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Copper in PDB 8d4t: Mammalian Civ with Gdn Bound

Enzymatic activity of Mammalian Civ with Gdn Bound

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

Other elements in 8d4t:

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

Copper Binding Sites:

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 8d4t

Go back to Copper Binding Sites List in 8d4t
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 8d4t

Go back to Copper Binding Sites List in 8d4t
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 8d4t

Go back to Copper Binding Sites List in 8d4t
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

Reference:

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
Page generated: Wed Jul 31 09:37:16 2024

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