 HG2 B:GLU282 4.2 13.7 1.0 HZ2 B:LYS281 4.2 12.1 1.0 HG12 B:ILE528 4.3 13.6 1.0 HD11 B:ILE528 4.3 13.6 1.0 HG13 B:VAL273 4.3 11.5 1.0 HG22 B:VAL273 4.3 11.5 1.0 HD22 B:ASN451 4.3 20.7 1.0 HB B:ILE528 4.3 13.6 1.0 CB B:ILE528 4.4 13.6 1.0 HG B:SER453 4.4 20.2 1.0 CD1 B:ILE528 4.5 13.6 1.0 HG21 B:VAL273 4.6 11.5 1.0 OG B:SER453 4.6 20.2 1.0 HG22 B:ILE528 4.6 13.6 1.0 C B:GLY280 4.6 9.8 1.0 N B:SER453 4.7 20.2 1.0 HD12 B:ILE528 4.7 13.6 1.0 HB B:THR452 4.7 16.4 1.0 O B:LEU279 4.7 9.4 1.0 CD B:GLU282 4.8 13.7 1.0 HG23 B:ILE528 4.8 13.6 1.0 CG2 B:VAL273 4.8 11.5 1.0 CA B:SER453 4.8 20.2 1.0 CE B:LYS281 4.9 12.1 1.0 CG B:GLU282 4.9 13.7 1.0 CB B:VAL273 5.0 11.5 1.0 NZ B:LYS281 5.0 12.1 1.0

Chlorine binding site 5 out of 6 in the Cryo-Em Structure of Mclc-3 with Atp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Cryo-Em Structure of Mclc-3 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl903 b:22.0 occ:1.00 HA3 B:GLY238 3.1 9.6 1.0 HA2 B:GLY519 3.2 12.3 1.0 HA2 B:GLY238 3.5 9.6 1.0 CA B:GLY238 3.7 9.6 1.0 HA3 B:GLY519 3.9 12.3 1.0 H B:SER239 4.0 9.2 1.0 CA B:GLY519 4.0 12.3 1.0 ND1 B:HIS633 4.4 8.9 1.0 N B:SER239 4.6 9.2 1.0 CE1 B:HIS633 4.6 8.9 1.0 HD22 B:ASN637 4.6 11.1 1.0 N B:GLY238 4.7 9.6 1.0 C B:GLY238 4.7 9.6 1.0 O B:PHE518 4.8 9.4 1.0 N B:GLY519 4.8 12.3 1.0 H B:ILE520 4.9 11.4 1.0 H B:GLY240 4.9 10.1 1.0

Chlorine binding site 6 out of 6 in the Cryo-Em Structure of Mclc-3 with Atp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Cryo-Em Structure of Mclc-3 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl904 b:10.4 occ:1.00 OG B:SER239 2.4 9.2 1.0 HG B:SER239 2.5 9.2 1.0 OH B:TYR630 2.6 11.9 1.0 H B:LEU526 2.6 10.8 1.0 HD12 B:ILE241 2.7 11.5 1.0 HB2 B:SER239 2.9 9.2 1.0 HE1 B:TYR630 2.9 11.9 1.0 HA3 B:GLY283 3.1 10.9 1.0 CB B:SER239 3.1 9.2 1.0 HH B:TYR630 3.2 11.9 1.0 CZ B:TYR630 3.4 11.9 1.0 HB3 B:LEU526 3.4 10.8 1.0 CE1 B:TYR630 3.4 11.9 1.0 HB3 B:SER239 3.4 9.2 1.0 N B:LEU526 3.4 10.8 1.0 HA2 B:GLY525 3.5 8.9 1.0 CD1 B:ILE241 3.6 11.5 1.0 HD11 B:ILE241 3.7 11.5 1.0 HB2 B:LEU526 3.8 10.8 1.0 CA B:GLY283 3.9 10.9 1.0 HZ B:PHE518 3.9 9.4 1.0 HA2 B:GLY283 3.9 10.9 1.0 HB B:ILE241 4.0 11.5 1.0 CB B:LEU526 4.0 10.8 1.0 H B:PHE527 4.1 12.8 1.0 CA B:GLY525 4.2 8.9 1.0 HE1 B:PHE518 4.2 9.4 1.0 HD13 B:ILE241 4.2 11.5 1.0 CA B:LEU526 4.2 10.8 1.0 HD3 B:PRO284 4.3 9.9 1.0 C B:GLY525 4.3 8.9 1.0 HG13 B:ILE241 4.3 11.5 1.0 HA3 B:GLY525 4.3 8.9 1.0 CG1 B:ILE241 4.4 11.5 1.0 CA B:SER239 4.5 9.2 1.0 CZ B:PHE518 4.5 9.4 1.0 C B:GLY283 4.5 10.9 1.0 N B:PHE527 4.6 12.8 1.0 HA B:SER239 4.6 9.2 1.0 CE2 B:TYR630 4.6 11.9 1.0 CE2 B:PHE527 4.6 12.8 1.0 CE1 B:PHE518 4.6 9.4 1.0 CD2 B:PHE527 4.7 12.8 1.0 CD1 B:TYR630 4.7 11.9 1.0 CB B:ILE241 4.7 11.5 1.0 HE2 B:PHE527 4.7 12.8 1.0 HD2 B:PHE527 4.7 12.8 1.0 C B:LEU526 4.8 10.8 1.0 H B:ILE241 4.8 11.5 1.0 H B:GLY283 4.9 10.9 1.0 HE2 B:TYR630 4.9 11.9 1.0 O B:GLY283 4.9 10.9 1.0 N B:GLY283 5.0 10.9 1.0 HD3 B:PRO242 5.0 10.3 1.0

Y.Wan, S.Guo, W.Zhen, L.Xu, X.Chen, F.Liu, Y.Shen, S.Liu, L.Hu, X.Wang, F.Ye, Q.Wang, H.Wen, F.Yang. Structural Basis of Adenine Nucleotides Regulation and Neurodegenerative Pathology in Clc-3 Exchanger. Nat Commun V. 15 6654 2024.
ISSN: ESSN 2041-1723
PubMed: 39107281
DOI: 10.1038/S41467-024-50975-W