Iron in PDB 7ose: Cytochrome Bd-II Type Oxidase with Bound Aurachin D
Enzymatic activity of Cytochrome Bd-II Type Oxidase with Bound Aurachin D
All present enzymatic activity of Cytochrome Bd-II Type Oxidase with Bound Aurachin D:
1.10.3.10;
7.1.1.3;
Iron Binding Sites:
The binding sites of Iron atom in the Cytochrome Bd-II Type Oxidase with Bound Aurachin D
(pdb code 7ose). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Cytochrome Bd-II Type Oxidase with Bound Aurachin D, PDB code: 7ose:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 7ose
Go back to
Iron Binding Sites List in 7ose
Iron binding site 1 out
of 6 in the Cytochrome Bd-II Type Oxidase with Bound Aurachin D
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Cytochrome Bd-II Type Oxidase with Bound Aurachin D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:72.8
occ:1.00
|
FE
|
A:HEB601
|
0.0
|
72.8
|
1.0
|
NA
|
A:HEB601
|
2.0
|
72.8
|
1.0
|
NC
|
A:HEB601
|
2.0
|
72.8
|
1.0
|
NB
|
A:HEB601
|
2.0
|
72.8
|
1.0
|
ND
|
A:HEB601
|
2.1
|
72.8
|
1.0
|
NE2
|
A:HIS186
|
2.6
|
64.1
|
1.0
|
SD
|
A:MET393
|
2.8
|
76.9
|
1.0
|
C1C
|
A:HEB601
|
3.0
|
72.8
|
1.0
|
C1A
|
A:HEB601
|
3.0
|
72.8
|
1.0
|
C4A
|
A:HEB601
|
3.0
|
72.8
|
1.0
|
C4C
|
A:HEB601
|
3.1
|
72.8
|
1.0
|
C4B
|
A:HEB601
|
3.2
|
72.8
|
1.0
|
C1B
|
A:HEB601
|
3.2
|
72.8
|
1.0
|
C4D
|
A:HEB601
|
3.2
|
72.8
|
1.0
|
C1D
|
A:HEB601
|
3.3
|
72.8
|
1.0
|
CHC
|
A:HEB601
|
3.4
|
72.8
|
1.0
|
CHA
|
A:HEB601
|
3.5
|
72.8
|
1.0
|
CHB
|
A:HEB601
|
3.5
|
72.8
|
1.0
|
CD2
|
A:HIS186
|
3.5
|
64.1
|
1.0
|
CE1
|
A:HIS186
|
3.5
|
64.1
|
1.0
|
CHD
|
A:HEB601
|
3.6
|
72.8
|
1.0
|
CG
|
A:MET393
|
3.9
|
76.9
|
1.0
|
CE
|
A:MET393
|
3.9
|
76.9
|
1.0
|
C3A
|
A:HEB601
|
4.2
|
72.8
|
1.0
|
C2C
|
A:HEB601
|
4.2
|
72.8
|
1.0
|
C2A
|
A:HEB601
|
4.2
|
72.8
|
1.0
|
C3C
|
A:HEB601
|
4.2
|
72.8
|
1.0
|
C3B
|
A:HEB601
|
4.4
|
72.8
|
1.0
|
C2B
|
A:HEB601
|
4.4
|
72.8
|
1.0
|
CA
|
A:GLY238
|
4.5
|
70.1
|
1.0
|
C3D
|
A:HEB601
|
4.5
|
72.8
|
1.0
|
C2D
|
A:HEB601
|
4.5
|
72.8
|
1.0
|
ND1
|
A:HIS186
|
4.6
|
64.1
|
1.0
|
CG
|
A:HIS186
|
4.7
|
64.1
|
1.0
|
|
Iron binding site 2 out
of 6 in 7ose
Go back to
Iron Binding Sites List in 7ose
Iron binding site 2 out
of 6 in the Cytochrome Bd-II Type Oxidase with Bound Aurachin D
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Cytochrome Bd-II Type Oxidase with Bound Aurachin D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe602
b:76.4
occ:1.00
|
FE
|
A:HEB602
|
0.0
|
76.4
|
1.0
|
NA
|
A:HEB602
|
2.0
|
76.4
|
1.0
|
NC
|
A:HEB602
|
2.0
|
76.4
|
1.0
|
NB
|
A:HEB602
|
2.0
|
76.4
|
1.0
|
ND
|
A:HEB602
|
2.1
|
76.4
|
1.0
|
C1C
|
A:HEB602
|
3.0
|
76.4
|
1.0
|
C1A
|
A:HEB602
|
3.0
|
76.4
|
1.0
|
C4A
|
A:HEB602
|
3.0
|
76.4
|
1.0
|
C4C
|
A:HEB602
|
3.0
|
76.4
|
1.0
|
C4B
|
A:HEB602
|
3.2
|
76.4
|
1.0
|
C1B
|
A:HEB602
|
3.2
|
76.4
|
1.0
|
C4D
|
A:HEB602
|
3.2
|
76.4
|
1.0
|
C1D
|
A:HEB602
|
3.3
|
76.4
|
1.0
|
OE1
|
A:GLU445
|
3.4
|
75.9
|
1.0
|
CHC
|
A:HEB602
|
3.4
|
76.4
|
1.0
|
CE1
|
A:PHE12
|
3.5
|
74.5
|
1.0
|
CHA
|
A:HEB602
|
3.5
|
76.4
|
1.0
|
CHB
|
A:HEB602
|
3.5
|
76.4
|
1.0
|
CD
|
A:GLU445
|
3.5
|
75.9
|
1.0
|
CHD
|
A:HEB602
|
3.6
|
76.4
|
1.0
|
CG
|
A:GLU445
|
3.7
|
75.9
|
1.0
|
CD1
|
A:PHE12
|
3.8
|
74.5
|
1.0
|
C3A
|
A:HEB602
|
4.2
|
76.4
|
1.0
|
C2C
|
A:HEB602
|
4.2
|
76.4
|
1.0
|
C2A
|
A:HEB602
|
4.2
|
76.4
|
1.0
|
OE2
|
A:GLU445
|
4.2
|
75.9
|
1.0
|
C3C
|
A:HEB602
|
4.2
|
76.4
|
1.0
|
CB
|
A:GLU445
|
4.3
|
75.9
|
1.0
|
C3B
|
A:HEB602
|
4.4
|
76.4
|
1.0
|
C2B
|
A:HEB602
|
4.4
|
76.4
|
1.0
|
C3D
|
A:HEB602
|
4.5
|
76.4
|
1.0
|
C2D
|
A:HEB602
|
4.5
|
76.4
|
1.0
|
CZ
|
A:PHE12
|
4.5
|
74.5
|
1.0
|
NH2
|
A:ARG448
|
4.7
|
79.5
|
1.0
|
CB
|
A:ALA16
|
4.8
|
70.3
|
1.0
|
|
Iron binding site 3 out
of 6 in 7ose
Go back to
Iron Binding Sites List in 7ose
Iron binding site 3 out
of 6 in the Cytochrome Bd-II Type Oxidase with Bound Aurachin D
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Cytochrome Bd-II Type Oxidase with Bound Aurachin D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe603
b:72.2
occ:1.00
|
FE
|
A:HDD603
|
0.0
|
72.2
|
1.0
|
NB
|
A:HDD603
|
1.9
|
72.2
|
1.0
|
NA
|
A:HDD603
|
1.9
|
72.2
|
1.0
|
NC
|
A:HDD603
|
1.9
|
72.2
|
1.0
|
ND
|
A:HDD603
|
1.9
|
72.2
|
1.0
|
NE2
|
A:HIS19
|
2.6
|
66.3
|
1.0
|
C4B
|
A:HDD603
|
2.9
|
72.2
|
1.0
|
C1C
|
A:HDD603
|
2.9
|
72.2
|
1.0
|
C1A
|
A:HDD603
|
2.9
|
72.2
|
1.0
|
C4C
|
A:HDD603
|
2.9
|
72.2
|
1.0
|
C4A
|
A:HDD603
|
2.9
|
72.2
|
1.0
|
C4D
|
A:HDD603
|
2.9
|
72.2
|
1.0
|
C1B
|
A:HDD603
|
2.9
|
72.2
|
1.0
|
C1D
|
A:HDD603
|
3.0
|
72.2
|
1.0
|
CHC
|
A:HDD603
|
3.2
|
72.2
|
1.0
|
CHA
|
A:HDD603
|
3.2
|
72.2
|
1.0
|
CHD
|
A:HDD603
|
3.3
|
72.2
|
1.0
|
CHB
|
A:HDD603
|
3.3
|
72.2
|
1.0
|
CE1
|
A:HIS19
|
3.3
|
66.3
|
1.0
|
CD2
|
A:HIS19
|
3.7
|
66.3
|
1.0
|
C2A
|
A:HDD603
|
4.1
|
72.2
|
1.0
|
C2C
|
A:HDD603
|
4.1
|
72.2
|
1.0
|
C3A
|
A:HDD603
|
4.1
|
72.2
|
1.0
|
C3C
|
A:HDD603
|
4.1
|
72.2
|
1.0
|
C2B
|
A:HDD603
|
4.1
|
72.2
|
1.0
|
C3B
|
A:HDD603
|
4.2
|
72.2
|
1.0
|
C2D
|
A:HDD603
|
4.2
|
72.2
|
1.0
|
C3D
|
A:HDD603
|
4.2
|
72.2
|
1.0
|
ND1
|
A:HIS19
|
4.5
|
66.3
|
1.0
|
CZ
|
A:PHE104
|
4.6
|
76.7
|
1.0
|
OND
|
A:HDD603
|
4.6
|
72.2
|
1.0
|
CG
|
A:HIS19
|
4.7
|
66.3
|
1.0
|
CA
|
A:GLY70
|
4.8
|
74.1
|
1.0
|
CG2
|
A:VAL23
|
4.9
|
65.8
|
1.0
|
|
Iron binding site 4 out
of 6 in 7ose
Go back to
Iron Binding Sites List in 7ose
Iron binding site 4 out
of 6 in the Cytochrome Bd-II Type Oxidase with Bound Aurachin D
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Cytochrome Bd-II Type Oxidase with Bound Aurachin D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe601
b:72.7
occ:1.00
|
FE
|
D:HEB601
|
0.0
|
72.7
|
1.0
|
NA
|
D:HEB601
|
2.0
|
72.7
|
1.0
|
NC
|
D:HEB601
|
2.0
|
72.7
|
1.0
|
NB
|
D:HEB601
|
2.0
|
72.7
|
1.0
|
ND
|
D:HEB601
|
2.1
|
72.7
|
1.0
|
NE2
|
D:HIS186
|
2.6
|
64.0
|
1.0
|
SD
|
D:MET393
|
2.8
|
76.9
|
1.0
|
C1C
|
D:HEB601
|
3.0
|
72.7
|
1.0
|
C1A
|
D:HEB601
|
3.0
|
72.7
|
1.0
|
C4A
|
D:HEB601
|
3.0
|
72.7
|
1.0
|
C4C
|
D:HEB601
|
3.1
|
72.7
|
1.0
|
C4B
|
D:HEB601
|
3.2
|
72.7
|
1.0
|
C1B
|
D:HEB601
|
3.2
|
72.7
|
1.0
|
C4D
|
D:HEB601
|
3.2
|
72.7
|
1.0
|
C1D
|
D:HEB601
|
3.3
|
72.7
|
1.0
|
CHC
|
D:HEB601
|
3.4
|
72.7
|
1.0
|
CHA
|
D:HEB601
|
3.5
|
72.7
|
1.0
|
CHB
|
D:HEB601
|
3.5
|
72.7
|
1.0
|
CD2
|
D:HIS186
|
3.5
|
64.0
|
1.0
|
CE1
|
D:HIS186
|
3.5
|
64.0
|
1.0
|
CHD
|
D:HEB601
|
3.6
|
72.7
|
1.0
|
CG
|
D:MET393
|
3.9
|
76.9
|
1.0
|
CE
|
D:MET393
|
3.9
|
76.9
|
1.0
|
C3A
|
D:HEB601
|
4.2
|
72.7
|
1.0
|
C2C
|
D:HEB601
|
4.2
|
72.7
|
1.0
|
C2A
|
D:HEB601
|
4.2
|
72.7
|
1.0
|
C3C
|
D:HEB601
|
4.2
|
72.7
|
1.0
|
C3B
|
D:HEB601
|
4.4
|
72.7
|
1.0
|
C2B
|
D:HEB601
|
4.4
|
72.7
|
1.0
|
CA
|
D:GLY238
|
4.5
|
70.2
|
1.0
|
C3D
|
D:HEB601
|
4.5
|
72.7
|
1.0
|
C2D
|
D:HEB601
|
4.5
|
72.7
|
1.0
|
ND1
|
D:HIS186
|
4.6
|
64.0
|
1.0
|
CG
|
D:HIS186
|
4.7
|
64.0
|
1.0
|
|
Iron binding site 5 out
of 6 in 7ose
Go back to
Iron Binding Sites List in 7ose
Iron binding site 5 out
of 6 in the Cytochrome Bd-II Type Oxidase with Bound Aurachin D
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Cytochrome Bd-II Type Oxidase with Bound Aurachin D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe602
b:76.2
occ:1.00
|
FE
|
D:HEB602
|
0.0
|
76.2
|
1.0
|
NA
|
D:HEB602
|
2.0
|
76.2
|
1.0
|
NC
|
D:HEB602
|
2.0
|
76.2
|
1.0
|
NB
|
D:HEB602
|
2.0
|
76.2
|
1.0
|
ND
|
D:HEB602
|
2.1
|
76.2
|
1.0
|
C1C
|
D:HEB602
|
3.0
|
76.2
|
1.0
|
C1A
|
D:HEB602
|
3.0
|
76.2
|
1.0
|
C4A
|
D:HEB602
|
3.0
|
76.2
|
1.0
|
C4C
|
D:HEB602
|
3.0
|
76.2
|
1.0
|
C4B
|
D:HEB602
|
3.2
|
76.2
|
1.0
|
C1B
|
D:HEB602
|
3.2
|
76.2
|
1.0
|
C4D
|
D:HEB602
|
3.2
|
76.2
|
1.0
|
C1D
|
D:HEB602
|
3.3
|
76.2
|
1.0
|
OE1
|
D:GLU445
|
3.4
|
75.7
|
1.0
|
CHC
|
D:HEB602
|
3.4
|
76.2
|
1.0
|
CE1
|
D:PHE12
|
3.5
|
74.9
|
1.0
|
CHA
|
D:HEB602
|
3.5
|
76.2
|
1.0
|
CHB
|
D:HEB602
|
3.5
|
76.2
|
1.0
|
CD
|
D:GLU445
|
3.5
|
75.7
|
1.0
|
CHD
|
D:HEB602
|
3.6
|
76.2
|
1.0
|
CG
|
D:GLU445
|
3.7
|
75.7
|
1.0
|
CD1
|
D:PHE12
|
3.8
|
74.9
|
1.0
|
C3A
|
D:HEB602
|
4.2
|
76.2
|
1.0
|
C2C
|
D:HEB602
|
4.2
|
76.2
|
1.0
|
C2A
|
D:HEB602
|
4.2
|
76.2
|
1.0
|
OE2
|
D:GLU445
|
4.2
|
75.7
|
1.0
|
C3C
|
D:HEB602
|
4.2
|
76.2
|
1.0
|
CB
|
D:GLU445
|
4.3
|
75.7
|
1.0
|
C3B
|
D:HEB602
|
4.4
|
76.2
|
1.0
|
C2B
|
D:HEB602
|
4.4
|
76.2
|
1.0
|
C3D
|
D:HEB602
|
4.5
|
76.2
|
1.0
|
C2D
|
D:HEB602
|
4.5
|
76.2
|
1.0
|
CZ
|
D:PHE12
|
4.5
|
74.9
|
1.0
|
NH2
|
D:ARG448
|
4.7
|
79.4
|
1.0
|
CB
|
D:ALA16
|
4.8
|
70.4
|
1.0
|
|
Iron binding site 6 out
of 6 in 7ose
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Iron Binding Sites List in 7ose
Iron binding site 6 out
of 6 in the Cytochrome Bd-II Type Oxidase with Bound Aurachin D
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Cytochrome Bd-II Type Oxidase with Bound Aurachin D within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe603
b:72.2
occ:1.00
|
FE
|
D:HDD603
|
0.0
|
72.2
|
1.0
|
NB
|
D:HDD603
|
1.9
|
72.2
|
1.0
|
NA
|
D:HDD603
|
1.9
|
72.2
|
1.0
|
NC
|
D:HDD603
|
1.9
|
72.2
|
1.0
|
ND
|
D:HDD603
|
2.0
|
72.2
|
1.0
|
NE2
|
D:HIS19
|
2.6
|
66.2
|
1.0
|
C4B
|
D:HDD603
|
2.9
|
72.2
|
1.0
|
C1C
|
D:HDD603
|
2.9
|
72.2
|
1.0
|
C1A
|
D:HDD603
|
2.9
|
72.2
|
1.0
|
C4C
|
D:HDD603
|
2.9
|
72.2
|
1.0
|
C4A
|
D:HDD603
|
2.9
|
72.2
|
1.0
|
C4D
|
D:HDD603
|
2.9
|
72.2
|
1.0
|
C1B
|
D:HDD603
|
2.9
|
72.2
|
1.0
|
C1D
|
D:HDD603
|
3.0
|
72.2
|
1.0
|
CHC
|
D:HDD603
|
3.2
|
72.2
|
1.0
|
CHA
|
D:HDD603
|
3.2
|
72.2
|
1.0
|
CHD
|
D:HDD603
|
3.3
|
72.2
|
1.0
|
CHB
|
D:HDD603
|
3.3
|
72.2
|
1.0
|
CE1
|
D:HIS19
|
3.3
|
66.2
|
1.0
|
CD2
|
D:HIS19
|
3.7
|
66.2
|
1.0
|
C2A
|
D:HDD603
|
4.1
|
72.2
|
1.0
|
C2C
|
D:HDD603
|
4.1
|
72.2
|
1.0
|
C3A
|
D:HDD603
|
4.1
|
72.2
|
1.0
|
C3C
|
D:HDD603
|
4.1
|
72.2
|
1.0
|
C2B
|
D:HDD603
|
4.1
|
72.2
|
1.0
|
C3B
|
D:HDD603
|
4.2
|
72.2
|
1.0
|
C2D
|
D:HDD603
|
4.2
|
72.2
|
1.0
|
C3D
|
D:HDD603
|
4.2
|
72.2
|
1.0
|
ND1
|
D:HIS19
|
4.5
|
66.2
|
1.0
|
CZ
|
D:PHE104
|
4.6
|
76.7
|
1.0
|
OND
|
D:HDD603
|
4.6
|
72.2
|
1.0
|
CG
|
D:HIS19
|
4.7
|
66.2
|
1.0
|
CA
|
D:GLY70
|
4.8
|
74.1
|
1.0
|
CG2
|
D:VAL23
|
4.9
|
66.0
|
1.0
|
|
Reference:
A.Grauel,
J.Kaegi,
T.Rasmussen,
I.Makarchuk,
S.Oppermann,
A.F.A.Moumbock,
D.Wohlwend,
R.Mueller,
F.Melin,
S.Guenther,
P.Hellwig,
B.Boettcher,
T.Friedrich.
Structure of Escherichia Coli Cytochrome Bd-II Type Oxidase with Bound Aurachin D Nat Commun 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-26835-2
Page generated: Thu Aug 8 14:45:25 2024
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