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Iron in PDB 6qq6: Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) VAL495ALA Mutant From Alcaligenes Xylosoxidans

Enzymatic activity of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) VAL495ALA Mutant From Alcaligenes Xylosoxidans

All present enzymatic activity of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) VAL495ALA Mutant From Alcaligenes Xylosoxidans:
1.7.2.5;

Other elements in 6qq6:

The structure of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) VAL495ALA Mutant 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) VAL495ALA Mutant From Alcaligenes Xylosoxidans (pdb code 6qq6). 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) VAL495ALA Mutant From Alcaligenes Xylosoxidans, PDB code: 6qq6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 6qq6

Go back to Iron Binding Sites List in 6qq6
Iron binding site 1 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) VAL495ALA Mutant 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) VAL495ALA Mutant From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:43.4
occ:1.00
 FE A:HEM801 0.0 43.4 1.0
NE2 A:HIS331 1.9 43.4 1.0
NE2 A:HIS631 2.0 55.9 1.0
ND A:HEM801 2.0 43.4 1.0
NB A:HEM801 2.0 43.4 1.0
NC A:HEM801 2.0 43.4 1.0
NA A:HEM801 2.0 43.4 1.0
CE1 A:HIS331 2.4 43.4 1.0
CD2 A:HIS631 3.0 55.9 1.0
CE1 A:HIS631 3.0 55.9 1.0
C1C A:HEM801 3.0 43.4 1.0
C4D A:HEM801 3.0 43.4 1.0
C1D A:HEM801 3.0 43.4 1.0
C1B A:HEM801 3.1 43.4 1.0
C4B A:HEM801 3.1 43.4 1.0
C1A A:HEM801 3.1 43.4 1.0
C4A A:HEM801 3.1 43.4 1.0
C4C A:HEM801 3.1 43.4 1.0
CD2 A:HIS331 3.2 43.4 1.0
CHC A:HEM801 3.4 43.4 1.0
CHA A:HEM801 3.4 43.4 1.0
CHB A:HEM801 3.4 43.4 1.0
CHD A:HEM801 3.4 43.4 1.0
ND1 A:HIS331 3.7 43.4 1.0
ND1 A:HIS631 4.0 55.9 1.0
CG A:HIS631 4.1 55.9 1.0
CG A:HIS331 4.1 43.4 1.0
C3D A:HEM801 4.2 43.4 1.0
C2C A:HEM801 4.2 43.4 1.0
C2D A:HEM801 4.3 43.4 1.0
C2A A:HEM801 4.3 43.4 1.0
C3A A:HEM801 4.3 43.4 1.0
C2B A:HEM801 4.3 43.4 1.0
C3B A:HEM801 4.3 43.4 1.0
C3C A:HEM801 4.3 43.4 1.0
NE2 A:GLN296 4.6 36.0 1.0
CA A:GLY300 5.0 39.0 1.0

Iron binding site 2 out of 6 in 6qq6

Go back to Iron Binding Sites List in 6qq6
Iron binding site 2 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) VAL495ALA Mutant 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) VAL495ALA Mutant From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe802

b:43.4
occ:1.00
 FE A:HEM802 0.0 43.4 1.0
NE2 A:HIS629 1.9 30.6 1.0
NC A:HEM802 2.0 43.4 1.0
NA A:HEM802 2.0 43.4 1.0
ND A:HEM802 2.0 43.4 1.0
NB A:HEM802 2.1 43.4 1.0
O A:HOH905 2.7 32.1 1.0
CE1 A:HIS629 2.8 30.6 1.0
CD2 A:HIS629 3.0 30.6 1.0
C1C A:HEM802 3.0 43.4 1.0
C4A A:HEM802 3.0 43.4 1.0
C1B A:HEM802 3.0 43.4 1.0
C4D A:HEM802 3.1 43.4 1.0
C1A A:HEM802 3.1 43.4 1.0
C1D A:HEM802 3.1 43.4 1.0
C4C A:HEM802 3.1 43.4 1.0
C4B A:HEM802 3.1 43.4 1.0
CHA A:HEM802 3.4 43.4 1.0
CHB A:HEM802 3.4 43.4 1.0
CHD A:HEM802 3.4 43.4 1.0
CHC A:HEM802 3.4 43.4 1.0
ND1 A:HIS629 3.9 30.6 1.0
CG A:HIS629 4.0 30.6 1.0
FE A:FE803 4.2 41.8 1.0
C2C A:HEM802 4.2 43.4 1.0
C3A A:HEM802 4.2 43.4 1.0
C2A A:HEM802 4.3 43.4 1.0
C2B A:HEM802 4.3 43.4 1.0
C2D A:HEM802 4.3 43.4 1.0
C3D A:HEM802 4.3 43.4 1.0
C3C A:HEM802 4.3 43.4 1.0
C3B A:HEM802 4.3 43.4 1.0
CE1 A:HIS538 4.7 30.3 1.0
NE2 A:HIS537 4.8 31.4 1.0

Iron binding site 3 out of 6 in 6qq6

Go back to Iron Binding Sites List in 6qq6
Iron binding site 3 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) VAL495ALA Mutant 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) VAL495ALA Mutant From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe803

b:41.8
occ:1.00
 NE2 A:HIS538 2.0 30.3 1.0
ND1 A:HIS486 2.1 36.3 1.0
NE2 A:HIS537 2.1 31.4 1.0
O A:HOH905 2.2 32.1 1.0
CE1 A:HIS486 2.7 36.3 1.0
CE1 A:HIS537 2.9 31.4 1.0
CE1 A:HIS538 2.9 30.3 1.0
CD2 A:HIS538 3.0 30.3 1.0
CG A:HIS486 3.1 36.3 1.0
CD2 A:HIS537 3.1 31.4 1.0
CB A:HIS486 3.7 36.3 1.0
NE2 A:HIS486 3.7 36.3 1.0
CD2 A:HIS486 3.9 36.3 1.0
ND1 A:HIS537 4.0 31.4 1.0
ND1 A:HIS538 4.0 30.3 1.0
CG A:HIS538 4.0 30.3 1.0
CG A:HIS537 4.1 31.4 1.0
FE A:HEM802 4.2 43.4 1.0
ND A:HEM802 4.2 43.4 1.0
C1D A:HEM802 4.4 43.4 1.0
NC A:HEM802 4.5 43.4 1.0
C4D A:HEM802 4.6 43.4 1.0
O A:GLY534 4.6 37.8 1.0
C4C A:HEM802 4.6 43.4 1.0
CA A:HIS486 4.6 36.3 1.0
CHD A:HEM802 4.7 43.4 1.0
NA A:HEM802 4.8 43.4 1.0
C2D A:HEM802 4.9 43.4 1.0

Iron binding site 4 out of 6 in 6qq6

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Iron binding site 4 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) VAL495ALA Mutant 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) VAL495ALA Mutant From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:43.4
occ:1.00
 FE B:HEM801 0.0 43.4 1.0
NE2 B:HIS331 1.9 43.4 1.0
NE2 B:HIS631 2.0 58.3 1.0
ND B:HEM801 2.0 43.4 1.0
NB B:HEM801 2.0 43.4 1.0
NA B:HEM801 2.0 43.4 1.0
NC B:HEM801 2.0 43.4 1.0
CE1 B:HIS331 2.4 43.4 1.0
CD2 B:HIS631 2.9 58.3 1.0
CE1 B:HIS631 3.0 58.3 1.0
C1C B:HEM801 3.0 43.4 1.0
C4D B:HEM801 3.0 43.4 1.0
C1D B:HEM801 3.0 43.4 1.0
C1A B:HEM801 3.1 43.4 1.0
C4B B:HEM801 3.1 43.4 1.0
C1B B:HEM801 3.1 43.4 1.0
C4A B:HEM801 3.1 43.4 1.0
C4C B:HEM801 3.1 43.4 1.0
CD2 B:HIS331 3.2 43.4 1.0
CHC B:HEM801 3.4 43.4 1.0
CHA B:HEM801 3.4 43.4 1.0
CHB B:HEM801 3.4 43.4 1.0
CHD B:HEM801 3.4 43.4 1.0
ND1 B:HIS331 3.7 43.4 1.0
ND1 B:HIS631 4.1 58.3 1.0
CG B:HIS631 4.1 58.3 1.0
CG B:HIS331 4.1 43.4 1.0
C3D B:HEM801 4.2 43.4 1.0
C2C B:HEM801 4.2 43.4 1.0
C2D B:HEM801 4.3 43.4 1.0
C2A B:HEM801 4.3 43.4 1.0
C3A B:HEM801 4.3 43.4 1.0
C2B B:HEM801 4.3 43.4 1.0
C3B B:HEM801 4.3 43.4 1.0
C3C B:HEM801 4.3 43.4 1.0
NE2 B:GLN296 4.6 37.2 1.0
CA B:GLY300 5.0 39.5 1.0

Iron binding site 5 out of 6 in 6qq6

Go back to Iron Binding Sites List in 6qq6
Iron binding site 5 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) VAL495ALA Mutant 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) VAL495ALA Mutant From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe802

b:43.4
occ:1.00
 FE B:HEM802 0.0 43.4 1.0
NE2 B:HIS629 1.9 48.6 1.0
NC B:HEM802 2.0 43.4 1.0
NA B:HEM802 2.0 43.4 1.0
ND B:HEM802 2.0 43.4 1.0
NB B:HEM802 2.0 43.4 1.0
O B:HOH906 2.7 30.6 1.0
CE1 B:HIS629 2.8 48.6 1.0
CD2 B:HIS629 3.0 48.6 1.0
C1C B:HEM802 3.0 43.4 1.0
C4A B:HEM802 3.0 43.4 1.0
C1B B:HEM802 3.0 43.4 1.0
C4D B:HEM802 3.1 43.4 1.0
C1A B:HEM802 3.1 43.4 1.0
C1D B:HEM802 3.1 43.4 1.0
C4C B:HEM802 3.1 43.4 1.0
C4B B:HEM802 3.1 43.4 1.0
CHA B:HEM802 3.4 43.4 1.0
CHB B:HEM802 3.4 43.4 1.0
CHD B:HEM802 3.4 43.4 1.0
CHC B:HEM802 3.4 43.4 1.0
ND1 B:HIS629 4.0 48.6 1.0
CG B:HIS629 4.0 48.6 1.0
FE B:FE803 4.1 39.5 1.0
C2C B:HEM802 4.2 43.4 1.0
C3A B:HEM802 4.2 43.4 1.0
C2B B:HEM802 4.3 43.4 1.0
C2A B:HEM802 4.3 43.4 1.0
C2D B:HEM802 4.3 43.4 1.0
C3C B:HEM802 4.3 43.4 1.0
C3D B:HEM802 4.3 43.4 1.0
C3B B:HEM802 4.3 43.4 1.0
CE1 B:HIS538 4.7 31.0 1.0
NE2 B:HIS537 4.8 33.1 1.0

Iron binding site 6 out of 6 in 6qq6

Go back to Iron Binding Sites List in 6qq6
Iron binding site 6 out of 6 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) VAL495ALA Mutant 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) VAL495ALA Mutant From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe803

b:39.5
occ:1.00
 NE2 B:HIS538 2.0 31.0 1.0
ND1 B:HIS486 2.1 36.9 1.0
NE2 B:HIS537 2.1 33.1 1.0
O B:HOH906 2.3 30.6 1.0
CE1 B:HIS486 2.7 36.9 1.0
CE1 B:HIS538 2.9 31.0 1.0
CE1 B:HIS537 2.9 33.1 1.0
CD2 B:HIS538 3.0 31.0 1.0
CD2 B:HIS537 3.1 33.1 1.0
CG B:HIS486 3.1 36.9 1.0
NE2 B:HIS486 3.7 36.9 1.0
CB B:HIS486 3.8 36.9 1.0
CD2 B:HIS486 4.0 36.9 1.0
ND1 B:HIS538 4.0 31.0 1.0
ND1 B:HIS537 4.0 33.1 1.0
CG B:HIS538 4.1 31.0 1.0
CG B:HIS537 4.1 33.1 1.0
ND B:HEM802 4.1 43.4 1.0
FE B:HEM802 4.1 43.4 1.0
C1D B:HEM802 4.3 43.4 1.0
NC B:HEM802 4.4 43.4 1.0
C4D B:HEM802 4.5 43.4 1.0
C4C B:HEM802 4.6 43.4 1.0
CHD B:HEM802 4.6 43.4 1.0
O B:GLY534 4.7 37.2 1.0
CA B:HIS486 4.7 36.9 1.0
NA B:HEM802 4.8 43.4 1.0
C2D B:HEM802 4.8 43.4 1.0
C3D B:HEM802 5.0 43.4 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 08:17:49 2024

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