Copper in PDB 7e1w: Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203
Enzymatic activity of Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203
All present enzymatic activity of Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203:
7.1.1.8;
7.1.1.9;
Other elements in 7e1w:
The structure of Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203 also contains other interesting chemical elements:
Copper Binding Sites:
The binding sites of Copper atom in the Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203
(pdb code 7e1w). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the
Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203, PDB code: 7e1w:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Copper binding site 1 out
of 8 in 7e1w
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Copper Binding Sites List in 7e1w
Copper binding site 1 out
of 8 in the Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cu401
b:102.1
occ:1.00
|
CU
|
E:CU402
|
1.2
|
108.3
|
1.0
|
ND1
|
E:HIS281
|
2.1
|
73.0
|
1.0
|
SG
|
E:CYS277
|
2.2
|
74.8
|
1.0
|
SG
|
E:CYS273
|
2.2
|
75.7
|
1.0
|
CE1
|
E:HIS281
|
2.7
|
73.0
|
1.0
|
CB
|
E:CYS273
|
2.8
|
75.7
|
1.0
|
SD
|
E:MET284
|
3.1
|
76.7
|
1.0
|
CG
|
E:HIS281
|
3.4
|
73.0
|
1.0
|
CB
|
E:CYS277
|
3.4
|
74.8
|
1.0
|
O
|
E:HIS281
|
3.7
|
73.0
|
1.0
|
ND1
|
E:HIS232
|
3.9
|
70.2
|
1.0
|
CA
|
E:HIS281
|
3.9
|
73.0
|
1.0
|
NE2
|
E:HIS281
|
4.0
|
73.0
|
1.0
|
CB
|
E:HIS281
|
4.0
|
73.0
|
1.0
|
CA
|
E:CYS273
|
4.1
|
75.7
|
1.0
|
CG
|
E:MET284
|
4.2
|
76.7
|
1.0
|
CE
|
E:MET284
|
4.2
|
76.7
|
1.0
|
CD2
|
E:HIS281
|
4.3
|
73.0
|
1.0
|
C
|
E:HIS281
|
4.3
|
73.0
|
1.0
|
N
|
E:CYS277
|
4.3
|
74.8
|
1.0
|
C
|
E:CYS273
|
4.4
|
75.7
|
1.0
|
CA
|
E:CYS277
|
4.5
|
74.8
|
1.0
|
CB
|
E:MET284
|
4.6
|
76.7
|
1.0
|
CE1
|
E:HIS232
|
4.8
|
70.2
|
1.0
|
N
|
E:GLU275
|
4.8
|
76.7
|
1.0
|
O
|
E:CYS273
|
4.8
|
75.7
|
1.0
|
CG
|
E:HIS232
|
4.8
|
70.2
|
1.0
|
CB
|
E:HIS232
|
4.8
|
70.2
|
1.0
|
N
|
E:THR274
|
4.8
|
74.0
|
1.0
|
O
|
E:GLU275
|
4.9
|
76.7
|
1.0
|
C
|
E:GLU275
|
4.9
|
76.7
|
1.0
|
CA
|
E:HIS232
|
5.0
|
70.2
|
1.0
|
|
Copper binding site 2 out
of 8 in 7e1w
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Copper Binding Sites List in 7e1w
Copper binding site 2 out
of 8 in the Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cu402
b:108.3
occ:1.00
|
CU
|
E:CU401
|
1.2
|
102.1
|
1.0
|
SG
|
E:CYS277
|
2.2
|
74.8
|
1.0
|
SG
|
E:CYS273
|
2.2
|
75.7
|
1.0
|
SD
|
E:MET284
|
2.3
|
76.7
|
1.0
|
CB
|
E:CYS273
|
2.9
|
75.7
|
1.0
|
ND1
|
E:HIS232
|
3.0
|
70.2
|
1.0
|
CE
|
E:MET284
|
3.1
|
76.7
|
1.0
|
ND1
|
E:HIS281
|
3.3
|
73.0
|
1.0
|
CB
|
E:CYS277
|
3.5
|
74.8
|
1.0
|
CG
|
E:MET284
|
3.7
|
76.7
|
1.0
|
CE1
|
E:HIS281
|
3.8
|
73.0
|
1.0
|
CE1
|
E:HIS232
|
3.9
|
70.2
|
1.0
|
CG
|
E:HIS232
|
3.9
|
70.2
|
1.0
|
CB
|
E:HIS232
|
4.1
|
70.2
|
1.0
|
CB
|
E:MET284
|
4.1
|
76.7
|
1.0
|
CA
|
E:CYS273
|
4.4
|
75.7
|
1.0
|
O
|
E:HIS281
|
4.4
|
73.0
|
1.0
|
CG
|
E:HIS281
|
4.5
|
73.0
|
1.0
|
CA
|
E:HIS232
|
4.6
|
70.2
|
1.0
|
CA
|
E:HIS281
|
4.6
|
73.0
|
1.0
|
CA
|
E:CYS277
|
4.8
|
74.8
|
1.0
|
N
|
E:GLY233
|
4.8
|
74.1
|
1.0
|
N
|
E:CYS277
|
4.9
|
74.8
|
1.0
|
CB
|
E:HIS281
|
5.0
|
73.0
|
1.0
|
C
|
E:CYS273
|
5.0
|
75.7
|
1.0
|
|
Copper binding site 3 out
of 8 in 7e1w
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Copper Binding Sites List in 7e1w
Copper binding site 3 out
of 8 in the Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cu604
b:132.6
occ:1.00
|
O
|
F:HIS314
|
2.8
|
69.6
|
1.0
|
OH
|
F:TYR154
|
3.9
|
71.3
|
1.0
|
C
|
F:HIS314
|
4.0
|
69.6
|
1.0
|
O2A
|
F:HEA606
|
4.2
|
70.7
|
1.0
|
OD1
|
F:ASP390
|
4.4
|
73.7
|
1.0
|
OG1
|
F:THR389
|
4.5
|
73.0
|
1.0
|
OD2
|
F:ASP390
|
4.6
|
73.7
|
1.0
|
CA
|
F:MET315
|
4.8
|
74.2
|
1.0
|
N
|
F:MET315
|
4.8
|
74.2
|
1.0
|
CG
|
F:ASP390
|
4.8
|
73.7
|
1.0
|
CA
|
F:HIS314
|
4.9
|
69.6
|
1.0
|
CZ
|
F:TYR154
|
4.9
|
71.3
|
1.0
|
|
Copper binding site 4 out
of 8 in 7e1w
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Copper Binding Sites List in 7e1w
Copper binding site 4 out
of 8 in the Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cu605
b:139.1
occ:1.00
|
NE2
|
F:HIS314
|
1.4
|
69.6
|
1.0
|
ND1
|
F:HIS264
|
1.7
|
65.2
|
1.0
|
CE1
|
F:HIS264
|
2.1
|
65.2
|
1.0
|
CE1
|
F:HIS314
|
2.2
|
69.6
|
1.0
|
CE1
|
F:HIS313
|
2.6
|
71.0
|
1.0
|
CD2
|
F:HIS314
|
2.6
|
69.6
|
1.0
|
NE2
|
F:HIS313
|
2.9
|
71.0
|
1.0
|
CG
|
F:HIS264
|
2.9
|
65.2
|
1.0
|
NE2
|
F:HIS264
|
3.3
|
65.2
|
1.0
|
ND1
|
F:HIS314
|
3.3
|
69.6
|
1.0
|
CG
|
F:HIS314
|
3.5
|
69.6
|
1.0
|
ND1
|
F:HIS313
|
3.7
|
71.0
|
1.0
|
CD2
|
F:HIS264
|
3.7
|
65.2
|
1.0
|
CB
|
F:HIS264
|
3.8
|
65.2
|
1.0
|
CD2
|
F:HIS313
|
4.0
|
71.0
|
1.0
|
CG
|
F:HIS313
|
4.4
|
71.0
|
1.0
|
CA
|
F:HIS264
|
4.5
|
65.2
|
1.0
|
NA
|
F:HEA606
|
4.5
|
70.7
|
1.0
|
C1A
|
F:HEA606
|
4.6
|
70.7
|
1.0
|
CHA
|
F:HEA606
|
4.8
|
70.7
|
1.0
|
C4A
|
F:HEA606
|
4.9
|
70.7
|
1.0
|
C4D
|
F:HEA606
|
4.9
|
70.7
|
1.0
|
C2A
|
F:HEA606
|
4.9
|
70.7
|
1.0
|
ND
|
F:HEA606
|
5.0
|
70.7
|
1.0
|
FE
|
F:HEA606
|
5.0
|
70.7
|
1.0
|
|
Copper binding site 5 out
of 8 in 7e1w
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Copper Binding Sites List in 7e1w
Copper binding site 5 out
of 8 in the Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 5 of Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Cu401
b:93.3
occ:1.00
|
CU
|
Q:CU402
|
1.2
|
86.6
|
1.0
|
SG
|
Q:CYS277
|
2.1
|
59.6
|
1.0
|
SG
|
Q:CYS273
|
2.2
|
61.2
|
1.0
|
SD
|
Q:MET284
|
2.5
|
59.7
|
1.0
|
ND1
|
Q:HIS281
|
2.8
|
59.1
|
1.0
|
CB
|
Q:CYS273
|
2.9
|
61.2
|
1.0
|
ND1
|
Q:HIS232
|
3.4
|
54.4
|
1.0
|
CE1
|
Q:HIS281
|
3.4
|
59.1
|
1.0
|
CB
|
Q:CYS277
|
3.6
|
59.6
|
1.0
|
CE
|
Q:MET284
|
3.6
|
59.7
|
1.0
|
CG
|
Q:MET284
|
3.7
|
59.7
|
1.0
|
O
|
Q:HIS281
|
3.9
|
59.1
|
1.0
|
CG
|
Q:HIS281
|
4.0
|
59.1
|
1.0
|
CB
|
Q:MET284
|
4.2
|
59.7
|
1.0
|
CE1
|
Q:HIS232
|
4.2
|
54.4
|
1.0
|
CA
|
Q:HIS281
|
4.3
|
59.1
|
1.0
|
CA
|
Q:CYS273
|
4.3
|
61.2
|
1.0
|
CG
|
Q:HIS232
|
4.3
|
54.4
|
1.0
|
CB
|
Q:HIS232
|
4.5
|
54.4
|
1.0
|
CB
|
Q:HIS281
|
4.5
|
59.1
|
1.0
|
C
|
Q:HIS281
|
4.6
|
59.1
|
1.0
|
NE2
|
Q:HIS281
|
4.6
|
59.1
|
1.0
|
N
|
Q:CYS277
|
4.7
|
59.6
|
1.0
|
C
|
Q:CYS273
|
4.7
|
61.2
|
1.0
|
CA
|
Q:CYS277
|
4.7
|
59.6
|
1.0
|
CD1
|
Q:TRP138
|
4.8
|
57.5
|
1.0
|
CA
|
Q:HIS232
|
4.9
|
54.4
|
1.0
|
CD2
|
Q:HIS281
|
5.0
|
59.1
|
1.0
|
|
Copper binding site 6 out
of 8 in 7e1w
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Copper Binding Sites List in 7e1w
Copper binding site 6 out
of 8 in the Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 6 of Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Cu402
b:86.6
occ:1.00
|
CU
|
Q:CU401
|
1.2
|
93.3
|
1.0
|
ND1
|
Q:HIS281
|
2.0
|
59.1
|
1.0
|
SG
|
Q:CYS277
|
2.2
|
59.6
|
1.0
|
SG
|
Q:CYS273
|
2.2
|
61.2
|
1.0
|
CE1
|
Q:HIS281
|
2.3
|
59.1
|
1.0
|
CB
|
Q:CYS273
|
3.0
|
61.2
|
1.0
|
CG
|
Q:HIS281
|
3.3
|
59.1
|
1.0
|
NE2
|
Q:HIS281
|
3.6
|
59.1
|
1.0
|
SD
|
Q:MET284
|
3.7
|
59.7
|
1.0
|
CB
|
Q:CYS277
|
3.7
|
59.6
|
1.0
|
O
|
Q:HIS281
|
4.0
|
59.1
|
1.0
|
ND1
|
Q:HIS232
|
4.0
|
54.4
|
1.0
|
CD2
|
Q:HIS281
|
4.1
|
59.1
|
1.0
|
CB
|
Q:HIS281
|
4.1
|
59.1
|
1.0
|
N
|
Q:CYS277
|
4.1
|
59.6
|
1.0
|
CA
|
Q:CYS273
|
4.1
|
61.2
|
1.0
|
C
|
Q:CYS273
|
4.2
|
61.2
|
1.0
|
N
|
Q:GLU275
|
4.2
|
63.1
|
1.0
|
O
|
Q:GLU275
|
4.2
|
63.1
|
1.0
|
CA
|
Q:HIS281
|
4.3
|
59.1
|
1.0
|
C
|
Q:GLU275
|
4.3
|
63.1
|
1.0
|
O
|
Q:CYS273
|
4.4
|
61.2
|
1.0
|
N
|
Q:THR274
|
4.5
|
60.3
|
1.0
|
CA
|
Q:CYS277
|
4.5
|
59.6
|
1.0
|
C
|
Q:HIS281
|
4.6
|
59.1
|
1.0
|
CA
|
Q:GLU275
|
4.6
|
63.1
|
1.0
|
CB
|
Q:GLU275
|
4.6
|
63.1
|
1.0
|
CG
|
Q:MET284
|
4.7
|
59.7
|
1.0
|
CB
|
Q:HIS232
|
4.8
|
54.4
|
1.0
|
CA
|
Q:HIS232
|
4.8
|
54.4
|
1.0
|
CE
|
Q:MET284
|
4.8
|
59.7
|
1.0
|
N
|
Q:MET276
|
4.8
|
58.7
|
1.0
|
CG
|
Q:HIS232
|
4.8
|
54.4
|
1.0
|
C
|
Q:MET276
|
4.8
|
58.7
|
1.0
|
N
|
Q:GLY233
|
4.9
|
57.6
|
1.0
|
CE1
|
Q:HIS232
|
4.9
|
54.4
|
1.0
|
|
Copper binding site 7 out
of 8 in 7e1w
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Copper Binding Sites List in 7e1w
Copper binding site 7 out
of 8 in the Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 7 of Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Cu604
b:121.7
occ:1.00
|
OD1
|
R:ASP390
|
2.8
|
61.8
|
1.0
|
OD2
|
R:ASP390
|
2.9
|
61.8
|
1.0
|
CG
|
R:ASP390
|
3.2
|
61.8
|
1.0
|
OH
|
R:TYR154
|
3.3
|
61.1
|
1.0
|
OE2
|
Q:GLU275
|
3.8
|
63.1
|
1.0
|
CZ
|
R:TYR154
|
4.1
|
61.1
|
1.0
|
OE1
|
Q:GLU275
|
4.2
|
63.1
|
1.0
|
CE2
|
R:TYR154
|
4.4
|
61.1
|
1.0
|
CD
|
Q:GLU275
|
4.4
|
63.1
|
1.0
|
CB
|
R:ASP390
|
4.7
|
61.8
|
1.0
|
O
|
R:HIS314
|
5.0
|
58.6
|
1.0
|
OD1
|
Q:ASP244
|
5.0
|
64.8
|
1.0
|
|
Copper binding site 8 out
of 8 in 7e1w
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Copper Binding Sites List in 7e1w
Copper binding site 8 out
of 8 in the Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 8 of Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Cu605
b:138.9
occ:1.00
|
NE2
|
R:HIS314
|
2.1
|
58.6
|
1.0
|
ND1
|
R:HIS264
|
2.1
|
55.4
|
1.0
|
CE1
|
R:HIS313
|
2.5
|
58.6
|
1.0
|
NE2
|
R:HIS313
|
2.6
|
58.6
|
1.0
|
CE1
|
R:HIS314
|
2.7
|
58.6
|
1.0
|
CE1
|
R:HIS264
|
2.9
|
55.4
|
1.0
|
CD2
|
R:HIS314
|
3.2
|
58.6
|
1.0
|
CG
|
R:HIS264
|
3.3
|
55.4
|
1.0
|
ND1
|
R:HIS313
|
3.7
|
58.6
|
1.0
|
CB
|
R:HIS264
|
3.8
|
55.4
|
1.0
|
CD2
|
R:HIS313
|
3.9
|
58.6
|
1.0
|
ND1
|
R:HIS314
|
3.9
|
58.6
|
1.0
|
NE2
|
R:HIS264
|
4.1
|
55.4
|
1.0
|
CG
|
R:HIS314
|
4.2
|
58.6
|
1.0
|
NA
|
R:HEA606
|
4.3
|
58.5
|
1.0
|
CD2
|
R:HIS264
|
4.3
|
55.4
|
1.0
|
CG
|
R:HIS313
|
4.4
|
58.6
|
1.0
|
C1A
|
R:HEA606
|
4.5
|
58.5
|
1.0
|
C4A
|
R:HEA606
|
4.6
|
58.5
|
1.0
|
CA
|
R:HIS264
|
4.6
|
55.4
|
1.0
|
FE
|
R:HEA606
|
4.6
|
58.5
|
1.0
|
ND
|
R:HEA606
|
4.8
|
58.5
|
1.0
|
CHA
|
R:HEA606
|
4.9
|
58.5
|
1.0
|
C4D
|
R:HEA606
|
4.9
|
58.5
|
1.0
|
C3A
|
R:HEA606
|
4.9
|
58.5
|
1.0
|
C2A
|
R:HEA606
|
5.0
|
58.5
|
1.0
|
|
Reference:
S.Zhou,
W.Wang,
Y.Gao,
H.Gong,
Z.Rao.
Cryo-Em Structure of Hybrid Respiratory Supercomplex Consisting of Mycobacterium Tuberculosis Complexiii and Mycobacterium Smegmatis Complexiv in the Presence of Q203 To Be Published.
Page generated: Wed Jul 31 08:28:06 2024
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