Copper in PDB 9i6f: Cryo-Em Structure of HIGD2A Bound Complex IV

All present enzymatic activity of Cryo-Em Structure of HIGD2A Bound Complex IV:
7.1.1.9;

The structure of Cryo-Em Structure of HIGD2A Bound Complex IV also contains other interesting chemical elements:

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

The binding sites of Copper atom in the Cryo-Em Structure of HIGD2A Bound Complex IV (pdb code 9i6f). 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 HIGD2A Bound Complex IV, PDB code: 9i6f:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in the Cryo-Em Structure of HIGD2A Bound Complex IV


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 HIGD2A Bound Complex IV within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu601 b:114.8 occ:1.00 ND1 A:HIS240 2.0 48.4 1.0 NE2 A:HIS291 2.0 53.2 1.0 NE2 A:HIS290 2.0 56.7 1.0 CE1 A:HIS240 2.3 59.5 1.0 HE1 A:HIS240 2.3 60.5 1.0 CE1 A:HIS291 2.7 53.6 1.0 HE1 A:HIS291 2.8 52.8 1.0 CE1 A:HIS290 2.9 63.0 1.0 HE1 A:HIS290 3.0 63.0 1.0 CG A:HIS240 3.0 46.6 1.0 CD2 A:HIS291 3.1 46.2 1.0 CD2 A:HIS290 3.1 53.8 1.0 NE2 A:HIS240 3.3 66.9 1.0 HD2 A:HIS290 3.4 56.9 1.0 HD2 A:HIS291 3.4 52.0 1.0 HB2 A:HIS240 3.7 52.1 1.0 CD2 A:HIS240 3.7 59.8 1.0 HA A:HIS240 3.8 61.5 1.0 ND1 A:HIS291 3.9 55.0 1.0 CB A:HIS240 3.9 49.0 1.0 HG22 A:VAL243 3.9 60.5 1.0 HE2 A:HIS240 4.0 61.3 0.0 ND1 A:HIS290 4.0 59.0 1.0 CG A:HIS291 4.1 52.8 1.0 NA A:HEA605 4.1 49.5 1.0 CG A:HIS290 4.1 46.7 1.0 FE A:HEA605 4.2 70.0 1.0 C1A A:HEA605 4.3 45.8 1.0 CA A:HIS240 4.4 60.4 1.0 C4A A:HEA605 4.4 40.8 1.0 ND A:HEA605 4.5 51.6 1.0 HD2 A:HIS240 4.6 59.9 1.0 HD1 A:HIS291 4.6 54.8 0.0 CHA A:HEA605 4.7 51.1 1.0 HB3 A:HIS240 4.7 52.8 1.0 C4D A:HEA605 4.7 51.8 1.0 HG12 A:VAL243 4.7 56.1 1.0 HD1 A:HIS290 4.7 59.0 0.0 C2A A:HEA605 4.8 43.9 1.0 CG2 A:VAL243 4.8 62.4 1.0 NB A:HEA605 4.8 52.9 1.0 HE2 A:TYR244 4.9 47.0 1.0 C3A A:HEA605 4.9 42.6 1.0 HG13 A:VAL243 4.9 55.5 1.0 HG21 A:VAL243 5.0 61.9 1.0 CHB A:HEA605 5.0 45.7 1.0

Copper binding site 2 out of 3 in the Cryo-Em Structure of HIGD2A Bound Complex IV


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 HIGD2A Bound Complex IV within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu301 b:120.5 occ:1.00 HD2 B:HIS204 1.4 73.8 1.0 CD2 B:HIS204 2.0 73.9 1.0 SG B:CYS200 2.1 89.7 1.0 O B:GLU198 2.1 69.7 1.0 SG B:CYS196 2.5 94.1 1.0 CU B:CU302 2.7 128.4 1.0 NE2 B:HIS204 2.8 63.6 1.0 HA B:HIS204 3.0 67.3 1.0 CG B:HIS204 3.1 59.8 1.0 H B:CYS200 3.1 71.7 1.0 C B:GLU198 3.2 71.1 1.0 CB B:CYS200 3.3 74.7 1.0 HB3 B:CYS196 3.3 78.1 1.0 HB3 B:CYS200 3.3 72.3 1.0 N B:CYS200 3.3 70.5 1.0 HA B:ILE199 3.4 71.5 1.0 H B:GLU198 3.5 76.8 1.0 CB B:CYS196 3.5 77.6 1.0 SD B:MET207 3.6 92.2 1.0 O B:HIS204 3.6 80.9 1.0 CA B:HIS204 3.7 65.8 1.0 CB B:HIS204 3.8 63.6 1.0 C B:ILE199 3.8 66.4 1.0 CA B:CYS200 3.9 67.2 1.0 CE1 B:HIS204 3.9 53.6 1.0 CA B:ILE199 3.9 70.0 1.0 HB2 B:HIS204 3.9 66.8 1.0 N B:ILE199 4.0 71.9 1.0 ND1 B:HIS204 4.0 53.5 1.0 HB2 B:CYS196 4.0 77.1 1.0 HB2 B:CYS200 4.1 72.4 1.0 N B:GLU198 4.1 79.7 1.0 C B:HIS204 4.1 73.3 1.0 HD1 B:HIS161 4.2 70.9 0.0 HE1 A:TYR440 4.2 72.1 1.0 CA B:GLU198 4.3 69.2 1.0 HE2 B:MET207 4.3 73.7 1.0 HG3 B:MET207 4.4 75.3 1.0 HE1 B:MET207 4.4 70.3 1.0 CE B:MET207 4.4 68.3 1.0 HB3 B:GLU198 4.5 72.1 1.0 CG B:MET207 4.5 75.1 1.0 HG2 B:MET207 4.6 76.4 1.0 HA B:CYS200 4.6 67.7 1.0 O B:ILE199 4.7 68.9 1.0 C B:CYS196 4.7 66.5 1.0 HB3 B:HIS204 4.7 69.1 1.0 HE1 B:HIS204 4.7 61.0 1.0 CA B:CYS196 4.7 65.4 1.0 C B:CYS200 4.8 65.9 1.0 HA B:HIS161 4.8 67.8 1.0 HD1 B:HIS204 4.8 62.9 0.0 H B:ILE199 4.8 70.8 1.0 N B:SER197 4.9 65.9 1.0 O B:CYS196 4.9 84.6 1.0 CB B:GLU198 5.0 69.1 1.0

Copper binding site 3 out of 3 in the Cryo-Em Structure of HIGD2A Bound Complex IV


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 HIGD2A Bound Complex IV within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu302 b:128.4 occ:1.00 HE2 B:MET207 1.6 73.7 1.0 SG B:CYS196 1.8 94.1 1.0 HB2 B:CYS196 1.8 77.1 1.0 SD B:MET207 2.0 92.2 1.0 CE B:MET207 2.0 68.3 1.0 CB B:CYS196 2.0 77.6 1.0 HB3 B:CYS196 2.3 78.1 1.0 HE1 B:MET207 2.4 70.3 1.0 HG3 B:MET207 2.5 75.3 1.0 CU B:CU301 2.7 120.5 1.0 CG B:MET207 2.8 75.1 1.0 HE3 B:MET207 2.9 71.1 1.0 SG B:CYS200 3.0 89.7 1.0 HG2 B:MET207 3.4 76.4 1.0 HD2 B:HIS204 3.4 73.8 1.0 CA B:CYS196 3.5 65.4 1.0 HZ2 B:TRP106 3.7 66.9 1.0 HA B:CYS196 3.7 69.7 1.0 HD1 B:HIS161 3.8 70.9 0.0 HB2 B:MET207 3.8 73.0 1.0 HB3 B:HIS161 3.8 67.8 1.0 CB B:MET207 3.9 68.6 1.0 H B:CYS196 4.1 75.8 1.0 O B:GLU198 4.1 69.7 1.0 H B:SER162 4.2 70.9 1.0 HB3 B:CYS200 4.2 72.3 1.0 ND1 B:HIS161 4.2 71.0 1.0 O B:HIS204 4.3 80.9 1.0 CB B:CYS200 4.3 74.7 1.0 CZ2 B:TRP106 4.3 69.2 1.0 CD2 B:HIS204 4.3 73.9 1.0 C B:CYS196 4.3 66.5 1.0 H B:GLU198 4.3 76.8 1.0 N B:CYS196 4.4 76.2 1.0 O B:MET207 4.4 77.2 1.0 HB3 B:MET207 4.4 72.6 1.0 HE1 B:TRP106 4.4 64.0 1.0 HA B:HIS204 4.4 67.3 1.0 HA B:HIS161 4.5 67.8 1.0 CB B:HIS161 4.6 66.3 1.0 HB2 B:CYS200 4.7 72.4 1.0 H B:SER197 4.7 71.0 1.0 CG B:HIS161 4.7 68.5 1.0 HA B:TRP104 4.8 76.0 1.0 N B:SER197 4.8 65.9 1.0 CE2 B:TRP106 4.8 62.7 1.0 NE1 B:TRP106 4.8 61.2 1.0 O B:SER162 4.9 79.5 1.0 N B:SER162 5.0 71.0 1.0 O B:CYS196 5.0 84.6 1.0

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