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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

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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

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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

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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

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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

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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 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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