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:
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 Sites List in 6qq5
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 Sites List in 6qq5
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 Sites List in 6qq5
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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