Copper in PDB 2ybb: Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)

All present enzymatic activity of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876):
1.10.2.2; 1.6.5.3; 1.6.99.5; 1.9.3.1;

The structure of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) also contains other interesting chemical elements:

Magnesium	(Mg)	7 atoms
Calcium	(Ca)	1 atom
Iron	(Fe)	45 atoms
Zinc	(Zn)	1 atom

The binding sites of Copper atom in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) (pdb code 2ybb). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876), PDB code: 2ybb:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range: probe atom residue distance (Å) B Occ L:Cu517 b:15.3 occ:1.00 ND1 L:HIS240 1.9 26.2 1.0 NE2 L:HIS291 2.2 7.0 1.0 NE2 L:HIS290 2.2 7.0 1.0 CE1 L:HIS240 2.6 27.2 1.0 CD2 L:HIS291 3.0 18.9 1.0 CG L:HIS240 3.1 18.8 1.0 CE1 L:HIS290 3.1 7.0 1.0 CE1 L:HIS291 3.2 23.1 1.0 CD2 L:HIS290 3.2 17.6 1.0 CB L:HIS240 3.6 11.4 1.0 NE2 L:HIS240 3.9 7.0 1.0 CD2 L:HIS240 4.1 15.7 1.0 CG L:HIS291 4.2 20.1 1.0 CA L:HIS240 4.2 13.6 1.0 ND1 L:HIS291 4.2 23.8 1.0 ND1 L:HIS290 4.2 7.9 1.0 CG L:HIS290 4.3 14.5 1.0 NA L:HEA516 4.4 14.8 1.0 C1A L:HEA516 4.5 7.0 1.0 C4A L:HEA516 4.7 14.3 1.0 FE L:HEA516 4.7 8.0 1.0 C2A L:HEA516 4.9 7.0 1.0 C3A L:HEA516 4.9 7.0 1.0 CHA L:HEA516 4.9 8.6 1.0

Copper binding site 2 out of 3 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range: probe atom residue distance (Å) B Occ M:Cu228 b:25.9 occ:1.00 ND1 M:HIS161 1.9 7.0 1.0 SG M:CYS196 2.3 10.8 1.0 SG M:CYS200 2.3 10.4 1.0 CU M:CU229 2.4 13.4 1.0 SD M:MET207 2.5 14.2 1.0 CE1 M:HIS161 2.6 7.0 1.0 CG M:HIS161 3.1 7.0 1.0 CE M:MET207 3.2 10.6 1.0 CB M:CYS200 3.3 11.0 1.0 CB M:CYS196 3.5 17.1 1.0 CB M:HIS161 3.7 7.0 1.0 CG M:MET207 3.7 10.4 1.0 O M:GLU198 3.8 20.2 1.0 NE2 M:HIS161 3.9 7.0 1.0 CD2 M:HIS161 4.1 7.0 1.0 CA M:HIS161 4.1 7.0 1.0 ND1 M:HIS204 4.2 16.2 1.0 O M:LEU160 4.6 7.0 1.0 CA M:CYS200 4.7 10.1 1.0 O M:HIS204 4.8 17.7 1.0 CA M:CYS196 4.8 8.4 1.0 N M:CYS200 4.9 16.8 1.0 CA M:HIS204 5.0 9.2 1.0 CD1 M:TRP104 5.0 16.1 1.0

Copper binding site 3 out of 3 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range: probe atom residue distance (Å) B Occ M:Cu229 b:13.4 occ:1.00 ND1 M:HIS204 1.9 16.2 1.0 O M:GLU198 2.2 20.2 1.0 SG M:CYS200 2.2 10.4 1.0 SG M:CYS196 2.3 10.8 1.0 CU M:CU228 2.4 25.9 1.0 CE1 M:HIS204 2.8 19.0 1.0 CG M:HIS204 3.0 9.0 1.0 CB M:CYS200 3.3 11.0 1.0 C M:GLU198 3.4 11.5 1.0 CB M:CYS196 3.4 17.1 1.0 CB M:HIS204 3.5 12.8 1.0 N M:CYS200 3.6 16.8 1.0 CA M:HIS204 3.6 9.2 1.0 O M:HIS204 3.6 17.7 1.0 NE2 M:HIS204 3.9 10.2 1.0 C M:HIS204 4.0 10.3 1.0 ND1 M:HIS161 4.1 7.0 1.0 CD2 M:HIS204 4.1 11.1 1.0 CA M:CYS200 4.1 10.1 1.0 SD M:MET207 4.1 14.2 1.0 C M:ILE199 4.1 12.8 1.0 CA M:ILE199 4.3 11.1 1.0 N M:ILE199 4.3 13.2 1.0 N M:GLU198 4.3 16.7 1.0 CA M:GLU198 4.4 8.4 1.0 O M:CYS196 4.5 15.9 1.0 CG M:MET207 4.5 10.4 1.0 C M:CYS196 4.6 14.1 1.0 CE1 M:HIS161 4.7 7.0 1.0 CA M:CYS196 4.7 8.4 1.0 N M:HIS204 4.9 15.7 1.0 C M:CYS200 4.9 7.5 1.0 O M:ILE199 4.9 8.4 1.0

T.Althoff, D.J.Mills, J.-L.Popot, W.Kuehlbrandt. Arrangement of Electron Transport Chain Components in Bovine Mitochondrial Supercomplex I(1)III(2)IV(1). Embo J. V. 30 4652 2011.
ISSN: ISSN 0261-4189
PubMed: 21909073
DOI: 10.1038/EMBOJ.2011.324