Copper in PDB 7deg: Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism

The structure of Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Copper atom in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism (pdb code 7deg). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism, PDB code: 7deg:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu603 b:55.8 occ:1.00 CE1 A:HIS273 1.2 32.6 1.0 CE1 A:HIS222 1.8 30.1 1.0 ND1 A:HIS222 1.9 30.1 1.0 NE2 A:HIS273 1.9 32.6 1.0 NE2 A:HIS274 2.1 30.5 1.0 NE2 A:HIS222 2.2 30.1 1.0 CG A:HIS222 2.3 30.1 1.0 ND1 A:HIS273 2.3 32.6 1.0 CD2 A:HIS222 2.5 30.1 1.0 CD2 A:HIS274 2.6 30.5 1.0 CD2 A:HIS273 3.0 32.6 1.0 CG A:HIS273 3.2 32.6 1.0 CE1 A:HIS274 3.3 30.5 1.0 CB A:HIS222 3.5 30.1 1.0 CG A:HIS274 3.8 30.5 1.0 O A:VAL270 4.0 32.8 1.0 ND1 A:HIS274 4.1 30.5 1.0 CG2 A:VAL270 4.3 32.8 1.0 C1D A:HAS601 4.4 24.4 1.0 CA A:GLY271 4.6 32.1 1.0 C A:VAL270 4.6 32.8 1.0 CB A:HIS273 4.6 32.6 1.0 CA A:HIS222 4.6 30.1 1.0 ND A:HAS601 4.7 24.4 1.0 C2D A:HAS601 4.7 24.4 1.0 CHB A:HAS601 4.7 24.4 1.0 CG1 A:VAL270 4.7 32.8 1.0 N A:HIS274 4.8 30.5 1.0 C A:HIS273 4.8 32.6 1.0 OH A:TYR226 4.9 25.7 1.0 C4D A:HAS601 4.9 24.4 1.0 CG2 A:THR293 5.0 32.3 1.0

Copper binding site 2 out of 6 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu600 b:34.5 occ:1.00 CU1 B:CUA600 0.0 34.5 1.0 ND1 B:HIS139 1.8 25.9 1.0 CE1 B:HIS139 2.2 25.9 1.0 O B:GLU133 2.5 29.9 1.0 CU2 B:CUA600 2.7 34.5 1.0 SG B:CYS135 2.8 28.1 1.0 SG B:CYS131 2.8 23.6 1.0 CB B:CYS135 3.1 28.1 1.0 CG B:HIS139 3.1 25.9 1.0 NE2 B:HIS139 3.4 25.9 1.0 N B:CYS135 3.4 28.1 1.0 C B:GLU133 3.7 29.9 1.0 CD2 B:HIS139 3.8 25.9 1.0 CA B:CYS135 3.8 28.1 1.0 C B:PHE134 3.9 26.3 1.0 CB B:HIS139 3.9 25.9 1.0 ND1 B:HIS96 4.0 31.1 1.0 CB B:CYS131 4.1 23.6 1.0 CA B:PHE134 4.1 26.3 1.0 CE1 B:HIS96 4.3 31.1 1.0 N B:PHE134 4.4 26.3 1.0 O B:CYS131 4.4 23.6 1.0 O B:PHE134 4.6 26.3 1.0 CA B:HIS139 4.6 25.9 1.0 C B:CYS131 4.7 23.6 1.0 C B:CYS135 4.8 28.1 1.0 CA B:GLU133 4.8 29.9 1.0 O B:HIS132 4.8 25.2 1.0 C B:HIS132 4.8 25.2 1.0 N B:GLU133 4.9 29.9 1.0 SD B:MET142 4.9 26.6 1.0 O B:HIS139 4.9 25.9 1.0

Copper binding site 3 out of 6 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu600 b:34.5 occ:1.00 CU2 B:CUA600 0.0 34.5 1.0 ND1 B:HIS96 1.8 31.1 1.0 CE1 B:HIS96 2.0 31.1 1.0 CU1 B:CUA600 2.7 34.5 1.0 SD B:MET142 2.7 26.6 1.0 SG B:CYS135 2.8 28.1 1.0 CE B:MET142 3.0 26.6 1.0 SG B:CYS131 3.0 23.6 1.0 CG B:HIS96 3.2 31.1 1.0 NE2 B:HIS96 3.3 31.1 1.0 CB B:CYS135 3.3 28.1 1.0 CD2 B:HIS96 3.8 31.1 1.0 CG B:MET142 3.9 26.6 1.0 CB B:CYS131 4.0 23.6 1.0 ND1 B:HIS139 4.0 25.9 1.0 CB B:HIS96 4.1 31.1 1.0 CA B:HIS96 4.5 31.1 1.0 CB B:MET142 4.5 26.6 1.0 CE1 B:HIS139 4.5 25.9 1.0 CA B:CYS135 4.8 28.1 1.0 N B:TRP66 4.8 31.4 1.0 O B:GLU133 4.9 29.9 1.0 O B:ARG64 4.9 36.0 1.0

Copper binding site 4 out of 6 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu604 b:55.8 occ:1.00 CE1 D:HIS273 1.2 32.6 1.0 CE1 D:HIS222 1.8 30.1 1.0 ND1 D:HIS222 1.9 30.1 1.0 NE2 D:HIS273 1.9 32.6 1.0 NE2 D:HIS274 2.1 30.5 1.0 NE2 D:HIS222 2.2 30.1 1.0 CG D:HIS222 2.3 30.1 1.0 ND1 D:HIS273 2.3 32.6 1.0 CD2 D:HIS222 2.5 30.1 1.0 CD2 D:HIS274 2.6 30.5 1.0 CD2 D:HIS273 3.0 32.6 1.0 CG D:HIS273 3.2 32.6 1.0 CE1 D:HIS274 3.3 30.5 1.0 CB D:HIS222 3.5 30.1 1.0 CG D:HIS274 3.8 30.5 1.0 O D:VAL270 4.0 32.8 1.0 ND1 D:HIS274 4.1 30.5 1.0 CG2 D:VAL270 4.3 32.8 1.0 C1D D:HAS602 4.4 24.4 1.0 CA D:GLY271 4.6 32.1 1.0 C D:VAL270 4.6 32.8 1.0 CB D:HIS273 4.6 32.6 1.0 CA D:HIS222 4.6 30.1 1.0 ND D:HAS602 4.7 24.4 1.0 C2D D:HAS602 4.7 24.4 1.0 CHB D:HAS602 4.7 24.4 1.0 CG1 D:VAL270 4.7 32.8 1.0 N D:HIS274 4.8 30.5 1.0 C D:HIS273 4.8 32.6 1.0 OH D:TYR226 4.9 25.7 1.0 C4D D:HAS602 4.9 24.4 1.0 CG2 D:THR293 5.0 32.3 1.0

Copper binding site 5 out of 6 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu600 b:34.5 occ:1.00 CU1 E:CUA600 0.0 34.5 1.0 ND1 E:HIS139 1.8 25.9 1.0 CE1 E:HIS139 2.2 25.9 1.0 O E:GLU133 2.5 29.9 1.0 CU2 E:CUA600 2.7 34.5 1.0 SG E:CYS135 2.8 28.1 1.0 SG E:CYS131 2.8 23.6 1.0 CB E:CYS135 3.1 28.1 1.0 CG E:HIS139 3.1 25.9 1.0 NE2 E:HIS139 3.4 25.9 1.0 N E:CYS135 3.4 28.1 1.0 C E:GLU133 3.7 29.9 1.0 CD2 E:HIS139 3.8 25.9 1.0 CA E:CYS135 3.8 28.1 1.0 C E:PHE134 3.9 26.3 1.0 CB E:HIS139 3.9 25.9 1.0 ND1 E:HIS96 4.0 31.1 1.0 CB E:CYS131 4.1 23.6 1.0 CA E:PHE134 4.1 26.3 1.0 CE1 E:HIS96 4.3 31.1 1.0 N E:PHE134 4.4 26.3 1.0 O E:CYS131 4.4 23.6 1.0 O E:PHE134 4.6 26.3 1.0 CA E:HIS139 4.6 25.9 1.0 C E:CYS131 4.7 23.6 1.0 C E:CYS135 4.8 28.1 1.0 CA E:GLU133 4.8 29.9 1.0 O E:HIS132 4.8 25.2 1.0 C E:HIS132 4.8 25.2 1.0 N E:GLU133 4.9 29.9 1.0 SD E:MET142 4.9 26.6 1.0 O E:HIS139 4.9 25.9 1.0

Copper binding site 6 out of 6 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu600 b:34.5 occ:1.00 CU2 E:CUA600 0.0 34.5 1.0 ND1 E:HIS96 1.8 31.1 1.0 CE1 E:HIS96 2.0 31.1 1.0 CU1 E:CUA600 2.7 34.5 1.0 SD E:MET142 2.7 26.6 1.0 SG E:CYS135 2.8 28.1 1.0 CE E:MET142 3.0 26.6 1.0 SG E:CYS131 3.0 23.6 1.0 CG E:HIS96 3.2 31.1 1.0 NE2 E:HIS96 3.3 31.1 1.0 CB E:CYS135 3.3 28.1 1.0 CD2 E:HIS96 3.8 31.1 1.0 CG E:MET142 3.9 26.6 1.0 CB E:CYS131 4.0 23.6 1.0 ND1 E:HIS139 4.0 25.9 1.0 CB E:HIS96 4.1 31.1 1.0 CA E:HIS96 4.5 31.1 1.0 CB E:MET142 4.5 26.6 1.0 CE1 E:HIS139 4.5 25.9 1.0 CA E:CYS135 4.8 28.1 1.0 N E:TRP66 4.8 31.4 1.0 O E:GLU133 4.8 29.9 1.0 O E:ARG64 4.9 36.0 1.0

G.Zhu, H.Zeng, S.Zhang, J.Juli, L.Tai, D.Zhang, X.Pang, Y.Zhang, S.M.Lam, Y.Zhu, G.Peng, H.Michel, F.Sun. The Unusual Homodimer of A Heme-Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors. Angew.Chem.Int.Ed.Engl. V. 60 13323 2021.
ISSN: ESSN 1521-3773
PubMed: 33665933
DOI: 10.1002/ANIE.202016785