Copper in PDB 9dm1: Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly
Enzymatic activity of Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly
Other elements in 9dm1:
The structure of Mycobacterial Supercomplex Malate:Quinone Oxidoreductase Assembly also contains other interesting chemical elements:
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
Go back to
Copper Binding Sites List in 9dm1
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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