Copper in PDB 3fyi: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide
Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide
All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide:
1.9.3.1;
Protein crystallography data
The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide, PDB code: 3fyi
was solved by
L.Qin,
D.A.Mills,
D.A.Proshlyakov,
C.Hiser,
S.Ferguson-Miller,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
124.344,
131.877,
176.160,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.4 /
21.9
|
Other elements in 3fyi:
The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide also contains other interesting chemical elements:
Copper Binding Sites:
The binding sites of Copper atom in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide
(pdb code 3fyi). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the
Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide, PDB code: 3fyi:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
Copper binding site 1 out
of 6 in 3fyi
Go back to
Copper Binding Sites List in 3fyi
Copper binding site 1 out
of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu569
b:36.0
occ:1.00
|
N
|
A:CYN572
|
1.8
|
32.3
|
1.0
|
NE2
|
A:HIS334
|
2.1
|
33.8
|
1.0
|
ND1
|
A:HIS284
|
2.1
|
33.4
|
1.0
|
C
|
A:CYN572
|
2.9
|
31.7
|
1.0
|
NE2
|
A:HIS333
|
3.0
|
39.2
|
1.0
|
CE1
|
A:HIS284
|
3.0
|
32.7
|
1.0
|
CG
|
A:HIS284
|
3.0
|
31.2
|
1.0
|
CE1
|
A:HIS334
|
3.0
|
32.5
|
1.0
|
CD2
|
A:HIS334
|
3.1
|
31.6
|
1.0
|
CB
|
A:HIS284
|
3.3
|
29.6
|
1.0
|
CE1
|
A:HIS333
|
3.7
|
39.6
|
1.0
|
CA
|
A:HIS284
|
3.8
|
30.0
|
1.0
|
CD2
|
A:HIS333
|
4.0
|
37.2
|
1.0
|
CD2
|
A:HIS284
|
4.1
|
33.0
|
1.0
|
NE2
|
A:HIS284
|
4.1
|
33.2
|
1.0
|
ND1
|
A:HIS334
|
4.2
|
32.7
|
1.0
|
CG
|
A:HIS334
|
4.2
|
32.8
|
1.0
|
CG2
|
A:VAL287
|
4.6
|
29.7
|
1.0
|
N
|
A:HIS284
|
4.6
|
29.8
|
1.0
|
O
|
A:HOH647
|
4.7
|
39.9
|
1.0
|
ND1
|
A:HIS333
|
4.8
|
38.5
|
1.0
|
ND
|
A:HEA568
|
4.8
|
26.4
|
1.0
|
CG2
|
A:VAL330
|
4.9
|
35.2
|
1.0
|
C
|
A:HIS284
|
4.9
|
30.5
|
1.0
|
O
|
A:HIS284
|
4.9
|
30.5
|
1.0
|
|
Copper binding site 2 out
of 6 in 3fyi
Go back to
Copper Binding Sites List in 3fyi
Copper binding site 2 out
of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu3
b:25.8
occ:1.00
|
ND1
|
B:HIS260
|
2.1
|
22.0
|
1.0
|
SG
|
B:CYS252
|
2.2
|
24.9
|
1.0
|
SG
|
B:CYS256
|
2.3
|
24.3
|
1.0
|
O
|
B:GLU254
|
2.5
|
25.2
|
1.0
|
CU
|
B:CU14
|
2.6
|
25.6
|
1.0
|
CE1
|
B:HIS260
|
2.9
|
21.8
|
1.0
|
CG
|
B:HIS260
|
3.2
|
22.6
|
1.0
|
CB
|
B:CYS252
|
3.3
|
24.4
|
1.0
|
CB
|
B:CYS256
|
3.5
|
25.4
|
1.0
|
C
|
B:GLU254
|
3.5
|
24.8
|
1.0
|
CA
|
B:HIS260
|
3.6
|
22.6
|
1.0
|
CB
|
B:HIS260
|
3.6
|
21.8
|
1.0
|
N
|
B:CYS256
|
3.8
|
24.4
|
1.0
|
O
|
B:HIS260
|
3.9
|
22.0
|
1.0
|
NE2
|
B:HIS260
|
4.1
|
23.7
|
1.0
|
O
|
B:CYS252
|
4.1
|
24.2
|
1.0
|
N
|
B:GLU254
|
4.1
|
25.0
|
1.0
|
C
|
B:CYS252
|
4.1
|
24.6
|
1.0
|
CA
|
B:LEU255
|
4.2
|
24.5
|
1.0
|
C
|
B:HIS260
|
4.2
|
22.1
|
1.0
|
CD2
|
B:HIS260
|
4.2
|
21.8
|
1.0
|
N
|
B:LEU255
|
4.2
|
24.4
|
1.0
|
C
|
B:LEU255
|
4.3
|
24.3
|
1.0
|
CA
|
B:CYS256
|
4.3
|
25.0
|
1.0
|
ND1
|
B:HIS217
|
4.3
|
21.6
|
1.0
|
CA
|
B:CYS252
|
4.3
|
24.8
|
1.0
|
CA
|
B:GLU254
|
4.5
|
24.9
|
1.0
|
SD
|
B:MET263
|
4.5
|
23.5
|
1.0
|
N
|
B:SER253
|
4.6
|
24.8
|
1.0
|
CG
|
B:MET263
|
4.7
|
24.4
|
1.0
|
N
|
B:HIS260
|
4.8
|
22.9
|
1.0
|
CA
|
B:HIS217
|
4.9
|
24.6
|
1.0
|
|
Copper binding site 3 out
of 6 in 3fyi
Go back to
Copper Binding Sites List in 3fyi
Copper binding site 3 out
of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu4
b:25.6
occ:1.00
|
ND1
|
B:HIS217
|
2.1
|
21.6
|
1.0
|
SG
|
B:CYS252
|
2.3
|
24.9
|
1.0
|
SG
|
B:CYS256
|
2.4
|
24.3
|
1.0
|
SD
|
B:MET263
|
2.4
|
23.5
|
1.0
|
CU
|
B:CU13
|
2.6
|
25.8
|
1.0
|
CE1
|
B:HIS217
|
3.0
|
20.3
|
1.0
|
CE
|
B:MET263
|
3.1
|
21.1
|
1.0
|
CG
|
B:HIS217
|
3.2
|
23.5
|
1.0
|
CB
|
B:CYS256
|
3.4
|
25.4
|
1.0
|
CG
|
B:MET263
|
3.5
|
24.4
|
1.0
|
CB
|
B:CYS252
|
3.5
|
24.4
|
1.0
|
CB
|
B:HIS217
|
3.6
|
23.9
|
1.0
|
NE2
|
B:HIS217
|
4.1
|
21.9
|
1.0
|
CA
|
B:HIS217
|
4.2
|
24.6
|
1.0
|
CD2
|
B:HIS217
|
4.3
|
22.2
|
1.0
|
O
|
B:GLU254
|
4.3
|
25.2
|
1.0
|
CD1
|
B:TRP143
|
4.5
|
25.9
|
1.0
|
ND1
|
B:HIS260
|
4.6
|
22.0
|
1.0
|
O
|
B:TYR141
|
4.6
|
26.8
|
1.0
|
CA
|
B:HIS260
|
4.7
|
22.6
|
1.0
|
CA
|
B:CYS256
|
4.8
|
25.0
|
1.0
|
CB
|
B:MET263
|
4.9
|
25.5
|
1.0
|
CA
|
B:CYS252
|
4.9
|
24.8
|
1.0
|
|
Copper binding site 4 out
of 6 in 3fyi
Go back to
Copper Binding Sites List in 3fyi
Copper binding site 4 out
of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu569
b:42.5
occ:1.00
|
N
|
C:CYN572
|
1.8
|
37.9
|
1.0
|
NE2
|
C:HIS334
|
2.1
|
39.2
|
1.0
|
ND1
|
C:HIS284
|
2.3
|
45.4
|
1.0
|
NE2
|
C:HIS333
|
2.9
|
43.4
|
1.0
|
C
|
C:CYN572
|
2.9
|
36.8
|
1.0
|
CD2
|
C:HIS334
|
3.0
|
38.5
|
1.0
|
CG
|
C:HIS284
|
3.1
|
43.6
|
1.0
|
CE1
|
C:HIS334
|
3.1
|
38.7
|
1.0
|
CE1
|
C:HIS284
|
3.2
|
45.5
|
1.0
|
CB
|
C:HIS284
|
3.3
|
41.1
|
1.0
|
CE1
|
C:HIS333
|
3.6
|
42.9
|
1.0
|
CA
|
C:HIS284
|
3.9
|
41.1
|
1.0
|
CD2
|
C:HIS333
|
3.9
|
42.0
|
1.0
|
CD2
|
C:HIS284
|
4.2
|
45.2
|
1.0
|
CG
|
C:HIS334
|
4.2
|
38.5
|
1.0
|
ND1
|
C:HIS334
|
4.2
|
39.4
|
1.0
|
NE2
|
C:HIS284
|
4.3
|
45.3
|
1.0
|
CG2
|
C:VAL287
|
4.6
|
41.1
|
1.0
|
N
|
C:HIS284
|
4.7
|
40.4
|
1.0
|
ND1
|
C:HIS333
|
4.7
|
43.7
|
1.0
|
O
|
C:HOH1122
|
4.8
|
44.1
|
1.0
|
ND
|
C:HEA568
|
4.9
|
30.6
|
1.0
|
CG
|
C:HIS333
|
4.9
|
40.7
|
1.0
|
C
|
C:HIS284
|
5.0
|
41.1
|
1.0
|
CG2
|
C:VAL330
|
5.0
|
44.7
|
1.0
|
FE
|
C:HEA568
|
5.0
|
37.1
|
1.0
|
|
Copper binding site 5 out
of 6 in 3fyi
Go back to
Copper Binding Sites List in 3fyi
Copper binding site 5 out
of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 5 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cu3
b:33.2
occ:1.00
|
ND1
|
D:HIS260
|
2.0
|
33.0
|
1.0
|
SG
|
D:CYS252
|
2.3
|
29.8
|
1.0
|
SG
|
D:CYS256
|
2.3
|
31.6
|
1.0
|
CU
|
D:CU14
|
2.6
|
33.1
|
1.0
|
O
|
D:GLU254
|
2.6
|
30.7
|
1.0
|
CE1
|
D:HIS260
|
2.8
|
31.9
|
1.0
|
CG
|
D:HIS260
|
3.1
|
31.3
|
1.0
|
CB
|
D:CYS252
|
3.3
|
28.5
|
1.0
|
CB
|
D:CYS256
|
3.4
|
31.5
|
1.0
|
C
|
D:GLU254
|
3.5
|
30.8
|
1.0
|
CA
|
D:HIS260
|
3.6
|
31.5
|
1.0
|
CB
|
D:HIS260
|
3.7
|
31.8
|
1.0
|
N
|
D:CYS256
|
3.7
|
31.2
|
1.0
|
O
|
D:HIS260
|
3.9
|
31.3
|
1.0
|
NE2
|
D:HIS260
|
4.0
|
30.6
|
1.0
|
C
|
D:CYS252
|
4.1
|
29.1
|
1.0
|
CD2
|
D:HIS260
|
4.2
|
30.5
|
1.0
|
N
|
D:GLU254
|
4.2
|
30.4
|
1.0
|
CA
|
D:CYS256
|
4.2
|
31.6
|
1.0
|
O
|
D:CYS252
|
4.2
|
28.5
|
1.0
|
CA
|
D:LEU255
|
4.2
|
31.1
|
1.0
|
C
|
D:HIS260
|
4.2
|
31.1
|
1.0
|
ND1
|
D:HIS217
|
4.2
|
27.2
|
1.0
|
N
|
D:LEU255
|
4.3
|
30.4
|
1.0
|
C
|
D:LEU255
|
4.3
|
30.9
|
1.0
|
CA
|
D:CYS252
|
4.3
|
29.1
|
1.0
|
SD
|
D:MET263
|
4.5
|
31.4
|
1.0
|
CA
|
D:GLU254
|
4.5
|
30.7
|
1.0
|
N
|
D:SER253
|
4.6
|
29.7
|
1.0
|
CG
|
D:MET263
|
4.7
|
31.6
|
1.0
|
N
|
D:HIS260
|
4.9
|
32.0
|
1.0
|
CA
|
D:HIS217
|
4.9
|
31.5
|
1.0
|
|
Copper binding site 6 out
of 6 in 3fyi
Go back to
Copper Binding Sites List in 3fyi
Copper binding site 6 out
of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 6 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cu4
b:33.1
occ:1.00
|
ND1
|
D:HIS217
|
2.1
|
27.2
|
1.0
|
SG
|
D:CYS252
|
2.3
|
29.8
|
1.0
|
SG
|
D:CYS256
|
2.4
|
31.6
|
1.0
|
SD
|
D:MET263
|
2.4
|
31.4
|
1.0
|
CU
|
D:CU13
|
2.6
|
33.2
|
1.0
|
CE1
|
D:HIS217
|
3.0
|
28.0
|
1.0
|
CE
|
D:MET263
|
3.0
|
27.5
|
1.0
|
CG
|
D:HIS217
|
3.2
|
29.4
|
1.0
|
CB
|
D:CYS256
|
3.3
|
31.5
|
1.0
|
CB
|
D:CYS252
|
3.4
|
28.5
|
1.0
|
CG
|
D:MET263
|
3.5
|
31.6
|
1.0
|
CB
|
D:HIS217
|
3.6
|
31.4
|
1.0
|
NE2
|
D:HIS217
|
4.1
|
25.7
|
1.0
|
CA
|
D:HIS217
|
4.2
|
31.5
|
1.0
|
CD2
|
D:HIS217
|
4.3
|
27.9
|
1.0
|
O
|
D:GLU254
|
4.3
|
30.7
|
1.0
|
CD1
|
D:TRP143
|
4.4
|
37.1
|
1.0
|
ND1
|
D:HIS260
|
4.5
|
33.0
|
1.0
|
CA
|
D:CYS256
|
4.7
|
31.6
|
1.0
|
O
|
D:TYR141
|
4.7
|
35.1
|
1.0
|
CA
|
D:HIS260
|
4.8
|
31.5
|
1.0
|
CB
|
D:MET263
|
4.8
|
31.6
|
1.0
|
CA
|
D:CYS252
|
4.8
|
29.1
|
1.0
|
O
|
D:HIS260
|
5.0
|
31.3
|
1.0
|
|
Reference:
L.Qin,
J.Liu,
D.Mills,
D.A.Proshlyakov,
C.Hiser,
S.Ferguson-Miller.
Redox Dependent Conformational Changes in Cytochrome C Oxidase Suggest A Gating Mechanism For Proton Uptake. Biochemistry V. 48 5121 2009.
ISSN: ISSN 0006-2960
PubMed: 19397279
DOI: 10.1021/BI9001387
Page generated: Wed Jul 31 00:56:16 2024
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