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Iron in PDB 6qq5: Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans

Enzymatic activity of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans

All present enzymatic activity of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans:
1.7.2.5;

Other elements in 6qq5:

The structure of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans (pdb code 6qq5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans, PDB code: 6qq5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 6qq5

Go back to Iron Binding Sites List in 6qq5
Iron binding site 1 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

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

b:40.1
occ:1.00
 FE A:HEM801 0.0 40.1 1.0
ND A:HEM801 2.0 40.1 1.0
NB A:HEM801 2.0 40.1 1.0
NC A:HEM801 2.0 40.1 1.0
NA A:HEM801 2.0 40.1 1.0
NE2 A:HIS631 2.1 33.2 1.0
NE2 A:HIS331 2.2 40.1 1.0
CE1 A:HIS331 2.9 40.1 1.0
CD2 A:HIS631 2.9 33.2 1.0
C4D A:HEM801 3.0 40.1 1.0
C1C A:HEM801 3.0 40.1 1.0
C1A A:HEM801 3.0 40.1 1.0
C4B A:HEM801 3.0 40.1 1.0
C1D A:HEM801 3.0 40.1 1.0
C4A A:HEM801 3.0 40.1 1.0
C1B A:HEM801 3.0 40.1 1.0
C4C A:HEM801 3.1 40.1 1.0
CE1 A:HIS631 3.1 33.2 1.0
CD2 A:HIS331 3.3 40.1 1.0
CHA A:HEM801 3.4 40.1 1.0
CHC A:HEM801 3.4 40.1 1.0
CHB A:HEM801 3.4 40.1 1.0
CHD A:HEM801 3.4 40.1 1.0
CG A:HIS631 4.1 33.2 1.0
ND1 A:HIS331 4.1 40.1 1.0
ND1 A:HIS631 4.1 33.2 1.0
C2A A:HEM801 4.2 40.1 1.0
C3A A:HEM801 4.2 40.1 1.0
C3D A:HEM801 4.2 40.1 1.0
C2D A:HEM801 4.2 40.1 1.0
C2C A:HEM801 4.2 40.1 1.0
C2B A:HEM801 4.2 40.1 1.0
C3B A:HEM801 4.2 40.1 1.0
C3C A:HEM801 4.3 40.1 1.0
CG A:HIS331 4.3 40.1 1.0
NE2 A:GLN296 4.9 32.6 1.0

Iron binding site 2 out of 6 in 6qq5

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Iron binding site 2 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

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

b:40.1
occ:1.00
 FE A:HEM802 0.0 40.1 1.0
NE2 A:HIS629 1.9 40.1 1.0
NA A:HEM802 2.0 40.1 1.0
ND A:HEM802 2.0 40.1 1.0
NC A:HEM802 2.0 40.1 1.0
NB A:HEM802 2.0 40.1 1.0
CE1 A:HIS629 2.6 40.1 1.0
C1C A:HEM802 3.0 40.1 1.0
C1A A:HEM802 3.0 40.1 1.0
C4A A:HEM802 3.0 40.1 1.0
C4D A:HEM802 3.0 40.1 1.0
C1B A:HEM802 3.1 40.1 1.0
C4B A:HEM802 3.1 40.1 1.0
C1D A:HEM802 3.1 40.1 1.0
CD2 A:HIS629 3.1 40.1 1.0
C4C A:HEM802 3.1 40.1 1.0
CHC A:HEM802 3.4 40.1 1.0
CHA A:HEM802 3.4 40.1 1.0
CHB A:HEM802 3.4 40.1 1.0
CHD A:HEM802 3.5 40.1 1.0
ND1 A:HIS629 3.8 40.1 1.0
CG A:HIS629 4.1 40.1 1.0
FE A:FE803 4.1 34.6 1.0
C3A A:HEM802 4.2 40.1 1.0
C2A A:HEM802 4.2 40.1 1.0
C2C A:HEM802 4.2 40.1 1.0
C3D A:HEM802 4.3 40.1 1.0
C2B A:HEM802 4.3 40.1 1.0
C2D A:HEM802 4.3 40.1 1.0
C3B A:HEM802 4.3 40.1 1.0
C3C A:HEM802 4.3 40.1 1.0
CE1 A:HIS538 4.9 24.3 1.0

Iron binding site 3 out of 6 in 6qq5

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Iron binding site 3 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

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

b:34.6
occ:1.00
 CE1 A:HIS486 1.8 29.5 1.0
ND1 A:HIS486 1.9 29.5 1.0
NE2 A:HIS538 2.1 24.3 1.0
NE2 A:HIS537 2.4 24.4 1.0
CE1 A:HIS538 2.8 24.3 1.0
NE2 A:HIS486 2.8 29.5 1.0
CG A:HIS486 3.0 29.5 1.0
CD2 A:HIS537 3.2 24.4 1.0
CD2 A:HIS538 3.2 24.3 1.0
CE1 A:HIS537 3.3 24.4 1.0
CD2 A:HIS486 3.5 29.5 1.0
ND1 A:HIS538 3.9 24.3 1.0
ND A:HEM802 3.9 40.1 1.0
C1D A:HEM802 4.0 40.1 1.0
FE A:HEM802 4.1 40.1 1.0
CB A:HIS486 4.1 29.5 1.0
CG A:HIS538 4.1 24.3 1.0
NC A:HEM802 4.2 40.1 1.0
CHD A:HEM802 4.2 40.1 1.0
CG A:HIS537 4.2 24.4 1.0
C4C A:HEM802 4.3 40.1 1.0
ND1 A:HIS537 4.3 24.4 1.0
C4D A:HEM802 4.4 40.1 1.0
O A:GLY534 4.5 30.4 1.0
C2D A:HEM802 4.6 40.1 1.0
NA A:HEM802 4.7 40.1 1.0
C3D A:HEM802 4.8 40.1 1.0
C1C A:HEM802 4.9 40.1 1.0

Iron binding site 4 out of 6 in 6qq5

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Iron binding site 4 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:40.1
occ:1.00
 FE B:HEM801 0.0 40.1 1.0
ND B:HEM801 2.0 40.1 1.0
NB B:HEM801 2.0 40.1 1.0
NC B:HEM801 2.0 40.1 1.0
NA B:HEM801 2.0 40.1 1.0
NE2 B:HIS631 2.1 28.0 1.0
NE2 B:HIS331 2.1 40.1 1.0
CE1 B:HIS331 2.9 40.1 1.0
CD2 B:HIS631 2.9 28.0 1.0
C4A B:HEM801 3.0 40.1 1.0
C1B B:HEM801 3.0 40.1 1.0
C4C B:HEM801 3.0 40.1 1.0
C1D B:HEM801 3.0 40.1 1.0
C4D B:HEM801 3.0 40.1 1.0
C1A B:HEM801 3.0 40.1 1.0
C1C B:HEM801 3.0 40.1 1.0
C4B B:HEM801 3.0 40.1 1.0
CE1 B:HIS631 3.2 28.0 1.0
CD2 B:HIS331 3.3 40.1 1.0
CHB B:HEM801 3.4 40.1 1.0
CHD B:HEM801 3.4 40.1 1.0
CHA B:HEM801 3.4 40.1 1.0
CHC B:HEM801 3.4 40.1 1.0
CG B:HIS631 4.1 28.0 1.0
ND1 B:HIS331 4.1 40.1 1.0
ND1 B:HIS631 4.2 28.0 1.0
C3A B:HEM801 4.2 40.1 1.0
C2A B:HEM801 4.2 40.1 1.0
C2D B:HEM801 4.2 40.1 1.0
C2B B:HEM801 4.2 40.1 1.0
C2C B:HEM801 4.2 40.1 1.0
C3C B:HEM801 4.2 40.1 1.0
C3D B:HEM801 4.2 40.1 1.0
C3B B:HEM801 4.2 40.1 1.0
CG B:HIS331 4.3 40.1 1.0
NE2 B:GLN296 4.8 36.2 1.0

Iron binding site 5 out of 6 in 6qq5

Go back to Iron Binding Sites List in 6qq5
Iron binding site 5 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe802

b:40.1
occ:1.00
 FE B:HEM802 0.0 40.1 1.0
NE2 B:HIS629 1.9 40.1 1.0
NA B:HEM802 2.0 40.1 1.0
NC B:HEM802 2.0 40.1 1.0
ND B:HEM802 2.0 40.1 1.0
NB B:HEM802 2.0 40.1 1.0
CE1 B:HIS629 2.5 40.1 1.0
C1C B:HEM802 3.0 40.1 1.0
C4A B:HEM802 3.0 40.1 1.0
C1A B:HEM802 3.0 40.1 1.0
C4D B:HEM802 3.0 40.1 1.0
C1B B:HEM802 3.0 40.1 1.0
C4B B:HEM802 3.1 40.1 1.0
C1D B:HEM802 3.1 40.1 1.0
C4C B:HEM802 3.1 40.1 1.0
CD2 B:HIS629 3.1 40.1 1.0
CHC B:HEM802 3.4 40.1 1.0
CHA B:HEM802 3.4 40.1 1.0
CHB B:HEM802 3.4 40.1 1.0
CHD B:HEM802 3.5 40.1 1.0
ND1 B:HIS629 3.7 40.1 1.0
FE B:FE803 4.1 38.2 1.0
CG B:HIS629 4.1 40.1 1.0
C3A B:HEM802 4.2 40.1 1.0
C2A B:HEM802 4.2 40.1 1.0
C2C B:HEM802 4.2 40.1 1.0
C2B B:HEM802 4.3 40.1 1.0
C3D B:HEM802 4.3 40.1 1.0
C2D B:HEM802 4.3 40.1 1.0
C3C B:HEM802 4.3 40.1 1.0
C3B B:HEM802 4.3 40.1 1.0
CE1 B:HIS538 4.9 23.3 1.0
CE1 B:HIS486 5.0 29.6 1.0

Iron binding site 6 out of 6 in 6qq5

Go back to Iron Binding Sites List in 6qq5
Iron binding site 6 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe803

b:38.2
occ:1.00
 CE1 B:HIS486 1.8 29.6 1.0
ND1 B:HIS486 1.9 29.6 1.0
NE2 B:HIS538 2.1 23.3 1.0
NE2 B:HIS537 2.4 23.5 1.0
NE2 B:HIS486 2.8 29.6 1.0
CE1 B:HIS538 2.8 23.3 1.0
CG B:HIS486 3.0 29.6 1.0
CD2 B:HIS538 3.2 23.3 1.0
CD2 B:HIS537 3.2 23.5 1.0
CE1 B:HIS537 3.3 23.5 1.0
CD2 B:HIS486 3.4 29.6 1.0
ND B:HEM802 3.9 40.1 1.0
ND1 B:HIS538 4.0 23.3 1.0
C1D B:HEM802 4.0 40.1 1.0
FE B:HEM802 4.1 40.1 1.0
CB B:HIS486 4.1 29.6 1.0
CG B:HIS538 4.1 23.3 1.0
NC B:HEM802 4.2 40.1 1.0
CHD B:HEM802 4.2 40.1 1.0
CG B:HIS537 4.3 23.5 1.0
C4C B:HEM802 4.3 40.1 1.0
ND1 B:HIS537 4.3 23.5 1.0
C4D B:HEM802 4.4 40.1 1.0
O B:GLY534 4.5 29.1 1.0
C2D B:HEM802 4.6 40.1 1.0
NA B:HEM802 4.6 40.1 1.0
C3D B:HEM802 4.9 40.1 1.0
C1C B:HEM802 4.9 40.1 1.0
NB B:HEM802 5.0 40.1 1.0

Reference:

C.C.Gopalasingam, R.M.Johnson, G.N.Chiduza, T.Tosha, M.Yamamoto, Y.Shiro, S.V.Antonyuk, S.P.Muench, S.S.Hasnain. Dimeric Structures of Quinol-Dependent Nitric Oxide Reductases (Qnors) Revealed By Cryo-Electron Microscopy. Sci Adv V. 5 X1803 2019.
ISSN: ESSN 2375-2548
PubMed: 31489376
DOI: 10.1126/SCIADV.AAX1803
Page generated: Wed Aug 7 08:17:33 2024

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