Copper in PDB 8d4t: Mammalian Civ with Gdn Bound

All present enzymatic activity of Mammalian Civ with Gdn Bound:
7.1.1.9;

The structure of Mammalian Civ with Gdn Bound also contains other interesting chemical elements:

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

The binding sites of Copper atom in the Mammalian Civ with Gdn Bound (pdb code 8d4t). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Mammalian Civ with Gdn Bound, PDB code: 8d4t:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in the Mammalian Civ with Gdn Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Mammalian Civ with Gdn Bound within 5.0Å range: probe atom residue distance (Å) B Occ N:Cu601 b:21.0 occ:1.00 NE2 N:HIS291 2.0 23.3 1.0 NE2 N:HIS290 2.0 19.3 1.0 ND1 N:HIS240 2.0 20.3 1.0 HB2 N:HIS240 2.9 16.6 1.0 CD2 N:HIS291 2.9 24.5 1.0 CE1 N:HIS290 3.0 21.2 1.0 CG N:HIS240 3.0 21.1 1.0 CE1 N:HIS240 3.0 21.7 1.0 CE1 N:HIS291 3.0 23.9 1.0 CD2 N:HIS290 3.1 18.8 1.0 HD2 N:HIS291 3.1 24.5 1.0 HE1 N:HIS290 3.2 21.2 1.0 HE1 N:HIS240 3.2 21.7 1.0 HE1 N:HIS291 3.3 23.9 1.0 HD2 N:HIS290 3.3 18.8 1.0 HA N:HIS240 3.3 18.9 1.0 CB N:HIS240 3.3 16.6 1.0 CA N:HIS240 3.9 18.9 1.0 CG N:HIS291 4.1 24.6 1.0 ND1 N:HIS291 4.1 25.0 1.0 ND1 N:HIS290 4.1 18.6 1.0 NE2 N:HIS240 4.1 24.6 1.0 CD2 N:HIS240 4.1 21.2 1.0 HG21 N:VAL243 4.2 18.2 1.0 HB3 N:HIS240 4.2 16.6 1.0 CG N:HIS290 4.2 20.3 1.0 HG23 N:VAL287 4.3 19.7 1.0 HA N:TRP288 4.4 19.1 1.0 HG22 N:VAL243 4.4 18.2 1.0 C1A N:HEA605 4.7 18.5 1.0 N N:HIS240 4.7 18.6 1.0 CG2 N:VAL243 4.8 18.2 1.0 C4A N:HEA605 4.8 18.8 1.0 C2A N:HEA605 4.9 18.3 1.0 HG11 N:VAL243 4.9 17.1 1.0 HE3 N:TRP236 4.9 25.6 1.0 FE N:HEA605 4.9 19.3 1.0 NA N:HEA605 4.9 19.8 1.0 C3A N:HEA605 4.9 17.8 1.0 HD1 N:HIS290 4.9 18.6 1.0 HD1 N:HIS291 4.9 25.0 1.0 HG21 N:VAL287 5.0 19.7 1.0 HD2 N:HIS240 5.0 21.2 1.0

Copper binding site 2 out of 3 in the Mammalian Civ with Gdn Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Mammalian Civ with Gdn Bound within 5.0Å range: probe atom residue distance (Å) B Occ O:Cu301 b:26.7 occ:1.00 ND1 O:HIS161 2.0 25.0 1.0 SG O:CYS196 2.3 25.0 1.0 SG O:CYS200 2.3 21.7 1.0 CU O:CU302 2.4 22.4 1.0 SD O:MET207 2.7 25.6 1.0 HE2 O:MET207 2.9 19.5 1.0 CE1 O:HIS161 2.9 22.6 1.0 HE1 O:HIS161 3.0 22.6 1.0 CE O:MET207 3.1 19.5 1.0 CG O:HIS161 3.2 20.8 1.0 HE1 O:MET207 3.2 19.5 1.0 HB3 O:CYS200 3.2 27.7 1.0 HB3 O:HIS161 3.3 24.6 1.0 CB O:CYS200 3.3 27.7 1.0 HB2 O:CYS196 3.3 24.8 1.0 CB O:CYS196 3.4 24.8 1.0 HA O:HIS161 3.5 23.0 1.0 HB3 O:CYS196 3.6 24.8 1.0 HB2 O:CYS200 3.6 27.7 1.0 HG3 O:MET207 3.6 25.9 1.0 CB O:HIS161 3.6 24.6 1.0 CG O:MET207 3.6 25.9 1.0 HA O:HIS204 3.7 23.2 1.0 HG2 O:MET207 3.8 25.9 1.0 O O:GLU198 4.0 26.2 1.0 HE3 O:MET207 4.0 19.5 1.0 HD1 O:TRP104 4.1 24.9 1.0 NE2 O:HIS161 4.1 21.5 1.0 CA O:HIS161 4.2 23.0 1.0 CD2 O:HIS161 4.2 20.4 1.0 ND1 O:HIS204 4.4 26.7 1.0 HB2 O:HIS161 4.5 24.6 1.0 H O:SER162 4.5 22.0 1.0 HZ2 O:TRP106 4.6 30.1 1.0 CA O:HIS204 4.6 23.2 1.0 CA O:CYS200 4.7 25.9 1.0 H O:CYS200 4.7 28.9 1.0 CA O:CYS196 4.7 23.2 1.0 H O:TRP104 4.7 36.8 1.0 CD1 O:TRP104 4.8 24.9 1.0 N O:CYS200 4.8 28.9 1.0 H O:GLU198 4.8 22.6 1.0 O O:HIS102 4.9 23.4 1.0 HE2 O:HIS161 4.9 21.5 1.0 HA O:CYS196 4.9 23.2 1.0 HA O:TRP104 4.9 31.5 1.0 O O:HIS204 4.9 25.5 1.0 CZ2 O:TRP106 5.0 30.1 1.0

Copper binding site 3 out of 3 in the Mammalian Civ with Gdn Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Mammalian Civ with Gdn Bound within 5.0Å range: probe atom residue distance (Å) B Occ O:Cu302 b:22.4 occ:1.00 ND1 O:HIS204 2.1 26.7 1.0 SG O:CYS200 2.3 21.7 1.0 SG O:CYS196 2.3 25.0 1.0 CU O:CU301 2.4 26.7 1.0 O O:GLU198 2.4 26.2 1.0 HA O:HIS204 2.9 23.2 1.0 CE1 O:HIS204 3.0 23.9 1.0 HB3 O:CYS196 3.1 24.8 1.0 CG O:HIS204 3.1 24.2 1.0 HE1 O:HIS204 3.1 23.9 1.0 H O:CYS200 3.2 28.9 1.0 CB O:CYS196 3.3 24.8 1.0 HB3 O:CYS200 3.3 27.7 1.0 H O:GLU198 3.4 22.6 1.0 CB O:CYS200 3.4 27.7 1.0 HB2 O:HIS204 3.5 24.9 1.0 CB O:HIS204 3.5 24.9 1.0 C O:GLU198 3.5 23.7 1.0 CA O:HIS204 3.5 23.2 1.0 N O:CYS200 3.6 28.9 1.0 HA O:ILE199 3.8 24.5 1.0 HB2 O:CYS196 3.8 24.8 1.0 HA O:HIS161 4.0 23.0 1.0 ND1 O:HIS161 4.0 25.0 1.0 O O:HIS204 4.0 25.5 1.0 NE2 O:HIS204 4.0 24.1 1.0 CA O:CYS200 4.1 25.9 1.0 CD2 O:HIS204 4.1 24.1 1.0 C O:ILE199 4.1 29.4 1.0 N O:GLU198 4.1 22.6 1.0 HB2 O:CYS200 4.2 27.7 1.0 O O:CYS196 4.2 25.3 1.0 CA O:ILE199 4.2 24.5 1.0 C O:HIS204 4.3 23.2 1.0 N O:ILE199 4.3 23.4 1.0 C O:CYS196 4.3 26.9 1.0 CA O:CYS196 4.4 23.2 1.0 HB3 O:HIS204 4.5 24.9 1.0 HG2 O:MET207 4.5 25.9 1.0 CA O:GLU198 4.5 21.8 1.0 SD O:MET207 4.5 25.6 1.0 HG3 O:MET207 4.6 25.9 1.0 HE2 N:TYR440 4.6 26.2 1.0 HB3 O:HIS161 4.7 24.6 1.0 HE2 O:MET207 4.7 19.5 1.0 CG O:MET207 4.8 25.9 1.0 HE2 O:HIS204 4.8 24.1 1.0 N O:HIS204 4.8 25.5 1.0 HB3 O:GLU198 4.8 22.8 1.0 HE1 O:HIS161 4.8 22.6 1.0 N O:SER197 4.8 27.1 1.0 HA O:CYS200 4.8 25.9 1.0 CE1 O:HIS161 4.8 22.6 1.0 H O:SER162 4.9 22.0 1.0 CA O:HIS161 4.9 23.0 1.0 HA O:CYS196 4.9 23.2 1.0 HH N:TYR440 4.9 24.3 1.0 HD2 O:HIS204 5.0 24.1 1.0 CG O:HIS161 5.0 20.8 1.0 HD1 O:TRP104 5.0 24.9 1.0

J.M.Di Trani, A.Moe, D.Riepl, P.Saura, V.R.I.Kaila, P.Brzezinski, J.L.Rubinstein. Structural Basis of Mammalian Complex IV Inhibition By Steroids. Proc.Natl.Acad.Sci.Usa V. 119 28119 2022.
ISSN: ESSN 1091-6490
PubMed: 35858451
DOI: 10.1073/PNAS.2205228119