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:
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
|