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Copper in PDB 8ovd: 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 8ovd:

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

Magnesium (Mg) 2 atoms
Iron (Fe) 16 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 8ovd). 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: 8ovd:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 8ovd

Go back to Copper Binding Sites List in 8ovd
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:56.6
occ:1.00
 NE2 R:HIS314 2.0 10.8 1.0
NE2 R:HIS313 2.0 12.1 1.0
ND1 R:HIS264 2.1 10.2 1.0
CE1 R:HIS314 2.8 10.8 1.0
CD2 R:HIS314 2.9 10.8 1.0
CE1 R:HIS313 2.9 12.1 1.0
CE1 R:HIS264 3.0 10.2 1.0
CD2 R:HIS313 3.1 12.1 1.0
CG R:HIS264 3.3 10.2 1.0
CB R:HIS264 3.7 10.2 1.0
O R:HOH759 3.8 30.0 1.0
ND1 R:HIS314 3.9 10.8 1.0
CG R:HIS314 3.9 10.8 1.0
ND1 R:HIS313 4.1 12.1 1.0
C1A R:HEA602 4.2 13.1 1.0
NE2 R:HIS264 4.3 10.2 1.0
CG R:HIS313 4.3 12.1 1.0
NA R:HEA602 4.3 13.1 1.0
FE R:HEA602 4.3 13.1 1.0
CA R:HIS264 4.3 10.2 1.0
CD2 R:HIS264 4.4 10.2 1.0
C4A R:HEA602 4.5 13.1 1.0
C2A R:HEA602 4.5 13.1 1.0
CHA R:HEA602 4.6 13.1 1.0
ND R:HEA602 4.6 13.1 1.0
C3A R:HEA602 4.7 13.1 1.0
C4D R:HEA602 4.7 13.1 1.0
CG2 R:VAL267 4.8 8.5 1.0
O R:HOH711 4.8 18.3 1.0
NB R:HEA602 5.0 13.1 1.0

Copper binding site 2 out of 6 in 8ovd

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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:42.9
occ:1.00
 ND1 Q:HIS232 2.0 9.9 1.0
SG Q:CYS277 2.3 9.4 1.0
SD Q:MET284 2.4 10.3 1.0
SG Q:CYS273 2.5 10.8 1.0
CU Q:CU402 2.6 42.4 1.0
CE1 Q:HIS232 2.9 9.9 1.0
CG Q:HIS232 3.1 9.9 1.0
CB Q:CYS277 3.2 9.4 1.0
CE Q:MET284 3.2 10.3 1.0
CB Q:HIS232 3.5 9.9 1.0
CB Q:CYS273 3.7 10.8 1.0
CG Q:MET284 3.8 10.3 1.0
NE2 Q:HIS232 4.0 9.9 1.0
CA Q:HIS232 4.1 9.9 1.0
O Q:GLU275 4.1 11.3 1.0
CD2 Q:HIS232 4.1 9.9 1.0
ND1 Q:HIS281 4.4 9.3 1.0
CD1 Q:TRP138 4.5 10.8 1.0
CA Q:CYS277 4.6 9.4 1.0
O Q:PHE136 4.7 10.6 1.0
N Q:CYS277 4.9 9.4 1.0
N Q:GLY233 5.0 10.5 1.0
CA Q:HIS281 5.0 9.3 1.0

Copper binding site 3 out of 6 in 8ovd

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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:42.4
occ:1.00
 ND1 Q:HIS281 1.9 9.3 1.0
SG Q:CYS273 2.1 10.8 1.0
SG Q:CYS277 2.2 9.4 1.0
CU Q:CU401 2.6 42.9 1.0
O Q:GLU275 2.6 11.3 1.0
CE1 Q:HIS281 2.7 9.3 1.0
CG Q:HIS281 3.0 9.3 1.0
CB Q:CYS273 3.2 10.8 1.0
CB Q:CYS277 3.4 9.4 1.0
CB Q:HIS281 3.5 9.3 1.0
C Q:GLU275 3.6 11.3 1.0
CA Q:HIS281 3.7 9.3 1.0
N Q:CYS277 3.7 9.4 1.0
O Q:HIS281 3.8 9.3 1.0
NE2 Q:HIS281 3.9 9.3 1.0
CD2 Q:HIS281 4.0 9.3 1.0
SD Q:MET284 4.1 10.3 1.0
N Q:GLU275 4.2 11.3 1.0
CA Q:CYS277 4.2 9.4 1.0
C Q:HIS281 4.2 9.3 1.0
ND1 Q:HIS232 4.3 9.9 1.0
C Q:CYS273 4.3 10.8 1.0
C Q:MET276 4.4 8.5 1.0
CA Q:CYS273 4.4 10.8 1.0
N Q:MET276 4.4 8.5 1.0
CA Q:MET276 4.4 8.5 1.0
O Q:CYS273 4.5 10.8 1.0
CA Q:GLU275 4.5 11.3 1.0
CG Q:MET284 4.6 10.3 1.0
N Q:THR274 4.7 11.3 1.0
CA Q:HIS232 4.9 9.9 1.0
N Q:HIS281 4.9 9.3 1.0

Copper binding site 4 out of 6 in 8ovd

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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:57.0
occ:1.00
 NE2 L:HIS314 1.9 10.8 1.0
NE2 L:HIS313 2.0 12.1 1.0
ND1 L:HIS264 2.3 10.2 1.0
CE1 L:HIS314 2.8 10.8 1.0
CD2 L:HIS314 2.9 10.8 1.0
CE1 L:HIS313 2.9 12.1 1.0
CD2 L:HIS313 3.1 12.1 1.0
CE1 L:HIS264 3.1 10.2 1.0
CG L:HIS264 3.4 10.2 1.0
CB L:HIS264 3.8 10.2 1.0
ND1 L:HIS314 3.8 10.8 1.0
CG L:HIS314 3.9 10.8 1.0
O L:HOH775 4.0 15.5 1.0
C1A L:HEA602 4.0 12.9 1.0
ND1 L:HIS313 4.1 12.1 1.0
NA L:HEA602 4.2 12.9 1.0
CG L:HIS313 4.2 12.1 1.0
FE L:HEA602 4.3 12.9 1.0
NE2 L:HIS264 4.3 10.2 1.0
C4A L:HEA602 4.3 12.9 1.0
C2A L:HEA602 4.4 12.9 1.0
CA L:HIS264 4.4 10.2 1.0
CHA L:HEA602 4.5 12.9 1.0
CD2 L:HIS264 4.5 10.2 1.0
ND L:HEA602 4.5 12.9 1.0
C3A L:HEA602 4.6 12.9 1.0
C4D L:HEA602 4.6 12.9 1.0
O L:HOH710 4.8 19.5 1.0
CG2 L:VAL267 4.8 8.5 1.0
NB L:HEA602 4.9 12.9 1.0

Copper binding site 5 out of 6 in 8ovd

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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:42.6
occ:1.00
 ND1 X:HIS281 1.9 9.7 1.0
SG X:CYS277 2.1 9.8 1.0
SG X:CYS273 2.2 11.1 1.0
O X:GLU275 2.5 11.6 1.0
CU X:CU402 2.6 41.9 1.0
CE1 X:HIS281 2.7 9.7 1.0
CG X:HIS281 3.0 9.7 1.0
CB X:CYS277 3.3 9.8 1.0
CB X:CYS273 3.3 11.1 1.0
CB X:HIS281 3.5 9.7 1.0
C X:GLU275 3.5 11.6 1.0
N X:CYS277 3.6 9.8 1.0
CA X:HIS281 3.7 9.7 1.0
NE2 X:HIS281 3.9 9.7 1.0
O X:HIS281 3.9 9.7 1.0
CD2 X:HIS281 4.0 9.7 1.0
CA X:CYS277 4.1 9.8 1.0
SD X:MET284 4.1 10.3 1.0
N X:GLU275 4.2 11.6 1.0
C X:MET276 4.2 8.8 1.0
ND1 X:HIS232 4.3 10.2 1.0
C X:HIS281 4.3 9.7 1.0
N X:MET276 4.3 8.8 1.0
CA X:MET276 4.3 8.8 1.0
C X:CYS273 4.4 11.1 1.0
CA X:GLU275 4.5 11.6 1.0
CA X:CYS273 4.5 11.1 1.0
O X:CYS273 4.6 11.1 1.0
CG X:MET284 4.7 10.3 1.0
N X:THR274 4.7 11.6 1.0
CA X:HIS232 4.9 10.2 1.0
N X:HIS281 4.9 9.7 1.0

Copper binding site 6 out of 6 in 8ovd

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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:41.9
occ:1.00
 ND1 X:HIS232 2.0 10.2 1.0
SG X:CYS277 2.3 9.8 1.0
SD X:MET284 2.4 10.3 1.0
SG X:CYS273 2.5 11.1 1.0
CU X:CU401 2.6 42.6 1.0
CE1 X:HIS232 2.9 10.2 1.0
CG X:HIS232 3.1 10.2 1.0
CB X:CYS277 3.2 9.8 1.0
CE X:MET284 3.2 10.3 1.0
CB X:HIS232 3.5 10.2 1.0
CB X:CYS273 3.7 11.1 1.0
CG X:MET284 3.8 10.3 1.0
NE2 X:HIS232 4.0 10.2 1.0
CA X:HIS232 4.1 10.2 1.0
O X:GLU275 4.1 11.6 1.0
CD2 X:HIS232 4.1 10.2 1.0
ND1 X:HIS281 4.4 9.7 1.0
CD1 X:TRP138 4.5 10.8 1.0
CA X:CYS277 4.6 9.8 1.0
N X:CYS277 4.9 9.8 1.0
CA X:HIS281 5.0 9.7 1.0
N X:GLY233 5.0 10.7 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 09:53:03 2024

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