Chlorine in PDB 8ijv: Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-02

The structure of Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-02 also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Fluorine	(F)	3 atoms

The binding sites of Chlorine atom in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-02 (pdb code 8ijv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-02, PDB code: 8ijv:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-02


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 the Gastric Proton Pump with Bound Dq-02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1106 b:55.3 occ:0.46 CL1 A:PWI1106 0.0 55.3 0.5 CL2 A:PWI1106 0.5 57.8 0.5 C10 A:PWI1106 1.6 48.5 0.5 C04 A:PWI1106 1.7 46.6 0.5 C09 A:PWI1106 2.4 42.8 0.5 C03 A:PWI1106 2.7 41.3 0.5 C05 A:PWI1106 2.7 47.6 0.5 C11 A:PWI1106 2.8 46.7 0.5 O A:LEU811 3.1 38.8 1.0 O A:HOH1294 3.6 47.8 1.0 C08 A:PWI1106 3.7 43.0 0.5 N A:CYS813 3.9 35.9 1.0 CD1 A:ILE816 4.0 28.6 1.0 C A:GLY812 4.0 29.4 1.0 C02 A:PWI1106 4.0 41.9 0.5 C06 A:PWI1106 4.0 46.5 0.5 C12 A:PWI1106 4.0 46.3 0.5 O A:HOH1228 4.1 60.9 1.0 C A:LEU811 4.2 29.2 1.0 CA A:GLY812 4.2 22.7 1.0 C07 A:PWI1106 4.4 45.9 0.5 CD2 A:LEU809 4.4 31.4 1.0 CD1 A:LEU809 4.4 24.1 1.0 CD1 A:TYR799 4.4 32.9 1.0 CA A:CYS813 4.4 42.6 1.0 O A:GLY812 4.5 37.9 1.0 C01 A:PWI1106 4.5 44.5 0.5 N A:GLY812 4.6 23.8 1.0 CB A:CYS813 4.8 38.1 1.0 C13 A:PWI1106 4.8 42.2 0.5 CG A:LEU809 4.8 30.4 1.0 CB A:TYR799 4.9 30.6 1.0 O01 A:PWI1106 5.0 45.3 0.5 CG A:TYR799 5.0 33.6 1.0

Chlorine binding site 2 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-02


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 the Gastric Proton Pump with Bound Dq-02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1106 b:65.2 occ:0.54 CL1 A:PWI1106 0.0 65.2 0.5 CL2 A:PWI1106 0.2 61.9 0.5 C10 A:PWI1106 1.6 47.4 0.5 C04 A:PWI1106 1.7 47.7 0.5 C11 A:PWI1106 2.5 47.0 0.5 C09 A:PWI1106 2.6 46.2 0.5 C05 A:PWI1106 2.7 46.0 0.5 C03 A:PWI1106 2.7 47.0 0.5 ND2 A:ASN138 3.4 54.7 1.0 CB A:ALA123 3.5 55.5 1.0 CA A:CYS120 3.8 46.0 1.0 C12 A:PWI1106 3.8 46.5 0.5 C08 A:PWI1106 3.9 43.4 0.5 C06 A:PWI1106 4.0 45.5 0.5 C02 A:PWI1106 4.0 46.6 0.5 O A:MET334 4.0 51.5 1.0 SG A:CYS120 4.0 55.4 1.0 CG2 A:VAL338 4.1 40.7 1.0 CA A:ALA335 4.1 42.2 1.0 O A:ILE119 4.2 52.2 1.0 N A:ALA335 4.2 47.1 1.0 C A:MET334 4.2 49.3 1.0 CG A:ASN138 4.2 58.9 1.0 N A:CYS120 4.3 44.1 1.0 C07 A:PWI1106 4.4 46.1 0.5 CB A:VAL338 4.4 41.2 1.0 CB A:CYS120 4.4 46.6 1.0 C A:ILE119 4.5 45.0 1.0 C01 A:PWI1106 4.5 46.3 0.5 O A:CYS120 4.6 53.5 1.0 OD1 A:ASN138 4.7 64.5 1.0 CG2 A:ILE119 4.7 44.6 1.0 C A:CYS120 4.7 48.2 1.0 CB A:ALA335 4.8 42.2 1.0 CB A:MET334 4.8 49.7 1.0 CG1 A:VAL338 4.8 39.1 1.0 CA A:ALA123 5.0 59.5 1.0

Chlorine binding site 3 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-02


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 the Gastric Proton Pump with Bound Dq-02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1106 b:61.9 occ:0.46 CL2 A:PWI1106 0.0 61.9 0.5 CL1 A:PWI1106 0.2 65.2 0.5 C10 A:PWI1106 1.7 47.4 0.5 C04 A:PWI1106 1.9 47.7 0.5 C09 A:PWI1106 2.7 46.2 0.5 C11 A:PWI1106 2.7 47.0 0.5 C03 A:PWI1106 2.8 47.0 0.5 C05 A:PWI1106 2.9 46.0 0.5 CB A:ALA123 3.5 55.5 1.0 ND2 A:ASN138 3.5 54.7 1.0 CA A:CYS120 3.8 46.0 1.0 O A:MET334 3.8 51.5 1.0 CG2 A:VAL338 3.9 40.7 1.0 C08 A:PWI1106 4.0 43.4 0.5 C12 A:PWI1106 4.0 46.5 0.5 CA A:ALA335 4.0 42.2 1.0 C A:MET334 4.0 49.3 1.0 N A:ALA335 4.0 47.1 1.0 O A:ILE119 4.0 52.2 1.0 C02 A:PWI1106 4.1 46.6 0.5 SG A:CYS120 4.1 55.4 1.0 C06 A:PWI1106 4.2 45.5 0.5 N A:CYS120 4.2 44.1 1.0 CB A:VAL338 4.3 41.2 1.0 C A:ILE119 4.4 45.0 1.0 CG A:ASN138 4.4 58.9 1.0 CG2 A:ILE119 4.5 44.6 1.0 CB A:CYS120 4.5 46.6 1.0 C07 A:PWI1106 4.5 46.1 0.5 CB A:MET334 4.5 49.7 1.0 C01 A:PWI1106 4.7 46.3 0.5 O A:CYS120 4.7 53.5 1.0 CB A:ALA335 4.7 42.2 1.0 C A:CYS120 4.8 48.2 1.0 CG1 A:VAL338 4.8 39.1 1.0 OD1 A:ASN138 4.9 64.5 1.0 CA A:MET334 4.9 52.4 1.0 CA A:ALA123 4.9 59.5 1.0

Chlorine binding site 4 out of 4 in the Cryo-Em Structure of the Gastric Proton Pump with Bound Dq-02


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 the Gastric Proton Pump with Bound Dq-02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1106 b:57.8 occ:0.54 CL2 A:PWI1106 0.0 57.8 0.5 CL1 A:PWI1106 0.5 55.3 0.5 C10 A:PWI1106 1.7 48.5 0.5 C04 A:PWI1106 1.9 46.6 0.5 C05 A:PWI1106 2.7 47.6 0.5 C09 A:PWI1106 2.7 42.8 0.5 C11 A:PWI1106 2.7 46.7 0.5 O A:LEU811 3.0 38.8 1.0 C03 A:PWI1106 3.0 41.3 0.5 O A:HOH1228 3.6 60.9 1.0 N A:CYS813 3.7 35.9 1.0 C A:GLY812 3.9 29.4 1.0 CA A:GLY812 3.9 22.7 1.0 CD2 A:LEU809 4.0 31.4 1.0 C12 A:PWI1106 4.0 46.3 0.5 C08 A:PWI1106 4.0 43.0 0.5 O A:HOH1294 4.0 47.8 1.0 C06 A:PWI1106 4.0 46.5 0.5 C A:LEU811 4.0 29.2 1.0 CD1 A:LEU809 4.2 24.1 1.0 C02 A:PWI1106 4.3 41.9 0.5 CD1 A:ILE816 4.3 28.6 1.0 CA A:CYS813 4.4 42.6 1.0 N A:GLY812 4.5 23.8 1.0 CG A:LEU809 4.5 30.4 1.0 O A:GLY812 4.5 37.9 1.0 C07 A:PWI1106 4.5 45.9 0.5 CD1 A:TYR799 4.6 32.9 1.0 CB A:CYS813 4.7 38.1 1.0 C01 A:PWI1106 4.7 44.5 0.5

K.Abe, S.Yokoshima, A.Yoshimori. Deep Learning Driven De Novo Drug Design Based on Gastric Proton Pump Structures To Be Published.