Atomistry » Iron » PDB 8bgw-8ca3 » 8bgw
Atomistry »
  Iron »
    PDB 8bgw-8ca3 »
      8bgw »

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

Go back to Iron Binding Sites List in 8bgw
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

Go back to Iron Binding Sites List in 8bgw
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

Go back to Iron Binding Sites List in 8bgw
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

Go back to Iron Binding Sites List in 8bgw
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

Go back to Iron Binding Sites List in 8bgw
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

Go back to Iron Binding Sites List in 8bgw
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy