Copper in PDB 6adq: Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis
Enzymatic activity of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis
All present enzymatic activity of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis:
1.10.2.2;
1.15.1.1;
1.9.3.1;
Other elements in 6adq:
The structure of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis also contains other interesting chemical elements:
Copper Binding Sites:
The binding sites of Copper atom in the Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis
(pdb code 6adq). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the
Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis, PDB code: 6adq:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Copper binding site 1 out
of 8 in 6adq
Go back to
Copper Binding Sites List in 6adq
Copper binding site 1 out
of 8 in the Respiratory Complex CIII2CIV2SOD2 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 Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cu401
b:48.4
occ:1.00
|
CU
|
E:CU402
|
1.6
|
64.4
|
1.0
|
ND1
|
E:HIS281
|
2.3
|
34.4
|
1.0
|
SG
|
E:CYS277
|
2.5
|
34.5
|
1.0
|
SG
|
E:CYS273
|
2.5
|
34.5
|
1.0
|
CE1
|
E:HIS281
|
2.5
|
34.4
|
1.0
|
SD
|
E:MET284
|
2.5
|
35.7
|
1.0
|
CB
|
E:CYS277
|
3.0
|
34.5
|
1.0
|
CB
|
E:HIS232
|
3.4
|
36.2
|
1.0
|
CE
|
E:MET284
|
3.5
|
35.7
|
1.0
|
CG
|
E:HIS232
|
3.6
|
36.2
|
1.0
|
CG
|
E:HIS281
|
3.6
|
34.4
|
1.0
|
NE2
|
E:HIS281
|
3.8
|
34.4
|
1.0
|
CB
|
E:CYS273
|
3.8
|
34.5
|
1.0
|
CD2
|
E:HIS232
|
4.0
|
36.2
|
1.0
|
N
|
E:CYS277
|
4.0
|
34.5
|
1.0
|
CA
|
E:CYS277
|
4.0
|
34.5
|
1.0
|
CG
|
E:MET284
|
4.1
|
35.7
|
1.0
|
ND1
|
E:HIS232
|
4.2
|
36.2
|
1.0
|
O
|
E:HIS281
|
4.3
|
34.4
|
1.0
|
CD2
|
E:HIS281
|
4.3
|
34.4
|
1.0
|
CB
|
E:HIS281
|
4.5
|
34.4
|
1.0
|
CA
|
E:HIS281
|
4.5
|
34.4
|
1.0
|
CB
|
E:MET284
|
4.5
|
35.7
|
1.0
|
NE2
|
E:HIS232
|
4.7
|
36.2
|
1.0
|
CE1
|
E:HIS232
|
4.8
|
36.2
|
1.0
|
C
|
E:MET276
|
4.8
|
32.4
|
1.0
|
CA
|
E:HIS232
|
4.9
|
36.2
|
1.0
|
C
|
E:HIS281
|
4.9
|
34.4
|
1.0
|
CA
|
E:CYS273
|
5.0
|
34.5
|
1.0
|
C
|
E:CYS273
|
5.0
|
34.5
|
1.0
|
|
Copper binding site 2 out
of 8 in 6adq
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Copper Binding Sites List in 6adq
Copper binding site 2 out
of 8 in the Respiratory Complex CIII2CIV2SOD2 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 Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cu402
b:64.4
occ:1.00
|
CU
|
E:CU401
|
1.6
|
48.4
|
1.0
|
CG
|
E:HIS232
|
2.4
|
36.2
|
1.0
|
SG
|
E:CYS277
|
2.4
|
34.5
|
1.0
|
SG
|
E:CYS273
|
2.4
|
34.5
|
1.0
|
CD2
|
E:HIS232
|
2.5
|
36.2
|
1.0
|
SD
|
E:MET284
|
2.5
|
35.7
|
1.0
|
CE
|
E:MET284
|
2.5
|
35.7
|
1.0
|
CB
|
E:HIS232
|
2.8
|
36.2
|
1.0
|
ND1
|
E:HIS232
|
2.9
|
36.2
|
1.0
|
NE2
|
E:HIS232
|
3.0
|
36.2
|
1.0
|
CE1
|
E:HIS232
|
3.3
|
36.2
|
1.0
|
CB
|
E:CYS277
|
3.7
|
34.5
|
1.0
|
ND1
|
E:HIS281
|
4.0
|
34.4
|
1.0
|
CE1
|
E:HIS281
|
4.0
|
34.4
|
1.0
|
CB
|
E:CYS273
|
4.0
|
34.5
|
1.0
|
CG
|
E:MET284
|
4.1
|
35.7
|
1.0
|
CA
|
E:HIS232
|
4.3
|
36.2
|
1.0
|
CB
|
E:MET284
|
4.4
|
35.7
|
1.0
|
CA
|
E:CYS277
|
4.9
|
34.5
|
1.0
|
N
|
E:GLY233
|
4.9
|
33.3
|
1.0
|
|
Copper binding site 3 out
of 8 in 6adq
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Copper Binding Sites List in 6adq
Copper binding site 3 out
of 8 in the Respiratory Complex CIII2CIV2SOD2 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 Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cu603
b:35.4
occ:1.00
|
ND1
|
F:HIS264
|
2.1
|
24.9
|
1.0
|
NE2
|
F:HIS314
|
2.2
|
27.8
|
1.0
|
CE1
|
F:HIS313
|
2.3
|
28.1
|
1.0
|
CE1
|
F:HIS314
|
2.3
|
27.8
|
1.0
|
NE2
|
F:HIS313
|
2.6
|
28.1
|
1.0
|
CE1
|
F:HIS264
|
2.9
|
24.9
|
1.0
|
CG
|
F:HIS264
|
3.0
|
24.9
|
1.0
|
ND1
|
F:HIS313
|
3.4
|
28.1
|
1.0
|
CD2
|
F:HIS314
|
3.4
|
27.8
|
1.0
|
CB
|
F:HIS264
|
3.5
|
24.9
|
1.0
|
ND1
|
F:HIS314
|
3.5
|
27.8
|
1.0
|
CD2
|
F:HIS313
|
3.8
|
28.1
|
1.0
|
NE2
|
F:HIS264
|
4.0
|
24.9
|
1.0
|
C1A
|
F:HEA601
|
4.1
|
27.5
|
1.0
|
CD2
|
F:HIS264
|
4.1
|
24.9
|
1.0
|
CG
|
F:HIS314
|
4.1
|
27.8
|
1.0
|
NA
|
F:HEA601
|
4.1
|
27.5
|
1.0
|
CG
|
F:HIS313
|
4.2
|
28.1
|
1.0
|
CA
|
F:HIS264
|
4.3
|
24.9
|
1.0
|
C4D
|
F:HEA601
|
4.3
|
27.5
|
1.0
|
ND
|
F:HEA601
|
4.3
|
27.5
|
1.0
|
CHA
|
F:HEA601
|
4.4
|
27.5
|
1.0
|
CG2
|
F:VAL267
|
4.5
|
24.6
|
1.0
|
C2A
|
F:HEA601
|
4.5
|
27.5
|
1.0
|
C4A
|
F:HEA601
|
4.5
|
27.5
|
1.0
|
FE
|
F:HEA601
|
4.7
|
27.5
|
1.0
|
C3A
|
F:HEA601
|
4.8
|
27.5
|
1.0
|
C3D
|
F:HEA601
|
4.9
|
27.5
|
1.0
|
C1D
|
F:HEA601
|
5.0
|
27.5
|
1.0
|
NB
|
F:HEA601
|
5.0
|
27.5
|
1.0
|
|
Copper binding site 4 out
of 8 in 6adq
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Copper Binding Sites List in 6adq
Copper binding site 4 out
of 8 in the Respiratory Complex CIII2CIV2SOD2 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 Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cu604
b:48.5
occ:1.00
|
OD2
|
F:ASP390
|
2.8
|
30.8
|
1.0
|
OE2
|
E:GLU275
|
3.0
|
34.1
|
1.0
|
OH
|
F:TYR154
|
3.2
|
31.4
|
1.0
|
OD1
|
F:ASP390
|
3.3
|
30.8
|
1.0
|
CG
|
F:ASP390
|
3.3
|
30.8
|
1.0
|
OE1
|
E:GLU275
|
3.3
|
34.1
|
1.0
|
CD
|
E:GLU275
|
3.6
|
34.1
|
1.0
|
O
|
F:HIS314
|
3.8
|
27.8
|
1.0
|
CZ
|
F:TYR154
|
4.1
|
31.4
|
1.0
|
CE2
|
F:TYR154
|
4.4
|
31.4
|
1.0
|
O2A
|
F:HEA601
|
4.6
|
27.5
|
1.0
|
CB
|
F:ASP390
|
4.7
|
30.8
|
1.0
|
OD2
|
E:ASP244
|
4.8
|
32.4
|
1.0
|
|
Copper binding site 5 out
of 8 in 6adq
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Copper Binding Sites List in 6adq
Copper binding site 5 out
of 8 in the Respiratory Complex CIII2CIV2SOD2 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 Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Cu401
b:47.9
occ:1.00
|
CU
|
Q:CU402
|
1.6
|
64.0
|
1.0
|
ND1
|
Q:HIS281
|
2.3
|
34.2
|
1.0
|
SG
|
Q:CYS277
|
2.5
|
34.4
|
1.0
|
SG
|
Q:CYS273
|
2.5
|
34.1
|
1.0
|
CE1
|
Q:HIS281
|
2.5
|
34.2
|
1.0
|
SD
|
Q:MET284
|
2.5
|
35.9
|
1.0
|
CB
|
Q:CYS277
|
3.0
|
34.4
|
1.0
|
CB
|
Q:HIS232
|
3.4
|
35.9
|
1.0
|
CE
|
Q:MET284
|
3.5
|
35.9
|
1.0
|
CG
|
Q:HIS232
|
3.6
|
35.9
|
1.0
|
CG
|
Q:HIS281
|
3.6
|
34.2
|
1.0
|
NE2
|
Q:HIS281
|
3.8
|
34.2
|
1.0
|
CB
|
Q:CYS273
|
3.8
|
34.1
|
1.0
|
CD2
|
Q:HIS232
|
4.0
|
35.9
|
1.0
|
N
|
Q:CYS277
|
4.0
|
34.4
|
1.0
|
CA
|
Q:CYS277
|
4.0
|
34.4
|
1.0
|
CG
|
Q:MET284
|
4.1
|
35.9
|
1.0
|
ND1
|
Q:HIS232
|
4.2
|
35.9
|
1.0
|
O
|
Q:HIS281
|
4.3
|
34.2
|
1.0
|
CD2
|
Q:HIS281
|
4.4
|
34.2
|
1.0
|
CB
|
Q:HIS281
|
4.5
|
34.2
|
1.0
|
CA
|
Q:HIS281
|
4.5
|
34.2
|
1.0
|
CB
|
Q:MET284
|
4.5
|
35.9
|
1.0
|
NE2
|
Q:HIS232
|
4.7
|
35.9
|
1.0
|
CE1
|
Q:HIS232
|
4.8
|
35.9
|
1.0
|
C
|
Q:MET276
|
4.8
|
32.5
|
1.0
|
CA
|
Q:HIS232
|
4.9
|
35.9
|
1.0
|
C
|
Q:HIS281
|
4.9
|
34.2
|
1.0
|
CA
|
Q:CYS273
|
5.0
|
34.1
|
1.0
|
C
|
Q:CYS273
|
5.0
|
34.1
|
1.0
|
|
Copper binding site 6 out
of 8 in 6adq
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Copper Binding Sites List in 6adq
Copper binding site 6 out
of 8 in the Respiratory Complex CIII2CIV2SOD2 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 Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Cu402
b:64.0
occ:1.00
|
CU
|
Q:CU401
|
1.6
|
47.9
|
1.0
|
CG
|
Q:HIS232
|
2.4
|
35.9
|
1.0
|
SG
|
Q:CYS277
|
2.4
|
34.4
|
1.0
|
SG
|
Q:CYS273
|
2.5
|
34.1
|
1.0
|
CD2
|
Q:HIS232
|
2.5
|
35.9
|
1.0
|
SD
|
Q:MET284
|
2.5
|
35.9
|
1.0
|
CE
|
Q:MET284
|
2.5
|
35.9
|
1.0
|
CB
|
Q:HIS232
|
2.8
|
35.9
|
1.0
|
ND1
|
Q:HIS232
|
2.9
|
35.9
|
1.0
|
NE2
|
Q:HIS232
|
3.0
|
35.9
|
1.0
|
CE1
|
Q:HIS232
|
3.3
|
35.9
|
1.0
|
CB
|
Q:CYS277
|
3.7
|
34.4
|
1.0
|
ND1
|
Q:HIS281
|
4.0
|
34.2
|
1.0
|
CE1
|
Q:HIS281
|
4.0
|
34.2
|
1.0
|
CB
|
Q:CYS273
|
4.0
|
34.1
|
1.0
|
CG
|
Q:MET284
|
4.1
|
35.9
|
1.0
|
CA
|
Q:HIS232
|
4.3
|
35.9
|
1.0
|
CB
|
Q:MET284
|
4.5
|
35.9
|
1.0
|
CA
|
Q:CYS277
|
4.9
|
34.4
|
1.0
|
N
|
Q:GLY233
|
4.9
|
32.8
|
1.0
|
|
Copper binding site 7 out
of 8 in 6adq
Go back to
Copper Binding Sites List in 6adq
Copper binding site 7 out
of 8 in the Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 7 of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Cu603
b:33.9
occ:1.00
|
ND1
|
R:HIS264
|
2.1
|
24.5
|
1.0
|
NE2
|
R:HIS314
|
2.2
|
27.5
|
1.0
|
CE1
|
R:HIS313
|
2.3
|
27.7
|
1.0
|
CE1
|
R:HIS314
|
2.3
|
27.5
|
1.0
|
NE2
|
R:HIS313
|
2.6
|
27.7
|
1.0
|
CE1
|
R:HIS264
|
2.9
|
24.5
|
1.0
|
CG
|
R:HIS264
|
3.0
|
24.5
|
1.0
|
ND1
|
R:HIS313
|
3.4
|
27.7
|
1.0
|
CD2
|
R:HIS314
|
3.4
|
27.5
|
1.0
|
CB
|
R:HIS264
|
3.5
|
24.5
|
1.0
|
ND1
|
R:HIS314
|
3.5
|
27.5
|
1.0
|
CD2
|
R:HIS313
|
3.8
|
27.7
|
1.0
|
NE2
|
R:HIS264
|
4.0
|
24.5
|
1.0
|
C1A
|
R:HEA601
|
4.1
|
27.4
|
1.0
|
CD2
|
R:HIS264
|
4.1
|
24.5
|
1.0
|
CG
|
R:HIS314
|
4.1
|
27.5
|
1.0
|
NA
|
R:HEA601
|
4.1
|
27.4
|
1.0
|
CG
|
R:HIS313
|
4.2
|
27.7
|
1.0
|
CA
|
R:HIS264
|
4.3
|
24.5
|
1.0
|
C4D
|
R:HEA601
|
4.3
|
27.4
|
1.0
|
ND
|
R:HEA601
|
4.3
|
27.4
|
1.0
|
CHA
|
R:HEA601
|
4.4
|
27.4
|
1.0
|
CG2
|
R:VAL267
|
4.5
|
24.2
|
1.0
|
C2A
|
R:HEA601
|
4.5
|
27.4
|
1.0
|
C4A
|
R:HEA601
|
4.5
|
27.4
|
1.0
|
FE
|
R:HEA601
|
4.7
|
27.4
|
1.0
|
C3A
|
R:HEA601
|
4.8
|
27.4
|
1.0
|
C3D
|
R:HEA601
|
4.9
|
27.4
|
1.0
|
C1D
|
R:HEA601
|
5.0
|
27.4
|
1.0
|
NB
|
R:HEA601
|
5.0
|
27.4
|
1.0
|
|
Copper binding site 8 out
of 8 in 6adq
Go back to
Copper Binding Sites List in 6adq
Copper binding site 8 out
of 8 in the Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 8 of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Cu604
b:46.9
occ:1.00
|
OD2
|
R:ASP390
|
2.8
|
31.0
|
1.0
|
OE2
|
Q:GLU275
|
3.0
|
34.3
|
1.0
|
OH
|
R:TYR154
|
3.2
|
30.9
|
1.0
|
OD1
|
R:ASP390
|
3.3
|
31.0
|
1.0
|
CG
|
R:ASP390
|
3.3
|
31.0
|
1.0
|
OE1
|
Q:GLU275
|
3.3
|
34.3
|
1.0
|
CD
|
Q:GLU275
|
3.6
|
34.3
|
1.0
|
O
|
R:HIS314
|
3.8
|
27.5
|
1.0
|
CZ
|
R:TYR154
|
4.1
|
30.9
|
1.0
|
CE2
|
R:TYR154
|
4.4
|
30.9
|
1.0
|
O2A
|
R:HEA601
|
4.6
|
27.4
|
1.0
|
CB
|
R:ASP390
|
4.7
|
31.0
|
1.0
|
OD2
|
Q:ASP244
|
4.8
|
32.4
|
1.0
|
|
Reference:
H.Gong,
J.Li,
A.Xu,
Y.Tang,
W.Ji,
R.Gao,
S.Wang,
L.Yu,
C.Tian,
J.Li,
H.Y.Yen,
S.Man Lam,
G.Shui,
X.Yang,
Y.Sun,
X.Li,
M.Jia,
C.Yang,
B.Jiang,
Z.Lou,
C.V.Robinson,
L.L.Wong,
L.W.Guddat,
F.Sun,
Q.Wang,
Z.Rao.
An Electron Transfer Path Connects Subunits of A Mycobacterial Respiratory Supercomplex. Science V. 362 2018.
ISSN: ESSN 1095-9203
PubMed: 30361386
DOI: 10.1126/SCIENCE.AAT8923
Page generated: Wed Jul 31 05:46:55 2024
|