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Iron in PDB 8bgw: Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution

Enzymatic activity of Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution

All present enzymatic activity of Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution:
1.7.2.5;

Other elements in 8bgw:

The structure of Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution (pdb code 8bgw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution, PDB code: 8bgw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 8bgw

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Iron binding site 1 out of 6 in the Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:34.3
occ:1.00
 FE A:HEM801 0.0 34.3 1.0
ND A:HEM801 1.8 34.6 1.0
NE2 A:HIS331 1.9 28.7 1.0
NE2 A:HIS631 1.9 37.4 1.0
NA A:HEM801 2.0 37.3 1.0
NC A:HEM801 2.1 35.1 1.0
NB A:HEM801 2.1 34.7 1.0
CD2 A:HIS331 2.8 29.2 1.0
C1D A:HEM801 2.8 41.0 1.0
CE1 A:HIS631 2.8 44.8 1.0
C4D A:HEM801 2.9 37.9 1.0
CE1 A:HIS331 2.9 32.1 1.0
C4C A:HEM801 3.0 41.5 1.0
C1A A:HEM801 3.0 36.2 1.0
C4A A:HEM801 3.0 35.3 1.0
CD2 A:HIS631 3.0 43.1 1.0
C1B A:HEM801 3.0 36.9 1.0
C4B A:HEM801 3.0 35.0 1.0
C1C A:HEM801 3.1 35.7 1.0
CHD A:HEM801 3.2 41.9 1.0
CHA A:HEM801 3.3 37.7 1.0
CHB A:HEM801 3.4 39.0 1.0
CHC A:HEM801 3.4 35.9 1.0
CG A:HIS331 3.9 33.9 1.0
ND1 A:HIS631 3.9 36.5 1.0
ND1 A:HIS331 4.0 32.8 1.0
C2D A:HEM801 4.0 39.1 1.0
CG A:HIS631 4.0 40.1 1.0
C3D A:HEM801 4.1 37.9 1.0
C2A A:HEM801 4.2 45.5 1.0
C3A A:HEM801 4.2 45.4 1.0
C3C A:HEM801 4.2 40.9 1.0
C2B A:HEM801 4.3 34.9 1.0
C2C A:HEM801 4.3 39.9 1.0
C3B A:HEM801 4.3 41.6 1.0
NH2 A:ARG720 4.6 73.0 1.0
NE2 A:GLN296 4.7 49.0 1.0
CA A:GLY300 4.8 40.3 1.0

Iron binding site 2 out of 6 in 8bgw

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Iron binding site 2 out of 6 in the Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe802

b:37.7
occ:1.00
 FE A:HEM802 0.0 37.7 1.0
O A:HOH935 1.9 25.0 1.0
ND A:HEM802 1.9 52.6 1.0
NE2 A:HIS629 1.9 28.6 1.0
NA A:HEM802 2.0 48.1 1.0
NC A:HEM802 2.0 47.6 1.0
NB A:HEM802 2.1 52.0 1.0
C1D A:HEM802 2.9 44.7 1.0
C4D A:HEM802 2.9 41.2 1.0
CD2 A:HIS629 2.9 36.3 1.0
C4C A:HEM802 2.9 44.6 1.0
C1A A:HEM802 2.9 47.9 1.0
CE1 A:HIS629 3.0 34.2 1.0
C4A A:HEM802 3.0 48.3 1.0
C1B A:HEM802 3.0 52.7 1.0
C4B A:HEM802 3.0 44.9 1.0
C1C A:HEM802 3.1 55.1 1.0
CHD A:HEM802 3.2 42.4 1.0
CHA A:HEM802 3.3 40.2 1.0
CHB A:HEM802 3.4 45.5 1.0
CHC A:HEM802 3.4 44.9 1.0
O A:HOH968 3.6 69.2 1.0
OE2 A:GLU490 3.6 97.8 1.0
FE A:FE803 3.9 49.5 1.0
CG A:HIS629 4.0 30.1 1.0
ND1 A:HIS629 4.1 32.4 1.0
C3D A:HEM802 4.1 50.0 1.0
C2A A:HEM802 4.1 49.3 1.0
C2D A:HEM802 4.1 50.1 1.0
C3C A:HEM802 4.2 55.6 1.0
C3A A:HEM802 4.2 47.9 1.0
C2C A:HEM802 4.2 54.0 1.0
C2B A:HEM802 4.3 52.2 1.0
C3B A:HEM802 4.3 58.6 1.0
CD A:GLU490 4.4 104.2 1.0
OE1 A:GLU490 4.4 96.3 1.0
NE2 A:HIS537 4.5 54.3 1.0
CE1 A:HIS538 4.7 42.5 1.0
CE1 A:HIS537 4.8 50.4 1.0
NE2 A:HIS538 4.9 45.0 1.0

Iron binding site 3 out of 6 in 8bgw

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Iron binding site 3 out of 6 in the Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe803

b:49.5
occ:1.00
 NE2 A:HIS537 2.1 54.3 1.0
O A:HOH935 2.1 25.0 1.0
ND1 A:HIS486 2.1 47.4 1.0
NE2 A:HIS538 2.1 45.0 1.0
OE2 A:GLU490 2.9 97.8 1.0
CE1 A:HIS537 3.0 50.4 1.0
O A:HOH968 3.0 69.2 1.0
CE1 A:HIS486 3.0 51.2 1.0
CE1 A:HIS538 3.1 42.5 1.0
CD2 A:HIS538 3.1 37.2 1.0
CG A:HIS486 3.1 52.4 1.0
CD2 A:HIS537 3.1 48.5 1.0
OE1 A:GLU490 3.2 96.3 1.0
CD A:GLU490 3.3 104.2 1.0
CB A:HIS486 3.4 47.8 1.0
FE A:HEM802 3.9 37.7 1.0
NC A:HEM802 4.0 47.6 1.0
ND A:HEM802 4.0 52.6 1.0
ND1 A:HIS537 4.1 51.8 1.0
ND1 A:HIS538 4.1 38.9 1.0
CG A:HIS538 4.2 39.0 1.0
NE2 A:HIS486 4.2 54.2 1.0
CG A:HIS537 4.2 51.6 1.0
CD2 A:HIS486 4.2 45.9 1.0
C1D A:HEM802 4.3 44.7 1.0
CA A:HIS486 4.3 64.5 1.0
C4C A:HEM802 4.3 44.6 1.0
O A:GLY534 4.3 74.4 1.0
CHD A:HEM802 4.4 42.4 1.0
NA A:HEM802 4.5 48.1 1.0
C4D A:HEM802 4.6 41.2 1.0
NB A:HEM802 4.6 52.0 1.0
C1C A:HEM802 4.7 55.1 1.0
CG A:GLU490 4.7 100.0 1.0
C2D A:HEM802 5.0 50.1 1.0

Iron binding site 4 out of 6 in 8bgw

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Iron binding site 4 out of 6 in the Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe802

b:34.3
occ:1.00
 FE B:HEM802 0.0 34.3 1.0
ND B:HEM802 1.8 34.6 1.0
NE2 B:HIS331 1.9 28.7 1.0
NE2 B:HIS631 1.9 37.5 1.0
NA B:HEM802 2.0 37.4 1.0
NC B:HEM802 2.1 35.1 1.0
NB B:HEM802 2.1 34.7 1.0
CD2 B:HIS331 2.8 29.2 1.0
C1D B:HEM802 2.8 41.0 1.0
CE1 B:HIS631 2.8 44.8 1.0
C4D B:HEM802 2.9 37.9 1.0
CE1 B:HIS331 2.9 32.1 1.0
C4C B:HEM802 3.0 41.4 1.0
C1A B:HEM802 3.0 36.1 1.0
CD2 B:HIS631 3.0 43.2 1.0
C4A B:HEM802 3.0 35.3 1.0
C1B B:HEM802 3.0 36.8 1.0
C4B B:HEM802 3.0 35.1 1.0
C1C B:HEM802 3.1 35.6 1.0
CHD B:HEM802 3.2 41.9 1.0
CHA B:HEM802 3.3 37.7 1.0
CHB B:HEM802 3.4 38.9 1.0
CHC B:HEM802 3.4 36.0 1.0
CG B:HIS331 3.9 33.9 1.0
ND1 B:HIS631 3.9 36.5 1.0
ND1 B:HIS331 4.0 32.8 1.0
C2D B:HEM802 4.0 39.0 1.0
CG B:HIS631 4.0 40.1 1.0
C3D B:HEM802 4.1 37.8 1.0
C2A B:HEM802 4.2 45.5 1.0
C3A B:HEM802 4.2 45.2 1.0
C3C B:HEM802 4.2 40.9 1.0
C2B B:HEM802 4.3 34.9 1.0
C2C B:HEM802 4.3 39.9 1.0
C3B B:HEM802 4.3 41.7 1.0
NH2 B:ARG720 4.6 72.6 1.0
NE2 B:GLN296 4.7 49.2 1.0
CA B:GLY300 4.8 40.4 1.0

Iron binding site 5 out of 6 in 8bgw

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Iron binding site 5 out of 6 in the Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe803

b:37.7
occ:1.00
 FE B:HEM803 0.0 37.7 1.0
O B:HOH930 1.9 24.9 1.0
ND B:HEM803 1.9 52.4 1.0
NE2 B:HIS629 1.9 28.6 1.0
NA B:HEM803 2.0 48.1 1.0
NC B:HEM803 2.0 47.7 1.0
NB B:HEM803 2.1 52.0 1.0
C1D B:HEM803 2.9 44.7 1.0
C4D B:HEM803 2.9 41.1 1.0
CD2 B:HIS629 2.9 36.1 1.0
C4C B:HEM803 2.9 44.5 1.0
C1A B:HEM803 2.9 48.0 1.0
CE1 B:HIS629 3.0 34.3 1.0
C4A B:HEM803 3.0 48.2 1.0
C1B B:HEM803 3.0 52.7 1.0
C4B B:HEM803 3.0 45.1 1.0
C1C B:HEM803 3.1 55.4 1.0
CHD B:HEM803 3.2 42.2 1.0
CHA B:HEM803 3.3 40.3 1.0
CHB B:HEM803 3.4 45.4 1.0
CHC B:HEM803 3.4 45.3 1.0
O B:HOH956 3.5 68.8 1.0
OE2 B:GLU490 3.6 98.1 1.0
FE B:FE804 3.9 49.6 1.0
CG B:HIS629 4.0 30.1 1.0
ND1 B:HIS629 4.1 32.5 1.0
C3D B:HEM803 4.1 50.2 1.0
C2A B:HEM803 4.1 49.2 1.0
C2D B:HEM803 4.1 49.8 1.0
C3C B:HEM803 4.2 55.6 1.0
C3A B:HEM803 4.2 47.9 1.0
C2C B:HEM803 4.2 54.1 1.0
C2B B:HEM803 4.3 52.3 1.0
C3B B:HEM803 4.3 58.7 1.0
CD B:GLU490 4.4 104.9 1.0
OE1 B:GLU490 4.5 96.8 1.0
NE2 B:HIS537 4.5 54.6 1.0
CE1 B:HIS538 4.7 42.3 1.0
CE1 B:HIS537 4.8 50.5 1.0
NE2 B:HIS538 4.9 45.0 1.0

Iron binding site 6 out of 6 in 8bgw

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Iron binding site 6 out of 6 in the Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe804

b:49.6
occ:1.00
 NE2 B:HIS537 2.1 54.6 1.0
O B:HOH930 2.1 24.9 1.0
ND1 B:HIS486 2.1 47.4 1.0
NE2 B:HIS538 2.1 45.0 1.0
OE2 B:GLU490 2.9 98.1 1.0
CE1 B:HIS537 3.0 50.5 1.0
O B:HOH956 3.0 68.8 1.0
CE1 B:HIS486 3.0 51.2 1.0
CE1 B:HIS538 3.1 42.3 1.0
CD2 B:HIS538 3.1 37.2 1.0
CG B:HIS486 3.1 52.3 1.0
CD2 B:HIS537 3.1 48.5 1.0
OE1 B:GLU490 3.2 96.8 1.0
CD B:GLU490 3.3 104.9 1.0
CB B:HIS486 3.4 47.6 1.0
FE B:HEM803 3.9 37.7 1.0
NC B:HEM803 4.0 47.7 1.0
ND B:HEM803 4.0 52.4 1.0
ND1 B:HIS537 4.1 51.8 1.0
ND1 B:HIS538 4.1 38.8 1.0
CG B:HIS538 4.2 39.1 1.0
NE2 B:HIS486 4.2 54.4 1.0
CG B:HIS537 4.2 51.5 1.0
CD2 B:HIS486 4.2 45.9 1.0
C1D B:HEM803 4.3 44.7 1.0
CA B:HIS486 4.3 64.4 1.0
C4C B:HEM803 4.3 44.5 1.0
O B:GLY534 4.3 74.3 1.0
CHD B:HEM803 4.4 42.2 1.0
NA B:HEM803 4.5 48.1 1.0
C4D B:HEM803 4.6 41.1 1.0
NB B:HEM803 4.6 52.0 1.0
C1C B:HEM803 4.7 55.4 1.0
CG B:GLU490 4.7 100.1 1.0
C2D B:HEM803 5.0 49.8 1.0

Reference:

A.J.Flynn, S.V.Antonyuk, R.R.Eady, S.P.Muench, S.S.Hasnain. A 2.2 Angstrom Cryoem Structure of A Quinol-Dependent No Reductase Shows Close Similarity to Respiratory Oxidases. Nat Commun V. 14 3416 2023.
ISSN: ESSN 2041-1723
PubMed: 37296134
DOI: 10.1038/S41467-023-39140-X
Page generated: Fri Aug 9 19:54:27 2024

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