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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:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 14 atoms
Calcium (Ca) 2 atoms

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

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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

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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

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