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Copper in PDB 7qhm: Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound)

Enzymatic activity of Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound)

All present enzymatic activity of Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound):
7.1.1.8; 7.1.1.9;

Other elements in 7qhm:

The structure of Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound) also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Calcium (Ca) 2 atoms
Iron (Fe) 16 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound) (pdb code 7qhm). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound), PDB code: 7qhm:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7qhm

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Copper binding site 1 out of 6 in the Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu603

b:67.4
occ:1.00
N1 D:AZI606 1.8 42.5 1.0
NE2 D:HIS315 1.8 33.6 1.0
N2 D:AZI606 2.1 42.5 1.0
NE2 D:HIS314 2.1 34.0 1.0
ND1 D:HIS265 2.3 32.1 1.0
CE1 D:HIS315 2.5 33.6 1.0
HE1 D:HIS315 2.5 33.6 1.0
HB2 D:HIS265 2.8 32.1 1.0
N3 D:AZI606 2.9 42.5 1.0
CE1 D:HIS314 3.0 34.0 1.0
CD2 D:HIS315 3.0 33.6 1.0
HE1 D:HIS314 3.1 34.0 1.0
CG D:HIS265 3.1 32.1 1.0
CE1 D:HIS265 3.2 32.1 1.0
CD2 D:HIS314 3.2 34.0 1.0
HD2 D:HIS315 3.4 33.6 1.0
CB D:HIS265 3.4 32.1 1.0
HE1 D:HIS265 3.4 32.1 1.0
HD2 D:HIS314 3.5 34.0 1.0
ND1 D:HIS315 3.6 33.6 1.0
HA D:HIS265 3.7 32.1 1.0
CG D:HIS315 3.9 33.6 1.0
ND1 D:HIS314 4.1 34.0 1.0
HB3 D:HIS265 4.2 32.1 1.0
CA D:HIS265 4.2 32.1 1.0
CD2 D:HIS265 4.2 32.1 1.0
NE2 D:HIS265 4.2 32.1 1.0
CG D:HIS314 4.2 34.0 1.0
HG21 D:VAL268 4.3 31.1 1.0
C4D D:HAS602 4.3 36.5 1.0
HG22 D:VAL268 4.3 31.1 1.0
ND D:HAS602 4.3 36.5 1.0
HD1 D:HIS315 4.3 33.6 1.0
C3D D:HAS602 4.6 36.5 1.0
C1D D:HAS602 4.6 36.5 1.0
FE D:HAS602 4.6 36.5 1.0
CHA D:HAS602 4.6 36.5 1.0
C1A D:HAS602 4.7 36.5 1.0
C2D D:HAS602 4.7 36.5 1.0
CG2 D:VAL268 4.7 31.1 1.0
NA D:HAS602 4.8 36.5 1.0
HD1 D:HIS314 4.8 34.0 1.0
HAD1 D:HAS602 4.9 36.5 1.0
HG23 D:VAL311 4.9 36.5 1.0
O D:VAL311 5.0 36.5 1.0

Copper binding site 2 out of 6 in 7qhm

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Copper binding site 2 out of 6 in the Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu401

b:57.4
occ:1.00
ND1 E:HIS244 1.9 28.8 1.0
SD E:MET296 2.4 33.1 1.0
SG E:CYS289 2.4 29.1 1.0
SG E:CYS285 2.5 30.9 1.0
CU2 E:CUA402 2.6 61.3 1.0
CE1 E:HIS244 2.7 28.8 1.0
HE1 E:HIS244 2.8 28.8 1.0
HB3 E:CYS289 2.9 29.1 1.0
HE1 E:MET296 3.0 33.1 1.0
CG E:HIS244 3.1 28.8 1.0
CE E:MET296 3.2 33.1 1.0
CB E:CYS289 3.2 29.1 1.0
HB3 E:HIS244 3.2 28.8 1.0
HE2 E:MET296 3.4 33.1 1.0
HB2 E:CYS289 3.5 29.1 1.0
HA E:HIS244 3.5 28.8 1.0
CB E:HIS244 3.6 28.8 1.0
HB2 E:CYS285 3.6 30.9 1.0
CB E:CYS285 3.7 30.9 1.0
HB3 E:CYS285 3.9 30.9 1.0
NE2 E:HIS244 3.9 28.8 1.0
CG E:MET296 4.0 33.1 1.0
HE3 E:MET296 4.0 33.1 1.0
HB2 E:MET296 4.1 33.1 1.0
CD2 E:HIS244 4.1 28.8 1.0
CA E:HIS244 4.1 28.8 1.0
O E:GLU287 4.2 30.1 1.0
H E:SER245 4.2 29.7 1.0
HG3 E:MET296 4.3 33.1 1.0
HA E:HIS293 4.3 29.0 1.0
HD1 E:TRP153 4.3 31.3 1.0
HB3 E:MET296 4.4 33.1 1.0
ND1 E:HIS293 4.4 29.0 1.0
CB E:MET296 4.4 33.1 1.0
HB2 E:HIS244 4.5 28.8 1.0
H E:CYS289 4.6 29.1 1.0
CA E:CYS289 4.6 29.1 1.0
HG2 E:MET296 4.6 33.1 1.0
HE2 E:HIS244 4.7 28.8 1.0
HB1 E:ALA150 4.8 30.1 1.0
N E:CYS289 4.8 29.1 1.0
N E:SER245 4.9 29.7 1.0
O E:ALA243 5.0 27.4 1.0
HB2 E:HIS293 5.0 29.0 1.0
HD2 E:HIS244 5.0 28.8 1.0

Copper binding site 3 out of 6 in 7qhm

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Copper binding site 3 out of 6 in the Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu402

b:61.3
occ:1.00
ND1 E:HIS293 1.9 29.0 1.0
SG E:CYS285 2.3 30.9 1.0
SG E:CYS289 2.4 29.1 1.0
O E:GLU287 2.5 30.1 1.0
CU1 E:CUA401 2.6 57.4 1.0
CE1 E:HIS293 2.8 29.0 1.0
HE1 E:HIS293 2.9 29.0 1.0
H E:CYS289 2.9 29.1 1.0
CG E:HIS293 3.0 29.0 1.0
HB3 E:CYS289 3.1 29.1 1.0
HB3 E:CYS285 3.1 30.9 1.0
HB2 E:HIS293 3.2 29.0 1.0
CB E:CYS289 3.3 29.1 1.0
N E:CYS289 3.4 29.1 1.0
HA E:HIS293 3.4 29.0 1.0
CB E:CYS285 3.4 30.9 1.0
CB E:HIS293 3.5 29.0 1.0
HA E:MET288 3.6 29.1 1.0
C E:GLU287 3.6 30.1 1.0
NE2 E:HIS293 3.9 29.0 1.0
CA E:HIS293 3.9 29.0 1.0
HB2 E:CYS285 3.9 30.9 1.0
CA E:CYS289 4.0 29.1 1.0
O E:HIS293 4.0 29.0 1.0
CD2 E:HIS293 4.1 29.0 1.0
C E:MET288 4.1 29.1 1.0
HB2 E:CYS289 4.1 29.1 1.0
CA E:MET288 4.2 29.1 1.0
H E:GLU287 4.2 30.1 1.0
ND1 E:HIS244 4.3 28.8 1.0
N E:MET288 4.3 29.1 1.0
HA E:HIS244 4.4 28.8 1.0
SD E:MET296 4.4 33.1 1.0
C E:HIS293 4.4 29.0 1.0
HB3 E:HIS293 4.5 29.0 1.0
C E:CYS285 4.5 30.9 1.0
N E:GLU287 4.5 30.1 1.0
H E:ALA286 4.5 29.5 1.0
HB2 E:MET296 4.5 33.1 1.0
CA E:CYS285 4.5 30.9 1.0
N E:ALA286 4.6 29.5 1.0
HA E:CYS289 4.6 29.1 1.0
HE2 E:HIS293 4.7 29.0 1.0
CA E:GLU287 4.7 30.1 1.0
H E:GLY290 4.7 28.7 1.0
O E:CYS285 4.8 30.9 1.0
HE1 E:HIS244 4.8 28.8 1.0
HA E:CYS285 4.9 30.9 1.0
HD2 E:HIS293 4.9 29.0 1.0
H E:SER245 4.9 29.7 1.0
C E:CYS289 5.0 29.1 1.0
CE1 E:HIS244 5.0 28.8 1.0
HD1 E:TRP153 5.0 31.3 1.0

Copper binding site 4 out of 6 in 7qhm

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Copper binding site 4 out of 6 in the Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Cu603

b:56.9
occ:1.00
NE2 Q:HIS314 1.8 21.8 1.0
N2 Q:AZI605 2.1 25.6 1.0
ND1 Q:HIS265 2.1 21.9 1.0
NE2 Q:HIS315 2.1 22.5 1.0
N1 Q:AZI605 2.1 25.6 1.0
N3 Q:AZI605 2.6 25.6 1.0
CE1 Q:HIS314 2.7 21.8 1.0
CD2 Q:HIS314 2.8 21.8 1.0
CD2 Q:HIS315 2.9 22.5 1.0
HB2 Q:HIS265 2.9 21.9 1.0
CE1 Q:HIS265 2.9 21.9 1.0
HE1 Q:HIS314 3.0 21.8 1.0
HD2 Q:HIS315 3.0 22.5 1.0
CG Q:HIS265 3.0 21.9 1.0
HD2 Q:HIS314 3.1 21.8 1.0
HE1 Q:HIS265 3.1 21.9 1.0
CE1 Q:HIS315 3.2 22.5 1.0
CB Q:HIS265 3.5 21.9 1.0
HE1 Q:HIS315 3.5 22.5 1.0
ND1 Q:HIS314 3.8 21.8 1.0
CG Q:HIS314 3.9 21.8 1.0
CG Q:HIS315 4.0 22.5 1.0
NE2 Q:HIS265 4.0 21.9 1.0
HA Q:HIS265 4.0 21.9 1.0
CD2 Q:HIS265 4.1 21.9 1.0
ND1 Q:HIS315 4.1 22.5 1.0
HB3 Q:HIS265 4.2 21.9 1.0
CA Q:HIS265 4.4 21.9 1.0
C4D Q:HAS602 4.5 28.8 1.0
HG23 Q:VAL311 4.6 24.4 1.0
C3D Q:HAS602 4.6 28.8 1.0
HD1 Q:HIS314 4.6 21.8 1.0
ND Q:HAS602 4.6 28.8 1.0
HG21 Q:VAL268 4.6 22.0 1.0
HA Q:TRP312 4.7 22.0 1.0
O Q:TRP312 4.7 22.0 1.0
C2D Q:HAS602 4.7 28.8 1.0
C1D Q:HAS602 4.7 28.8 1.0
HG22 Q:VAL268 4.7 22.0 1.0
O Q:VAL311 4.8 24.4 1.0
HD1 Q:HIS315 4.9 22.5 1.0
HD2 Q:HIS265 4.9 21.9 1.0
HAD1 Q:HAS602 4.9 28.8 1.0
CHA Q:HAS602 4.9 28.8 1.0
FE Q:HAS602 4.9 28.8 1.0

Copper binding site 5 out of 6 in 7qhm

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Copper binding site 5 out of 6 in the Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cu402

b:56.5
occ:1.00
ND1 R:HIS244 1.9 13.3 1.0
SD R:MET296 2.4 18.7 1.0
SG R:CYS285 2.4 18.1 1.0
SG R:CYS289 2.4 17.4 1.0
CU2 R:CUA403 2.6 50.3 1.0
CE1 R:HIS244 2.7 13.3 1.0
HE1 R:HIS244 2.7 13.3 1.0
CG R:HIS244 3.1 13.3 1.0
HE1 R:MET296 3.2 18.7 1.0
HB3 R:CYS289 3.2 17.4 1.0
HB3 R:HIS244 3.2 13.3 1.0
CE R:MET296 3.3 18.7 1.0
CB R:CYS289 3.4 17.4 1.0
HB2 R:CYS285 3.5 18.1 1.0
HE2 R:MET296 3.5 18.7 1.0
CB R:CYS285 3.5 18.1 1.0
HB2 R:CYS289 3.6 17.4 1.0
CB R:HIS244 3.6 13.3 1.0
HA R:HIS244 3.7 13.3 1.0
HB3 R:CYS285 3.7 18.1 1.0
HD1 R:TRP153 3.9 15.4 1.0
NE2 R:HIS244 3.9 13.3 1.0
CG R:MET296 4.0 18.7 1.0
ND1 R:HIS293 4.0 15.8 1.0
CD2 R:HIS244 4.1 13.3 1.0
HB3 R:MET296 4.1 18.7 1.0
HE3 R:MET296 4.2 18.7 1.0
CA R:HIS244 4.2 13.3 1.0
HA R:HIS293 4.2 15.8 1.0
O R:GLU287 4.2 18.3 1.0
HG2 R:MET296 4.3 18.7 1.0
HB2 R:MET296 4.4 18.7 1.0
CB R:MET296 4.4 18.7 1.0
H R:SER245 4.5 17.2 1.0
HB2 R:HIS244 4.5 13.3 1.0
HE1 R:HIS293 4.5 15.8 1.0
HE2 R:HIS244 4.6 13.3 1.0
HG3 R:MET296 4.6 18.7 1.0
CE1 R:HIS293 4.7 15.8 1.0
CD1 R:TRP153 4.7 15.4 1.0
CA R:CYS289 4.8 17.4 1.0
O R:ALA243 4.8 17.1 1.0
CA R:CYS285 4.9 18.1 1.0
HB1 R:ALA150 4.9 18.2 1.0
HA R:TRP153 4.9 15.4 1.0
HD2 R:HIS244 5.0 13.3 1.0
HA R:CYS285 5.0 18.1 1.0

Copper binding site 6 out of 6 in 7qhm

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Copper binding site 6 out of 6 in the Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Cytochrome Bcc-AA3 Supercomplex (Respiratory Supercomplex III2/IV2) From Corynebacterium Glutamicum (Stigmatellin and Azide Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cu403

b:50.3
occ:1.00
ND1 R:HIS293 1.6 15.8 1.0
CE1 R:HIS293 2.2 15.8 1.0
HE1 R:HIS293 2.2 15.8 1.0
SG R:CYS285 2.3 18.1 1.0
SG R:CYS289 2.4 17.4 1.0
O R:GLU287 2.5 18.3 1.0
CU1 R:CUA402 2.6 56.5 1.0
CG R:HIS293 2.9 15.8 1.0
HB3 R:CYS285 3.0 18.1 1.0
CB R:CYS285 3.3 18.1 1.0
HB3 R:CYS289 3.3 17.4 1.0
NE2 R:HIS293 3.4 15.8 1.0
H R:CYS289 3.4 17.4 1.0
CB R:CYS289 3.5 17.4 1.0
HA R:HIS293 3.5 15.8 1.0
H R:GLU287 3.5 18.3 1.0
HB2 R:HIS293 3.5 15.8 1.0
C R:GLU287 3.6 18.3 1.0
CB R:HIS293 3.6 15.8 1.0
N R:CYS289 3.7 17.4 1.0
CD2 R:HIS293 3.7 15.8 1.0
HA R:MET288 3.8 18.4 1.0
HB2 R:CYS285 3.8 18.1 1.0
CA R:HIS293 4.0 15.8 1.0
O R:HIS293 4.0 15.8 1.0
HE2 R:HIS293 4.1 15.8 1.0
ND1 R:HIS244 4.2 13.3 1.0
C R:MET288 4.2 18.4 1.0
CA R:CYS289 4.2 17.4 1.0
HB2 R:CYS289 4.2 17.4 1.0
N R:GLU287 4.3 18.3 1.0
CA R:MET288 4.3 18.4 1.0
HA R:HIS244 4.3 13.3 1.0
C R:CYS285 4.4 18.1 1.0
N R:MET288 4.4 18.4 1.0
C R:HIS293 4.4 15.8 1.0
CA R:CYS285 4.4 18.1 1.0
O R:CYS285 4.4 18.1 1.0
SD R:MET296 4.5 18.7 1.0
HB3 R:HIS293 4.5 15.8 1.0
CA R:GLU287 4.6 18.3 1.0
HD2 R:HIS293 4.6 15.8 1.0
HB3 R:MET296 4.7 18.7 1.0
HD1 R:TRP153 4.8 15.4 1.0
HE1 R:HIS244 4.8 13.3 1.0
N R:ALA286 4.8 16.6 1.0
HA R:CYS285 4.8 18.1 1.0
HB3 R:GLU287 4.9 18.3 1.0
CE1 R:HIS244 4.9 13.3 1.0
HB3 R:HIS244 4.9 13.3 1.0
HA R:CYS289 4.9 17.4 1.0
H R:ALA286 4.9 16.6 1.0

Reference:

W.C.Kao, C.Ortmann De Percin Northumberland, T.C.Cheng, J.Ortiz, A.Durand, O.Von Loeffelholz, O.Schilling, M.L.Biniossek, B.P.Klaholz, C.Hunte. Structural Basis For Safe and Efficient Energy Conversion in A Respiratory Supercomplex. Nat Commun V. 13 545 2022.
ISSN: ESSN 2041-1723
PubMed: 35087070
DOI: 10.1038/S41467-022-28179-X
Page generated: Wed Jul 31 09:01:14 2024

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