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Copper in PDB 8ovc: Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis

Enzymatic activity of Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis

All present enzymatic activity of Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis:
1.15.1.1; 7.1.1.8; 7.1.1.9;

Other elements in 8ovc:

The structure of Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis also contains other interesting chemical elements:

Iron (Fe) 16 atoms
Magnesium (Mg) 2 atoms
Calcium (Ca) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis (pdb code 8ovc). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis, PDB code: 8ovc:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 8ovc

Go back to Copper Binding Sites List in 8ovc
Copper binding site 1 out of 6 in the Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cu604

b:22.2
occ:1.00
 NE2 R:HIS314 1.9 18.4 1.0
NE2 R:HIS313 2.0 17.7 1.0
ND1 R:HIS264 2.0 13.3 1.0
CE1 R:HIS264 2.3 13.5 1.0
CD2 R:HIS313 2.4 17.8 1.0
CD2 R:HIS314 2.5 18.3 1.0
CE1 R:HIS314 2.9 18.3 1.0
CE1 R:HIS313 3.2 17.7 1.0
CG R:HIS264 3.2 13.2 1.0
NE2 R:HIS264 3.5 13.4 1.0
CG R:HIS314 3.5 18.3 1.0
ND1 R:HIS314 3.7 18.2 1.0
CG R:HIS313 3.7 17.8 1.0
CD2 R:HIS264 3.9 13.3 1.0
C4A R:HEA602 3.9 16.1 1.0
C1A R:HEA602 3.9 16.2 1.0
CB R:HIS264 4.0 13.0 1.0
ND1 R:HIS313 4.0 17.8 1.0
C3A R:HEA602 4.0 16.1 1.0
C2A R:HEA602 4.0 16.2 1.0
NA R:HEA602 4.0 16.1 1.0
FE R:HEA602 4.4 16.1 1.0
CHB R:HEA602 4.6 16.2 1.0
CHA R:HEA602 4.6 16.1 1.0
CMA R:HEA602 4.7 15.9 1.0
N R:HIS314 4.7 18.0 1.0
CAA R:HEA602 4.7 16.4 1.0
CB R:HIS314 4.8 18.2 1.0
OMA R:HEA602 4.8 15.8 1.0
O R:VAL310 4.9 17.6 1.0
ND R:HEA602 4.9 16.2 1.0
CB R:HIS313 5.0 17.8 1.0
NB R:HEA602 5.0 16.3 1.0

Copper binding site 2 out of 6 in 8ovc

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Copper binding site 2 out of 6 in the Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Cu401

b:13.1
occ:1.00
 ND1 Q:HIS281 2.0 14.3 1.0
SG Q:CYS277 2.1 14.0 1.0
SG Q:CYS273 2.6 14.3 1.0
CU Q:CU402 2.8 11.1 1.0
CE1 Q:HIS281 2.8 14.3 1.0
N Q:CYS277 2.8 14.1 1.0
CB Q:CYS277 2.8 14.0 1.0
CG Q:HIS281 3.0 14.3 1.0
CA Q:CYS277 3.4 13.9 1.0
CB Q:HIS281 3.5 14.3 1.0
N Q:MET276 3.7 14.5 1.0
C Q:MET276 3.8 14.1 1.0
NE2 Q:HIS281 3.9 14.2 1.0
CA Q:HIS281 4.0 14.4 1.0
CD2 Q:HIS281 4.0 14.3 1.0
CA Q:MET276 4.0 14.3 1.0
N Q:GLU275 4.1 14.6 1.0
CB Q:CYS273 4.1 14.4 1.0
ND1 Q:HIS232 4.2 14.4 1.0
O Q:HIS281 4.3 14.5 1.0
C Q:GLU275 4.3 14.6 1.0
C Q:CYS277 4.4 13.8 1.0
CA Q:GLU275 4.5 14.7 1.0
CB Q:GLU275 4.6 14.9 1.0
SD Q:MET284 4.6 15.1 1.0
C Q:HIS281 4.6 14.5 1.0
N Q:GLY278 4.7 13.7 1.0
C Q:CYS273 4.9 14.5 1.0
O Q:MET276 4.9 14.1 1.0
O Q:CYS273 5.0 14.5 1.0
CE1 Q:HIS232 5.0 14.4 1.0

Copper binding site 3 out of 6 in 8ovc

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Copper binding site 3 out of 6 in the Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Cu402

b:11.1
occ:1.00
 ND1 Q:HIS232 2.1 14.4 1.0
SG Q:CYS277 2.3 14.0 1.0
SD Q:MET284 2.3 15.1 1.0
SG Q:CYS273 2.6 14.3 1.0
CU Q:CU401 2.8 13.1 1.0
CE Q:MET284 2.8 15.2 1.0
CE1 Q:HIS232 2.9 14.4 1.0
CG Q:HIS232 3.2 14.5 1.0
CB Q:CYS277 3.3 14.0 1.0
CB Q:HIS232 3.6 14.6 1.0
CB Q:CYS273 3.8 14.4 1.0
CG Q:MET284 4.0 15.3 1.0
NE2 Q:HIS232 4.1 14.4 1.0
CD2 Q:HIS232 4.2 14.4 1.0
CA Q:HIS232 4.4 14.8 1.0
ND1 Q:HIS281 4.4 14.3 1.0
CB Q:MET284 4.5 15.4 1.0
CA Q:CYS277 4.6 13.9 1.0
N Q:CYS277 4.9 14.1 1.0
O Q:PHE136 5.0 20.4 1.0

Copper binding site 4 out of 6 in 8ovc

Go back to Copper Binding Sites List in 8ovc
Copper binding site 4 out of 6 in the Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cu604

b:19.4
occ:1.00
 ND1 L:HIS264 2.1 10.9 1.0
NE2 L:HIS314 2.3 14.3 1.0
NE2 L:HIS313 2.5 13.1 1.0
CE1 L:HIS264 2.6 11.0 1.0
CE1 L:HIS314 2.9 14.3 1.0
FE L:HEA602 3.1 16.1 1.0
NA L:HEA602 3.2 16.1 1.0
CD2 L:HIS314 3.3 14.2 1.0
CD2 L:HIS313 3.4 13.2 1.0
C4A L:HEA602 3.4 16.1 1.0
C1A L:HEA602 3.4 16.2 1.0
CE1 L:HIS313 3.5 13.1 1.0
CG L:HIS264 3.5 10.8 1.0
ND L:HEA602 3.8 16.2 1.0
NE2 L:HIS264 3.9 11.0 1.0
NB L:HEA602 3.9 16.3 1.0
C3A L:HEA602 4.0 16.1 1.0
C2A L:HEA602 4.0 16.2 1.0
ND1 L:HIS314 4.0 14.1 1.0
CHA L:HEA602 4.1 16.1 1.0
CHB L:HEA602 4.1 16.2 1.0
CB L:HIS264 4.2 10.7 1.0
C4D L:HEA602 4.2 16.2 1.0
CG L:HIS314 4.2 14.1 1.0
C1B L:HEA602 4.3 16.3 1.0
CD2 L:HIS264 4.3 10.9 1.0
NC L:HEA602 4.5 16.2 1.0
CG L:HIS313 4.5 13.2 1.0
ND1 L:HIS313 4.5 13.1 1.0
C1D L:HEA602 4.8 16.2 1.0
C4B L:HEA602 4.9 16.4 1.0
CG2 L:VAL267 4.9 10.9 1.0
CMA L:HEA602 4.9 15.9 1.0
CA L:HIS264 5.0 10.5 1.0
CAA L:HEA602 5.0 16.4 1.0

Copper binding site 5 out of 6 in 8ovc

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Copper binding site 5 out of 6 in the Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cu401

b:12.5
occ:1.00
 ND1 X:HIS281 2.0 11.0 1.0
O X:GLU275 2.2 11.1 1.0
SG X:CYS277 2.3 10.2 1.0
SG X:CYS273 2.4 12.1 1.0
CE1 X:HIS281 2.7 11.0 1.0
CU X:CU402 2.7 8.1 1.0
CG X:HIS281 3.1 11.0 1.0
CB X:CYS277 3.3 10.3 1.0
C X:GLU275 3.3 11.0 1.0
N X:CYS277 3.6 10.4 1.0
CB X:CYS273 3.7 12.1 1.0
CB X:HIS281 3.8 11.1 1.0
NE2 X:HIS281 3.9 11.0 1.0
CA X:HIS281 4.0 11.1 1.0
N X:GLU275 4.0 11.3 1.0
CA X:CYS277 4.0 10.3 1.0
CD2 X:HIS281 4.1 11.0 1.0
C X:MET276 4.1 10.6 1.0
O X:HIS281 4.1 11.2 1.0
N X:MET276 4.2 10.8 1.0
CA X:GLU275 4.2 11.2 1.0
CA X:MET276 4.3 10.7 1.0
SD X:MET284 4.3 11.8 1.0
ND1 X:HIS232 4.3 11.4 1.0
C X:HIS281 4.5 11.2 1.0
C X:CYS273 4.7 11.9 1.0
CA X:CYS273 4.8 12.1 1.0
CB X:GLU275 4.8 11.3 1.0
N X:THR274 4.8 11.7 1.0
O X:MET276 4.9 10.6 1.0
CA X:HIS232 4.9 11.8 1.0
O X:ILE231 5.0 11.9 1.0
O X:CYS273 5.0 11.9 1.0

Copper binding site 6 out of 6 in 8ovc

Go back to Copper Binding Sites List in 8ovc
Copper binding site 6 out of 6 in the Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Respiratory Supercomplex (III2-IV2) From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cu402

b:8.1
occ:1.00
 ND1 X:HIS232 2.1 11.4 1.0
SD X:MET284 2.3 11.8 1.0
SG X:CYS277 2.5 10.2 1.0
SG X:CYS273 2.6 12.1 1.0
CU X:CU401 2.7 12.5 1.0
CE1 X:HIS232 2.9 11.4 1.0
CE X:MET284 2.9 11.7 1.0
CG X:HIS232 3.2 11.5 1.0
CB X:CYS277 3.5 10.3 1.0
CB X:HIS232 3.7 11.6 1.0
CB X:CYS273 3.8 12.1 1.0
CG X:MET284 3.9 11.9 1.0
NE2 X:HIS232 4.1 11.4 1.0
CD2 X:HIS232 4.2 11.4 1.0
CA X:HIS232 4.3 11.8 1.0
O X:GLU275 4.4 11.1 1.0
ND1 X:HIS281 4.4 11.0 1.0
O X:ILE231 4.9 11.9 1.0
CA X:CYS277 4.9 10.3 1.0
N X:GLY233 5.0 12.0 1.0

Reference:

D.Riepl, A.P.Gamiz-Hernandez, T.Kovalova, S.M.Krol, S.L.Mader, D.Sjostrand, M.Hogbom, P.Brzezinski, V.R.I.Kaila. Long-Range Charge Transfer Mechanism of the III 2 IV 2 Mycobacterial Supercomplex. Nat Commun V. 15 5276 2024.
ISSN: ESSN 2041-1723
PubMed: 38902248
DOI: 10.1038/S41467-024-49628-9
Page generated: Wed Jul 31 09:52:54 2024

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