Copper in PDB 6t0b: The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae
Enzymatic activity of The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae
All present enzymatic activity of The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae:
1.9.3.1;
7.1.1.8;
Other elements in 6t0b:
The structure of The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae also contains other interesting chemical elements:
Copper Binding Sites:
The binding sites of Copper atom in the The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae
(pdb code 6t0b). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the
The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae, PDB code: 6t0b:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
Copper binding site 1 out
of 6 in 6t0b
Go back to
Copper Binding Sites List in 6t0b
Copper binding site 1 out
of 6 in the The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Cu601
b:84.8
occ:1.00
|
NE2
|
a:HIS290
|
2.2
|
68.5
|
1.0
|
ND1
|
a:HIS241
|
2.2
|
68.1
|
1.0
|
NE2
|
a:HIS291
|
2.2
|
68.5
|
1.0
|
CE1
|
a:HIS291
|
2.4
|
68.5
|
1.0
|
CE1
|
a:HIS241
|
3.0
|
68.1
|
1.0
|
CE1
|
a:HIS290
|
3.1
|
68.5
|
1.0
|
CD2
|
a:HIS290
|
3.2
|
68.5
|
1.0
|
CG
|
a:HIS241
|
3.2
|
68.1
|
1.0
|
CD2
|
a:HIS291
|
3.5
|
68.5
|
1.0
|
ND1
|
a:HIS291
|
3.6
|
68.5
|
1.0
|
CB
|
a:HIS241
|
3.6
|
68.1
|
1.0
|
CA
|
a:HIS241
|
4.2
|
68.1
|
1.0
|
NE2
|
a:HIS241
|
4.2
|
68.1
|
1.0
|
CG
|
a:HIS291
|
4.2
|
68.5
|
1.0
|
ND1
|
a:HIS290
|
4.2
|
68.5
|
1.0
|
CG
|
a:HIS290
|
4.3
|
68.5
|
1.0
|
CD2
|
a:HIS241
|
4.3
|
68.1
|
1.0
|
CG2
|
a:VAL244
|
4.4
|
67.8
|
1.0
|
C1A
|
a:HEA603
|
4.4
|
67.1
|
1.0
|
ND
|
a:HEA603
|
4.5
|
67.1
|
1.0
|
FE
|
a:HEA603
|
4.5
|
67.1
|
1.0
|
NA
|
a:HEA603
|
4.6
|
67.1
|
1.0
|
C4A
|
a:HEA603
|
4.7
|
67.1
|
1.0
|
C2A
|
a:HEA603
|
4.7
|
67.1
|
1.0
|
C4D
|
a:HEA603
|
4.7
|
67.1
|
1.0
|
C3A
|
a:HEA603
|
4.8
|
67.1
|
1.0
|
CHA
|
a:HEA603
|
4.9
|
67.1
|
1.0
|
C1D
|
a:HEA603
|
4.9
|
67.1
|
1.0
|
N
|
a:HIS241
|
5.0
|
68.1
|
1.0
|
|
Copper binding site 2 out
of 6 in 6t0b
Go back to
Copper Binding Sites List in 6t0b
Copper binding site 2 out
of 6 in the The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
b:Cu301
b:83.4
occ:1.00
|
CU1
|
b:CUA301
|
0.0
|
83.4
|
1.0
|
SG
|
b:CYS225
|
2.0
|
69.7
|
1.0
|
ND1
|
b:HIS186
|
2.1
|
69.2
|
1.0
|
SD
|
b:MET232
|
2.1
|
67.0
|
1.0
|
CE
|
b:MET232
|
2.1
|
67.0
|
1.0
|
SG
|
b:CYS221
|
2.3
|
69.5
|
1.0
|
CU2
|
b:CUA301
|
2.6
|
80.6
|
1.0
|
CE1
|
b:HIS186
|
3.0
|
69.2
|
1.0
|
CG
|
b:HIS186
|
3.1
|
69.2
|
1.0
|
CB
|
b:CYS225
|
3.3
|
69.7
|
1.0
|
CB
|
b:CYS221
|
3.4
|
69.5
|
1.0
|
CB
|
b:HIS186
|
3.5
|
69.2
|
1.0
|
CG
|
b:MET232
|
3.7
|
67.0
|
1.0
|
NE2
|
b:HIS186
|
4.1
|
69.2
|
1.0
|
CD2
|
b:HIS186
|
4.2
|
69.2
|
1.0
|
CA
|
b:HIS186
|
4.2
|
69.2
|
1.0
|
O
|
b:GLU223
|
4.4
|
69.2
|
1.0
|
CB
|
b:MET232
|
4.4
|
67.0
|
1.0
|
O
|
b:TYR122
|
4.6
|
68.7
|
1.0
|
CD1
|
b:TRP124
|
4.6
|
65.4
|
1.0
|
ND1
|
b:HIS229
|
4.6
|
66.0
|
1.0
|
CA
|
b:CYS225
|
4.7
|
69.7
|
1.0
|
CZ2
|
b:TRP126
|
4.7
|
68.5
|
1.0
|
CA
|
b:CYS221
|
4.8
|
69.5
|
1.0
|
N
|
b:CYS225
|
5.0
|
69.7
|
1.0
|
|
Copper binding site 3 out
of 6 in 6t0b
Go back to
Copper Binding Sites List in 6t0b
Copper binding site 3 out
of 6 in the The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
b:Cu301
b:80.6
occ:1.00
|
CU2
|
b:CUA301
|
0.0
|
80.6
|
1.0
|
SG
|
b:CYS225
|
1.9
|
69.7
|
1.0
|
ND1
|
b:HIS229
|
2.2
|
66.0
|
1.0
|
SG
|
b:CYS221
|
2.2
|
69.5
|
1.0
|
O
|
b:GLU223
|
2.4
|
69.2
|
1.0
|
CU1
|
b:CUA301
|
2.6
|
83.4
|
1.0
|
CE1
|
b:HIS229
|
2.7
|
66.0
|
1.0
|
CB
|
b:CYS225
|
3.0
|
69.7
|
1.0
|
CB
|
b:CYS221
|
3.2
|
69.5
|
1.0
|
N
|
b:CYS225
|
3.4
|
69.7
|
1.0
|
CG
|
b:HIS229
|
3.4
|
66.0
|
1.0
|
C
|
b:GLU223
|
3.6
|
69.2
|
1.0
|
SD
|
b:MET232
|
3.8
|
67.0
|
1.0
|
CA
|
b:CYS225
|
3.8
|
69.7
|
1.0
|
NE2
|
b:HIS229
|
4.0
|
66.0
|
1.0
|
CB
|
b:HIS229
|
4.0
|
66.0
|
1.0
|
CA
|
b:HIS229
|
4.0
|
66.0
|
1.0
|
ND1
|
b:HIS186
|
4.1
|
69.2
|
1.0
|
O
|
b:HIS229
|
4.1
|
66.0
|
1.0
|
C
|
b:LEU224
|
4.2
|
66.3
|
1.0
|
O
|
b:CYS221
|
4.2
|
69.5
|
1.0
|
CD2
|
b:HIS229
|
4.3
|
66.0
|
1.0
|
N
|
b:GLU223
|
4.3
|
69.2
|
1.0
|
C
|
b:CYS221
|
4.4
|
69.5
|
1.0
|
CA
|
b:LEU224
|
4.4
|
66.3
|
1.0
|
CA
|
b:CYS221
|
4.4
|
69.5
|
1.0
|
N
|
b:LEU224
|
4.5
|
66.3
|
1.0
|
CE
|
b:MET232
|
4.5
|
67.0
|
1.0
|
CA
|
b:GLU223
|
4.5
|
69.2
|
1.0
|
C
|
b:HIS229
|
4.6
|
66.0
|
1.0
|
CE1
|
b:HIS186
|
4.9
|
69.2
|
1.0
|
CA
|
b:HIS186
|
5.0
|
69.2
|
1.0
|
C
|
b:CYS225
|
5.0
|
69.7
|
1.0
|
|
Copper binding site 4 out
of 6 in 6t0b
Go back to
Copper Binding Sites List in 6t0b
Copper binding site 4 out
of 6 in the The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
n:Cu601
b:0.7
occ:1.00
|
ND1
|
n:HIS241
|
2.1
|
0.1
|
1.0
|
NE2
|
n:HIS291
|
2.2
|
0.2
|
1.0
|
NE2
|
n:HIS290
|
2.2
|
0.7
|
1.0
|
CE1
|
n:HIS291
|
2.7
|
0.2
|
1.0
|
CE1
|
n:HIS241
|
3.1
|
0.1
|
1.0
|
CE1
|
n:HIS290
|
3.1
|
0.7
|
1.0
|
CG
|
n:HIS241
|
3.1
|
0.1
|
1.0
|
CD2
|
n:HIS290
|
3.2
|
0.7
|
1.0
|
CD2
|
n:HIS291
|
3.3
|
0.2
|
1.0
|
CB
|
n:HIS241
|
3.5
|
0.1
|
1.0
|
ND1
|
n:HIS291
|
3.9
|
0.2
|
1.0
|
CG2
|
n:VAL244
|
4.0
|
0.9
|
1.0
|
CA
|
n:HIS241
|
4.1
|
0.1
|
1.0
|
NE2
|
n:HIS241
|
4.2
|
0.1
|
1.0
|
CG
|
n:HIS291
|
4.2
|
0.2
|
1.0
|
ND1
|
n:HIS290
|
4.2
|
0.7
|
1.0
|
CD2
|
n:HIS241
|
4.2
|
0.1
|
1.0
|
CG
|
n:HIS290
|
4.3
|
0.7
|
1.0
|
FE
|
n:HEA603
|
4.5
|
0.3
|
1.0
|
ND
|
n:HEA603
|
4.5
|
0.3
|
1.0
|
C1A
|
n:HEA603
|
4.6
|
0.3
|
1.0
|
C4D
|
n:HEA603
|
4.8
|
0.3
|
1.0
|
C2A
|
n:HEA603
|
4.8
|
0.3
|
1.0
|
NA
|
n:HEA603
|
4.8
|
0.3
|
1.0
|
N
|
n:HIS241
|
4.9
|
0.1
|
1.0
|
C4A
|
n:HEA603
|
4.9
|
0.3
|
1.0
|
C1D
|
n:HEA603
|
4.9
|
0.3
|
1.0
|
C3A
|
n:HEA603
|
5.0
|
0.3
|
1.0
|
|
Copper binding site 5 out
of 6 in 6t0b
Go back to
Copper Binding Sites List in 6t0b
Copper binding site 5 out
of 6 in the The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 5 of The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
o:Cu301
b:0.7
occ:1.00
|
CU1
|
o:CUA301
|
0.0
|
0.7
|
1.0
|
SG
|
o:CYS225
|
2.1
|
0.4
|
1.0
|
ND1
|
o:HIS186
|
2.1
|
0.3
|
1.0
|
SD
|
o:MET232
|
2.1
|
0.4
|
1.0
|
SG
|
o:CYS221
|
2.3
|
0.3
|
1.0
|
CU2
|
o:CUA301
|
2.6
|
0.1
|
1.0
|
CE
|
o:MET232
|
2.7
|
0.4
|
1.0
|
CG
|
o:HIS186
|
3.0
|
0.3
|
1.0
|
CE1
|
o:HIS186
|
3.1
|
0.3
|
1.0
|
CB
|
o:CYS221
|
3.2
|
0.3
|
1.0
|
CB
|
o:CYS225
|
3.2
|
0.4
|
1.0
|
CB
|
o:HIS186
|
3.3
|
0.3
|
1.0
|
CG
|
o:MET232
|
3.8
|
0.4
|
1.0
|
CA
|
o:HIS186
|
4.1
|
0.3
|
1.0
|
CD2
|
o:HIS186
|
4.2
|
0.3
|
1.0
|
NE2
|
o:HIS186
|
4.2
|
0.3
|
1.0
|
CB
|
o:MET232
|
4.4
|
0.4
|
1.0
|
CD1
|
o:TRP124
|
4.5
|
0.1
|
1.0
|
ND1
|
o:HIS229
|
4.6
|
0.5
|
1.0
|
O
|
o:GLU223
|
4.6
|
0.3
|
1.0
|
CA
|
o:CYS225
|
4.6
|
0.4
|
1.0
|
CA
|
o:CYS221
|
4.7
|
0.3
|
1.0
|
NE1
|
o:TRP126
|
4.8
|
0.2
|
1.0
|
CZ2
|
o:TRP126
|
4.9
|
0.2
|
1.0
|
N
|
o:CYS225
|
4.9
|
0.4
|
1.0
|
N
|
o:ASP187
|
5.0
|
0.9
|
1.0
|
|
Copper binding site 6 out
of 6 in 6t0b
Go back to
Copper Binding Sites List in 6t0b
Copper binding site 6 out
of 6 in the The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 6 of The III2-IV(5B)2 Respiratory Supercomplex From S. Cerevisiae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
o:Cu301
b:0.1
occ:1.00
|
CU2
|
o:CUA301
|
0.0
|
0.1
|
1.0
|
ND1
|
o:HIS229
|
2.1
|
0.5
|
1.0
|
SG
|
o:CYS225
|
2.2
|
0.4
|
1.0
|
SG
|
o:CYS221
|
2.3
|
0.3
|
1.0
|
O
|
o:GLU223
|
2.5
|
0.3
|
1.0
|
CU1
|
o:CUA301
|
2.6
|
0.7
|
1.0
|
CB
|
o:CYS225
|
2.8
|
0.4
|
1.0
|
CE1
|
o:HIS229
|
2.9
|
0.5
|
1.0
|
CG
|
o:HIS229
|
3.1
|
0.5
|
1.0
|
N
|
o:CYS225
|
3.2
|
0.4
|
1.0
|
CB
|
o:CYS221
|
3.4
|
0.3
|
1.0
|
CB
|
o:HIS229
|
3.5
|
0.5
|
1.0
|
CA
|
o:CYS225
|
3.6
|
0.4
|
1.0
|
CA
|
o:HIS229
|
3.7
|
0.5
|
1.0
|
C
|
o:GLU223
|
3.7
|
0.3
|
1.0
|
SD
|
o:MET232
|
3.9
|
0.4
|
1.0
|
O
|
o:HIS229
|
4.0
|
0.5
|
1.0
|
NE2
|
o:HIS229
|
4.0
|
0.5
|
1.0
|
CD2
|
o:HIS229
|
4.1
|
0.5
|
1.0
|
C
|
o:LEU224
|
4.2
|
0.2
|
1.0
|
ND1
|
o:HIS186
|
4.2
|
0.3
|
1.0
|
C
|
o:HIS229
|
4.3
|
0.5
|
1.0
|
CA
|
o:LEU224
|
4.5
|
0.2
|
1.0
|
N
|
o:GLU223
|
4.5
|
0.3
|
1.0
|
N
|
o:LEU224
|
4.6
|
0.2
|
1.0
|
CA
|
o:CYS221
|
4.6
|
0.3
|
1.0
|
C
|
o:CYS221
|
4.6
|
0.3
|
1.0
|
CA
|
o:GLU223
|
4.6
|
0.3
|
1.0
|
C
|
o:CYS225
|
4.7
|
0.4
|
1.0
|
O
|
o:CYS221
|
4.7
|
0.3
|
1.0
|
CD1
|
o:TRP124
|
4.8
|
0.1
|
1.0
|
N
|
o:HIS229
|
4.8
|
0.5
|
1.0
|
NE1
|
o:TRP124
|
5.0
|
0.1
|
1.0
|
CE1
|
o:HIS186
|
5.0
|
0.3
|
1.0
|
|
Reference:
A.M.Hartley,
B.Meunier,
N.Pinotsis,
A.Marechal.
RCF2 Revealed in Cryo-Em Structures of Hypoxic Isoforms of Mature Mitochondrial III-IV Supercomplexes. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
PubMed: 32291341
DOI: 10.1073/PNAS.1920612117
Page generated: Wed Jul 31 07:31:03 2024
|