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Copper in PDB 9dm1: Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly

Enzymatic activity of Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly

All present enzymatic activity of Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly:
1.1.5.4; 1.15.1.1; 7.1.1.8; 7.1.1.9;

Other elements in 9dm1:

The structure of Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly also contains other interesting chemical elements:

Iron (Fe) 16 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly (pdb code 9dm1). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly, PDB code: 9dm1:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 9dm1

Go back to Copper Binding Sites List in 9dm1
Copper binding site 1 out of 6 in the Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cu601

b:76.2
occ:1.00
 NE2 R:HIS314 2.0 51.6 1.0
ND1 R:HIS264 2.1 50.5 1.0
NE2 R:HIS313 2.2 52.3 1.0
CE1 R:HIS313 2.3 52.3 1.0
CE1 R:HIS314 2.6 51.6 1.0
CE1 R:HIS264 2.6 50.5 1.0
CD2 R:HIS314 3.2 51.6 1.0
CG R:HIS264 3.3 50.5 1.0
CD2 R:HIS313 3.5 52.3 1.0
ND1 R:HIS313 3.6 52.3 1.0
ND1 R:HIS314 3.7 51.6 1.0
NA R:HEA602 3.7 50.9 1.0
NE2 R:HIS264 3.9 50.5 1.0
CB R:HIS264 4.0 50.5 1.0
FE R:HEA602 4.0 50.9 1.0
CG R:HIS314 4.0 51.6 1.0
C1A R:HEA602 4.0 50.9 1.0
CG R:HIS313 4.1 52.3 1.0
C4A R:HEA602 4.2 50.9 1.0
CD2 R:HIS264 4.2 50.5 1.0
ND R:HEA602 4.3 50.9 1.0
CHA R:HEA602 4.4 50.9 1.0
CG2 R:VAL267 4.4 48.5 1.0
CA R:HIS264 4.5 50.5 1.0
C4D R:HEA602 4.5 50.9 1.0
NB R:HEA602 4.6 50.9 1.0
CHB R:HEA602 4.7 50.9 1.0
C2A R:HEA602 4.7 50.9 1.0
C3A R:HEA602 4.7 50.9 1.0
C1B R:HEA602 4.8 50.9 1.0

Copper binding site 2 out of 6 in 9dm1

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Copper binding site 2 out of 6 in the Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cu601

b:70.8
occ:1.00
 CD2 L:HIS264 1.9 46.5 1.0
NE2 L:HIS314 2.0 47.9 1.0
NE2 L:HIS313 2.3 48.5 1.0
CE1 L:HIS313 2.4 48.5 1.0
NE2 L:HIS264 2.6 46.5 1.0
CG L:HIS264 2.8 46.5 1.0
CE1 L:HIS314 2.8 47.9 1.0
CD2 L:HIS314 3.1 47.9 1.0
CD2 L:HIS313 3.5 48.5 1.0
CE1 L:HIS264 3.5 46.5 1.0
CB L:HIS264 3.6 46.5 1.0
ND1 L:HIS264 3.6 46.5 1.0
ND1 L:HIS313 3.6 48.5 1.0
ND1 L:HIS314 3.9 47.9 1.0
NA L:HEA602 4.0 47.9 1.0
FE L:HEA602 4.1 47.9 1.0
CG L:HIS314 4.1 47.9 1.0
CG L:HIS313 4.2 48.5 1.0
CA L:HIS264 4.3 46.5 1.0
CG2 L:VAL267 4.3 45.3 1.0
C1A L:HEA602 4.3 47.9 1.0
C4A L:HEA602 4.4 47.9 1.0
ND L:HEA602 4.5 47.9 1.0
NB L:HEA602 4.6 47.9 1.0
CHA L:HEA602 4.7 47.9 1.0
C4D L:HEA602 4.7 47.9 1.0
O L:VAL310 4.8 47.7 1.0
CHB L:HEA602 4.8 47.9 1.0
C1B L:HEA602 4.9 47.9 1.0

Copper binding site 3 out of 6 in 9dm1

Go back to Copper Binding Sites List in 9dm1
Copper binding site 3 out of 6 in the Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Cu401

b:71.3
occ:1.00
 ND1 Q:HIS281 2.0 51.1 1.0
SG Q:CYS273 2.1 52.7 1.0
CE1 Q:HIS281 2.2 51.1 1.0
SG Q:CYS277 2.2 51.9 1.0
CB Q:CYS273 2.3 52.7 1.0
CG Q:HIS281 3.4 51.1 1.0
CA Q:CYS273 3.4 52.7 1.0
C Q:CYS273 3.5 52.7 1.0
NE2 Q:HIS281 3.5 51.1 1.0
O Q:HIS281 3.5 51.1 1.0
O Q:CYS273 3.6 52.7 1.0
SD Q:MET284 3.9 53.1 1.0
CB Q:CYS277 3.9 51.9 1.0
O Q:GLU275 4.0 52.4 1.0
CD2 Q:HIS281 4.0 51.1 1.0
N Q:THR274 4.1 51.7 1.0
N Q:GLU275 4.2 52.4 1.0
CB Q:HIS281 4.2 51.1 1.0
CB Q:HIS232 4.3 53.9 1.0
C Q:HIS281 4.3 51.1 1.0
CA Q:HIS281 4.3 51.1 1.0
C Q:GLU275 4.4 52.4 1.0
N Q:CYS273 4.5 52.7 1.0
CB Q:MET284 4.5 53.1 1.0
CG Q:MET284 4.6 53.1 1.0
N Q:CYS277 4.6 51.9 1.0
N Q:GLY233 4.7 53.3 1.0
CA Q:GLU275 4.8 52.4 1.0
O Q:GLY233 4.8 53.3 1.0
CA Q:CYS277 4.9 51.9 1.0
CE Q:MET284 5.0 53.1 1.0

Copper binding site 4 out of 6 in 9dm1

Go back to Copper Binding Sites List in 9dm1
Copper binding site 4 out of 6 in the Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Cu402

b:65.3
occ:1.00
 ND1 Q:HIS232 2.0 53.9 1.0
CG Q:HIS232 2.2 53.9 1.0
CE1 Q:HIS232 2.3 53.9 1.0
CD2 Q:HIS232 2.5 53.9 1.0
NE2 Q:HIS232 2.6 53.9 1.0
CB Q:HIS232 3.1 53.9 1.0
O Q:PHE136 3.4 55.8 1.0
SD Q:MET284 3.4 53.1 1.0
CB Q:CYS277 3.4 51.9 1.0
SG Q:CYS277 3.7 51.9 1.0
CG1 Q:VAL230 3.8 52.6 1.0
CE Q:MET284 3.8 53.1 1.0
CA Q:CYS277 4.3 51.9 1.0
C Q:PHE136 4.3 55.8 1.0
N Q:TRP138 4.3 53.6 1.0
O Q:VAL230 4.3 52.6 1.0
NE2 Q:GLN137 4.4 54.5 1.0
CA Q:HIS232 4.5 53.9 1.0
O Q:ALA135 4.5 54.7 1.0
CA Q:GLN137 4.6 54.5 1.0
O Q:ILE231 4.6 52.2 1.0
SG Q:CYS273 4.7 52.7 1.0
N Q:HIS232 4.8 53.9 1.0
N Q:GLN137 4.8 54.5 1.0
O Q:CYS277 4.9 51.9 1.0
C Q:ILE231 4.9 52.2 1.0
C Q:ALA135 5.0 54.7 1.0

Copper binding site 5 out of 6 in 9dm1

Go back to Copper Binding Sites List in 9dm1
Copper binding site 5 out of 6 in the Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu401

b:67.6
occ:1.00
 ND1 K:HIS281 2.0 46.6 1.0
SG K:CYS273 2.2 48.5 1.0
SG K:CYS277 2.2 47.2 1.0
CE1 K:HIS281 2.4 46.6 1.0
CB K:CYS273 2.6 48.5 1.0
O K:GLU275 2.6 47.7 1.0
CG K:HIS281 3.3 46.6 1.0
C K:CYS273 3.3 48.5 1.0
O K:HIS281 3.3 46.6 1.0
CA K:CYS273 3.5 48.5 1.0
O K:CYS273 3.5 48.5 1.0
NE2 K:HIS281 3.6 46.6 1.0
N K:GLU275 3.8 47.7 1.0
N K:THR274 3.8 48.0 1.0
C K:GLU275 3.8 47.7 1.0
CB K:CYS277 4.0 47.2 1.0
CD2 K:HIS281 4.1 46.6 1.0
CB K:HIS281 4.1 46.6 1.0
C K:HIS281 4.1 46.6 1.0
SD K:MET284 4.1 49.4 1.0
CA K:HIS281 4.2 46.6 1.0
CB K:HIS232 4.2 48.9 1.0
N K:CYS277 4.4 47.2 1.0
CA K:GLU275 4.4 47.7 1.0
CA K:THR274 4.6 48.0 1.0
N K:CYS273 4.7 48.5 1.0
C K:THR274 4.7 48.0 1.0
CU K:CU402 4.8 65.5 1.0
CA K:CYS277 4.8 47.2 1.0
CB K:MET284 4.8 49.4 1.0
N K:MET276 4.8 45.8 1.0
C K:MET276 4.9 45.8 1.0
N K:GLY233 4.9 48.7 1.0
CE K:MET284 4.9 49.4 1.0

Copper binding site 6 out of 6 in 9dm1

Go back to Copper Binding Sites List in 9dm1
Copper binding site 6 out of 6 in the Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu402

b:65.5
occ:1.00
 ND1 K:HIS232 2.0 48.9 1.0
CG K:HIS232 2.2 48.9 1.0
CE1 K:HIS232 2.4 48.9 1.0
SD K:MET284 2.7 49.4 1.0
CD2 K:HIS232 2.7 48.9 1.0
NE2 K:HIS232 2.8 48.9 1.0
CE K:MET284 2.8 49.4 1.0
CB K:HIS232 3.0 48.9 1.0
CB K:CYS277 3.3 47.2 1.0
SG K:CYS277 3.4 47.2 1.0
O K:PHE136 3.5 51.2 1.0
SG K:CYS273 3.9 48.5 1.0
N K:TRP138 4.2 49.0 1.0
CA K:CYS277 4.3 47.2 1.0
C K:PHE136 4.4 51.2 1.0
CG K:MET284 4.5 49.4 1.0
CA K:HIS232 4.5 48.9 1.0
CA K:GLN137 4.7 49.0 1.0
CU K:CU401 4.8 67.6 1.0
CG1 K:VAL230 4.8 47.8 1.0
O K:ILE231 4.8 47.6 1.0
CB K:ALA135 4.9 50.3 1.0
N K:HIS232 4.9 48.9 1.0
O K:ALA135 4.9 50.3 1.0
CA K:TRP138 5.0 49.0 1.0
OE1 K:GLN137 5.0 49.0 1.0
C K:GLN137 5.0 49.0 1.0

Reference:

J.M.Di Trani, J.Yu, G.M.Courbon, A.P.Lobez Rodriguez, J.Cheung, Y.Liang, C.E.Coupland, S.A.Bueler, G.M.Cook, P.Brzezinski, J.L.Rubinstein. Cryo-Em of Native Membranes Reveals An Intimate Connection Between Krebs Cycle and Respiration in Mycobacteria To Be Published.
Page generated: Thu Oct 31 19:43:06 2024

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