Atomistry » Copper » PDB 8yk7-9fdl » 9dm1
Atomistry »
  Copper »
    PDB 8yk7-9fdl »
      9dm1 »

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

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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy