Copper in PDB 9i7u: Cryo-Em Structure of NDUFA4 Bound Complex IV Within the Respirasome Complex

All present enzymatic activity of Cryo-Em Structure of NDUFA4 Bound Complex IV Within the Respirasome Complex:
7.1.1.9;

The structure of Cryo-Em Structure of NDUFA4 Bound Complex IV Within the Respirasome Complex also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Zinc	(Zn)	1 atom
Magnesium	(Mg)	1 atom

The binding sites of Copper atom in the Cryo-Em Structure of NDUFA4 Bound Complex IV Within the Respirasome Complex (pdb code 9i7u). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Cryo-Em Structure of NDUFA4 Bound Complex IV Within the Respirasome Complex, PDB code: 9i7u:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in the Cryo-Em Structure of NDUFA4 Bound Complex IV Within the Respirasome Complex


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 NDUFA4 Bound Complex IV Within the Respirasome Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu601 b:111.1 occ:1.00 HE1 A:HIS290 1.2 60.6 1.0 NE2 A:HIS291 1.4 69.4 1.0 CE1 A:HIS291 2.0 56.7 1.0 HD1 A:HIS240 2.0 60.4 1.0 CE1 A:HIS290 2.0 59.2 1.0 ND1 A:HIS240 2.0 59.9 1.0 HE1 A:HIS291 2.1 54.5 1.0 CE1 A:HIS240 2.3 60.0 1.0 HE1 A:HIS240 2.4 58.8 1.0 CD2 A:HIS291 2.7 64.3 1.0 CG A:HIS240 2.9 53.6 1.0 NE2 A:HIS290 3.0 51.2 1.0 ND1 A:HIS290 3.0 54.4 1.0 ND1 A:HIS291 3.1 57.9 1.0 HD1 A:HIS290 3.1 56.1 1.0 NE2 A:HIS240 3.1 68.7 1.0 HD2 A:HIS291 3.2 62.5 1.0 CG A:HIS291 3.5 62.5 1.0 CD2 A:HIS240 3.5 64.2 1.0 HB2 A:HIS240 3.6 53.8 1.0 HE2 A:HIS240 3.8 69.3 1.0 CB A:HIS240 3.8 49.3 1.0 HD1 A:HIS291 3.8 56.0 1.0 HA A:HIS240 3.9 59.0 1.0 CD2 A:HIS290 4.1 61.7 1.0 CG A:HIS290 4.1 56.8 1.0 HD2 A:HIS240 4.3 63.0 1.0 ND A:HEA604 4.3 64.3 1.0 CA A:HIS240 4.4 55.8 1.0 NA A:HEA604 4.6 60.0 1.0 HB3 A:HIS240 4.6 54.2 1.0 C1D A:HEA604 4.6 51.5 1.0 FE A:HEA604 4.6 72.8 1.0 HG21 A:VAL243 4.6 59.0 1.0 C4D A:HEA604 4.7 73.8 1.0 HA A:TRP288 4.8 60.2 1.0 CHD A:HEA604 4.9 55.3 1.0 CB A:HIS291 4.9 60.0 1.0 HD2 A:HIS290 4.9 63.4 1.0 O A:VAL287 5.0 57.7 1.0

Copper binding site 2 out of 3 in the Cryo-Em Structure of NDUFA4 Bound Complex IV Within the Respirasome Complex


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 NDUFA4 Bound Complex IV Within the Respirasome Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu301 b:162.8 occ:1.00 SG B:CYS196 2.1 74.2 1.0 HD1 B:HIS161 2.1 73.8 1.0 HE2 B:MET207 2.3 74.7 1.0 HB3 B:HIS161 2.6 68.7 1.0 HB2 B:CYS196 2.6 74.6 1.0 HE1 B:MET207 2.7 71.5 1.0 CU B:CU302 2.7 175.7 1.0 H B:SER162 2.8 65.0 1.0 CE B:MET207 2.8 71.1 1.0 ND1 B:HIS161 2.8 76.1 1.0 CB B:CYS196 2.9 78.1 1.0 HA B:HIS161 3.1 67.4 1.0 SD B:MET207 3.2 90.2 1.0 CB B:HIS161 3.2 66.3 1.0 CG B:HIS161 3.3 64.3 1.0 HZ2 B:TRP106 3.3 61.5 1.0 HB3 B:CYS196 3.5 74.4 1.0 N B:SER162 3.5 62.0 1.0 CA B:HIS161 3.6 66.2 1.0 SG B:CYS200 3.7 81.6 1.0 HE3 B:MET207 3.7 73.0 1.0 CZ2 B:TRP106 3.8 63.8 1.0 HG3 B:MET207 3.8 79.0 1.0 CE1 B:HIS161 3.9 77.3 1.0 HH2 B:TRP106 3.9 64.7 1.0 HB3 B:CYS200 3.9 72.8 1.0 HA B:CYS196 4.0 69.8 1.0 O B:SER162 4.0 72.3 1.0 C B:HIS161 4.0 72.6 1.0 CA B:CYS196 4.1 70.3 1.0 CH2 B:TRP106 4.1 67.0 1.0 HB2 B:HIS161 4.1 68.9 1.0 CG B:MET207 4.2 85.0 1.0 HE1 B:HIS161 4.2 77.6 1.0 H B:SER197 4.3 72.2 1.0 O B:GLU198 4.3 59.3 1.0 CB B:CYS200 4.4 74.3 1.0 CD2 B:HIS161 4.5 67.9 1.0 HD1 B:HIS204 4.6 72.3 1.0 HB2 B:CYS200 4.6 73.3 1.0 CE2 B:TRP106 4.6 61.6 1.0 CA B:SER162 4.7 61.3 1.0 C B:SER162 4.7 66.5 1.0 N B:SER197 4.7 69.0 1.0 NE2 B:HIS161 4.8 74.4 1.0 HG2 B:MET207 4.8 79.4 1.0 C B:CYS196 4.8 68.3 1.0 HB3 B:SER162 4.8 68.0 1.0 H B:GLU198 4.8 69.8 1.0 HB2 B:MET207 4.9 76.5 1.0 N B:HIS161 4.9 69.7 1.0 HE1 B:HIS204 4.9 71.2 1.0

Copper binding site 3 out of 3 in the Cryo-Em Structure of NDUFA4 Bound Complex IV Within the Respirasome Complex


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 NDUFA4 Bound Complex IV Within the Respirasome Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu302 b:175.7 occ:1.00 SD B:MET207 2.0 90.2 1.0 SG B:CYS196 2.2 74.2 1.0 HB3 B:CYS196 2.3 74.4 1.0 HG3 B:MET207 2.4 79.0 1.0 SG B:CYS200 2.5 81.6 1.0 CG B:MET207 2.5 85.0 1.0 CB B:CYS196 2.5 78.1 1.0 HD1 B:HIS204 2.6 72.3 1.0 HG2 B:MET207 2.6 79.4 1.0 HB2 B:CYS196 2.7 74.6 1.0 CU B:CU301 2.7 162.8 1.0 O B:HIS204 3.1 76.7 1.0 HE2 B:MET207 3.2 74.7 1.0 CE B:MET207 3.2 71.1 1.0 ND1 B:HIS204 3.4 74.4 1.0 HA B:HIS204 3.4 66.5 1.0 HE1 B:MET207 3.6 71.5 1.0 HD1 B:HIS161 3.7 73.8 1.0 HE1 B:HIS204 3.9 71.2 1.0 C B:HIS204 3.9 67.6 1.0 HE3 B:MET207 4.0 73.0 1.0 CA B:CYS196 4.0 70.3 1.0 CB B:MET207 4.0 77.0 1.0 CE1 B:HIS204 4.0 73.0 1.0 CA B:HIS204 4.1 63.3 1.0 CB B:CYS200 4.2 74.3 1.0 HB3 B:CYS200 4.3 72.8 1.0 HB2 B:MET207 4.3 76.5 1.0 O B:GLU198 4.3 59.3 1.0 HB3 B:MET207 4.4 77.4 1.0 HD1 B:TRP104 4.4 70.3 1.0 H B:CYS196 4.4 76.6 1.0 ND1 B:HIS161 4.4 76.1 1.0 C B:CYS196 4.5 68.3 1.0 CG B:HIS204 4.5 57.3 1.0 HA B:CYS196 4.5 69.8 1.0 HB2 B:CYS200 4.5 73.3 1.0 HE1 A:TYR440 4.6 70.3 1.0 OH A:TYR440 4.7 66.4 1.0 O B:MET207 4.7 80.2 1.0 O B:ASN203 4.7 72.7 1.0 N B:CYS196 4.8 78.2 1.0 HE1 B:HIS161 4.8 77.6 1.0 HA B:TRP104 4.8 79.2 1.0 H B:MET207 4.8 75.7 1.0 CB B:HIS204 4.9 64.3 1.0 HZ2 B:TRP106 4.9 61.5 1.0 O B:CYS196 4.9 77.8 1.0 H B:PHE206 5.0 70.0 1.0 H B:CYS200 5.0 67.4 1.0 H B:SER197 5.0 72.2 1.0 N B:SER197 5.0 69.0 1.0

M.D.Nguyen, J.Rorbach. Structural Basis For Late Maturation Steps of Mitochondrial Respiratory Chain Complex IV Within the Human Respirasome To Be Published.