Chlorine in PDB 5zdq: Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B

The structure of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B, PDB code: 5zdq was solved by T.Shiba, D.K.Inaoka, G.Takahashi, C.Tsuge, Y.Kido, L.Young, S.Ueda, E.O.Balogun, T.Nara, T.Honma, A.Tanaka, M.Inoue, H.Saimoto, S.Harada, A.L.Moore, K.Kita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.89 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	228.017, 137.920, 63.058, 90.00, 106.08, 90.00
R / Rfree (%)	18.5 / 22

The structure of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Chlorine atom in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B (pdb code 5zdq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B, PDB code: 5zdq:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:36.2 occ:1.00 CL A:RNB504 0.0 36.2 1.0 CAT A:RNB504 1.8 32.9 1.0 CAR A:RNB504 2.7 32.2 1.0 CAQ A:RNB504 2.8 32.2 1.0 OAF A:RNB504 2.9 29.8 1.0 CAD A:RNB504 3.1 32.1 1.0 CG2 A:THR219 3.7 28.0 1.0 NE A:ARG118 3.8 23.8 1.0 SG A:CYS119 3.8 33.6 1.0 CD1 A:LEU122 3.9 29.1 1.0 CB A:THR219 4.0 29.5 1.0 CAV A:RNB504 4.0 35.7 1.0 CD A:ARG118 4.1 25.4 1.0 CAU A:RNB504 4.1 32.2 1.0 CZ A:TYR220 4.2 31.4 1.0 OG1 A:THR219 4.2 31.0 1.0 OH A:TYR220 4.3 33.3 1.0 CG A:ARG118 4.3 25.9 1.0 CE2 A:TYR220 4.4 30.2 1.0 CA A:CYS119 4.5 31.0 1.0 CAS A:RNB504 4.6 33.7 1.0 CE1 A:TYR220 4.6 31.9 1.0 CB A:CYS119 4.7 29.8 1.0 CB A:LEU122 4.7 28.6 1.0 N A:CYS119 4.8 31.0 1.0 CD2 A:TYR220 4.9 29.6 1.0 CZ A:ARG118 4.9 23.9 1.0 CG A:LEU122 4.9 28.2 1.0 CA A:ALA216 4.9 28.5 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl504 b:50.8 occ:1.00 CL B:RNB504 0.0 50.8 1.0 CAT B:RNB504 1.8 52.5 1.0 CAR B:RNB504 2.7 52.4 1.0 CAQ B:RNB504 2.8 50.9 1.0 OAF B:RNB504 3.0 52.0 1.0 CAD B:RNB504 3.0 47.1 1.0 CG2 B:THR219 3.3 34.5 1.0 SG B:CYS119 3.8 51.5 1.0 NE B:ARG118 3.9 46.0 1.0 CB B:THR219 3.9 34.3 1.0 CD1 B:LEU122 3.9 47.2 1.0 CAV B:RNB504 4.0 50.8 1.0 CAU B:RNB504 4.1 52.6 1.0 CZ B:TYR220 4.1 38.0 1.0 OH B:TYR220 4.2 40.6 1.0 CD B:ARG118 4.2 46.2 1.0 OG1 B:THR219 4.2 33.8 1.0 CE2 B:TYR220 4.3 37.0 1.0 CA B:CYS119 4.4 47.1 1.0 CB B:CYS119 4.5 48.2 1.0 CAS B:RNB504 4.6 50.7 1.0 CE1 B:TYR220 4.6 37.2 1.0 CG B:ARG118 4.7 45.2 1.0 CB B:LEU122 4.7 45.0 1.0 N B:CYS119 4.8 43.4 1.0 CD2 B:TYR220 4.9 36.3 1.0 CG B:LEU122 4.9 48.0 1.0 CZ B:ARG118 4.9 45.3 1.0 CA B:ALA216 5.0 31.1 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl504 b:45.7 occ:1.00 CL C:RNB504 0.0 45.7 1.0 CAT C:RNB504 1.8 44.9 1.0 CAR C:RNB504 2.7 47.0 1.0 CAQ C:RNB504 2.8 43.6 1.0 OAF C:RNB504 2.9 45.0 1.0 CAD C:RNB504 3.1 41.1 1.0 CG2 C:THR219 3.5 33.9 1.0 SG C:CYS119 3.5 46.7 1.0 CD1 C:LEU122 3.9 43.3 1.0 OH C:TYR220 4.0 45.5 1.0 CAV C:RNB504 4.0 47.8 1.0 CZ C:TYR220 4.1 45.1 1.0 CAU C:RNB504 4.1 45.7 1.0 CB C:THR219 4.1 34.5 1.0 CD C:ARG118 4.2 52.4 1.0 CA C:CYS119 4.2 49.7 1.0 CG C:ARG118 4.3 52.8 1.0 CE2 C:TYR220 4.4 45.7 1.0 CB C:CYS119 4.4 49.9 1.0 OG1 C:THR219 4.4 32.7 1.0 CE1 C:TYR220 4.5 45.4 1.0 CAS C:RNB504 4.6 46.8 1.0 CB C:LEU122 4.7 42.5 1.0 NH2 C:ARG118 4.7 48.0 1.0 N C:CYS119 4.8 47.5 1.0 CG C:LEU122 4.9 43.4 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl504 b:35.5 occ:1.00 CL D:RNB504 0.0 35.5 1.0 CAT D:RNB504 1.8 30.0 1.0 CAR D:RNB504 2.7 27.8 1.0 CAQ D:RNB504 2.7 29.3 1.0 OAF D:RNB504 2.9 26.0 1.0 CAD D:RNB504 3.0 28.6 1.0 CG2 D:THR219 3.4 24.9 1.0 SG D:CYS119 3.8 43.5 1.0 CD1 D:LEU122 3.8 28.5 1.0 CB D:THR219 3.9 26.2 1.0 CD D:ARG118 3.9 38.1 1.0 CAV D:RNB504 4.0 28.4 1.0 CAU D:RNB504 4.0 28.5 1.0 CG D:ARG118 4.0 36.0 1.0 CZ D:TYR220 4.3 31.5 1.0 OG1 D:THR219 4.3 27.2 1.0 OH D:TYR220 4.3 30.1 1.0 CE2 D:TYR220 4.5 31.1 1.0 CAS D:RNB504 4.5 28.4 1.0 NH2 D:ARG118 4.6 39.5 1.0 CA D:CYS119 4.6 37.8 1.0 CB D:LEU122 4.6 27.5 1.0 CE1 D:TYR220 4.6 33.0 1.0 CB D:CYS119 4.7 37.4 1.0 CG D:LEU122 4.8 27.9 1.0 CA D:ALA216 5.0 27.7 1.0

T.Shiba, D.K.Inaoka, G.Takahashi, C.Tsuge, Y.Kido, L.Young, S.Ueda, E.O.Balogun, T.Nara, T.Honma, A.Tanaka, M.Inoue, H.Saimoto, S.Harada, A.L.Moore, K.Kita. Insights Into the Ubiquinol/Dioxygen Binding and Proton Relay Pathways of the Alternative Oxidase. Biochim Biophys Acta V.1860 375 2019BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 30910528
DOI: 10.1016/J.BBABIO.2019.03.008