Iron in PDB 8zgp: Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis
Enzymatic activity of Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis
All present enzymatic activity of Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis:
1.7.99.7;
Other elements in 8zgp:
The structure of Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis
(pdb code 8zgp). 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 Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis, PDB code: 8zgp:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 8zgp
Go back to
Iron Binding Sites List in 8zgp
Iron binding site 1 out
of 6 in the Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis
 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 Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe801
b:16.5
occ:1.00
|
FE
|
A:HEM801
|
0.0
|
16.5
|
1.0
|
ND
|
A:HEM801
|
2.0
|
16.5
|
1.0
|
NA
|
A:HEM801
|
2.0
|
16.5
|
1.0
|
NB
|
A:HEM801
|
2.1
|
16.5
|
1.0
|
NC
|
A:HEM801
|
2.1
|
16.5
|
1.0
|
NE2
|
A:HIS335
|
2.2
|
17.1
|
1.0
|
NE2
|
A:HIS635
|
2.4
|
14.0
|
1.0
|
C1D
|
A:HEM801
|
3.0
|
16.5
|
1.0
|
C4D
|
A:HEM801
|
3.0
|
16.5
|
1.0
|
C1A
|
A:HEM801
|
3.0
|
16.5
|
1.0
|
C4A
|
A:HEM801
|
3.0
|
16.5
|
1.0
|
C1B
|
A:HEM801
|
3.0
|
16.5
|
1.0
|
C4C
|
A:HEM801
|
3.1
|
16.5
|
1.0
|
CD2
|
A:HIS635
|
3.1
|
14.0
|
1.0
|
C1C
|
A:HEM801
|
3.1
|
16.5
|
1.0
|
C4B
|
A:HEM801
|
3.1
|
16.5
|
1.0
|
CD2
|
A:HIS335
|
3.1
|
17.1
|
1.0
|
CE1
|
A:HIS335
|
3.2
|
17.1
|
1.0
|
CHB
|
A:HEM801
|
3.4
|
16.5
|
1.0
|
CHA
|
A:HEM801
|
3.4
|
16.5
|
1.0
|
CHD
|
A:HEM801
|
3.4
|
16.5
|
1.0
|
CE1
|
A:HIS635
|
3.4
|
14.0
|
1.0
|
CHC
|
A:HEM801
|
3.5
|
16.5
|
1.0
|
C3D
|
A:HEM801
|
4.2
|
16.5
|
1.0
|
C2D
|
A:HEM801
|
4.2
|
16.5
|
1.0
|
CG
|
A:HIS635
|
4.2
|
14.0
|
1.0
|
C2A
|
A:HEM801
|
4.2
|
16.5
|
1.0
|
C3A
|
A:HEM801
|
4.2
|
16.5
|
1.0
|
CG
|
A:HIS335
|
4.3
|
17.1
|
1.0
|
C2B
|
A:HEM801
|
4.3
|
16.5
|
1.0
|
C3C
|
A:HEM801
|
4.3
|
16.5
|
1.0
|
ND1
|
A:HIS335
|
4.3
|
17.1
|
1.0
|
C2C
|
A:HEM801
|
4.3
|
16.5
|
1.0
|
C3B
|
A:HEM801
|
4.3
|
16.5
|
1.0
|
ND1
|
A:HIS635
|
4.4
|
14.0
|
1.0
|
NH2
|
A:ARG724
|
4.5
|
24.1
|
1.0
|
NE2
|
A:GLN294
|
4.9
|
17.6
|
1.0
|
O
|
A:HOH935
|
4.9
|
30.0
|
1.0
|
|
Iron binding site 2 out
of 6 in 8zgp
Go back to
Iron Binding Sites List in 8zgp
Iron binding site 2 out
of 6 in the Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis
 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 Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe802
b:15.0
occ:1.00
|
FE
|
A:HEM802
|
0.0
|
15.0
|
1.0
|
NC
|
A:HEM802
|
2.0
|
15.0
|
1.0
|
NA
|
A:HEM802
|
2.0
|
15.0
|
1.0
|
NB
|
A:HEM802
|
2.1
|
15.0
|
1.0
|
ND
|
A:HEM802
|
2.1
|
15.0
|
1.0
|
NE2
|
A:HIS633
|
2.5
|
13.3
|
1.0
|
O
|
A:HOH905
|
2.5
|
30.0
|
1.0
|
C4C
|
A:HEM802
|
3.0
|
15.0
|
1.0
|
C1C
|
A:HEM802
|
3.1
|
15.0
|
1.0
|
C4A
|
A:HEM802
|
3.1
|
15.0
|
1.0
|
C1D
|
A:HEM802
|
3.1
|
15.0
|
1.0
|
C1A
|
A:HEM802
|
3.1
|
15.0
|
1.0
|
C4B
|
A:HEM802
|
3.1
|
15.0
|
1.0
|
C1B
|
A:HEM802
|
3.1
|
15.0
|
1.0
|
C4D
|
A:HEM802
|
3.1
|
15.0
|
1.0
|
CD2
|
A:HIS633
|
3.2
|
13.3
|
1.0
|
CHD
|
A:HEM802
|
3.4
|
15.0
|
1.0
|
CHC
|
A:HEM802
|
3.4
|
15.0
|
1.0
|
CHB
|
A:HEM802
|
3.4
|
15.0
|
1.0
|
CHA
|
A:HEM802
|
3.5
|
15.0
|
1.0
|
CE1
|
A:HIS633
|
3.6
|
13.3
|
1.0
|
FE
|
A:FE803
|
3.9
|
22.2
|
1.0
|
C3C
|
A:HEM802
|
4.3
|
15.0
|
1.0
|
C2C
|
A:HEM802
|
4.3
|
15.0
|
1.0
|
C2A
|
A:HEM802
|
4.3
|
15.0
|
1.0
|
C2D
|
A:HEM802
|
4.3
|
15.0
|
1.0
|
C3A
|
A:HEM802
|
4.3
|
15.0
|
1.0
|
C3B
|
A:HEM802
|
4.3
|
15.0
|
1.0
|
C2B
|
A:HEM802
|
4.3
|
15.0
|
1.0
|
C3D
|
A:HEM802
|
4.3
|
15.0
|
1.0
|
OE1
|
A:GLU494
|
4.3
|
22.2
|
0.5
|
OE2
|
A:GLU494
|
4.3
|
22.2
|
0.5
|
OE2
|
A:GLU494
|
4.4
|
22.2
|
0.5
|
CD
|
A:GLU494
|
4.4
|
22.2
|
0.5
|
CG
|
A:HIS633
|
4.5
|
13.3
|
1.0
|
OE1
|
A:GLU494
|
4.5
|
22.2
|
0.5
|
CE1
|
A:HIS542
|
4.5
|
15.3
|
1.0
|
CD
|
A:GLU494
|
4.5
|
22.2
|
0.5
|
ND1
|
A:HIS633
|
4.6
|
13.3
|
1.0
|
NE2
|
A:HIS542
|
4.8
|
15.3
|
1.0
|
NE2
|
A:HIS541
|
4.8
|
14.9
|
1.0
|
|
Iron binding site 3 out
of 6 in 8zgp
Go back to
Iron Binding Sites List in 8zgp
Iron binding site 3 out
of 6 in the Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis
 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 Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe803
b:22.2
occ:1.00
|
O
|
A:HOH905
|
2.1
|
30.0
|
1.0
|
ND1
|
A:HIS490
|
2.1
|
18.2
|
1.0
|
NE2
|
A:HIS542
|
2.1
|
15.3
|
1.0
|
NE2
|
A:HIS541
|
2.3
|
14.9
|
1.0
|
OE1
|
A:GLU494
|
2.4
|
22.2
|
0.5
|
OE1
|
A:GLU494
|
2.6
|
22.2
|
0.5
|
CE1
|
A:HIS490
|
2.9
|
18.2
|
1.0
|
CE1
|
A:HIS542
|
3.1
|
15.3
|
1.0
|
CE1
|
A:HIS541
|
3.1
|
14.9
|
1.0
|
CD2
|
A:HIS542
|
3.1
|
15.3
|
1.0
|
CD
|
A:GLU494
|
3.2
|
22.2
|
0.5
|
CG
|
A:HIS490
|
3.2
|
18.2
|
1.0
|
OE2
|
A:GLU494
|
3.2
|
22.2
|
0.5
|
CD2
|
A:HIS541
|
3.4
|
14.9
|
1.0
|
CB
|
A:HIS490
|
3.6
|
18.2
|
1.0
|
CD
|
A:GLU494
|
3.7
|
22.2
|
0.5
|
FE
|
A:HEM802
|
3.9
|
15.0
|
1.0
|
NC
|
A:HEM802
|
4.1
|
15.0
|
1.0
|
NE2
|
A:HIS490
|
4.1
|
18.2
|
1.0
|
ND1
|
A:HIS542
|
4.2
|
15.3
|
1.0
|
CG
|
A:HIS542
|
4.2
|
15.3
|
1.0
|
CD2
|
A:HIS490
|
4.2
|
18.2
|
1.0
|
ND
|
A:HEM802
|
4.3
|
15.0
|
1.0
|
ND1
|
A:HIS541
|
4.3
|
14.9
|
1.0
|
OE2
|
A:GLU494
|
4.3
|
22.2
|
0.5
|
CA
|
A:HIS490
|
4.4
|
18.2
|
1.0
|
C1D
|
A:HEM802
|
4.4
|
15.0
|
1.0
|
C4C
|
A:HEM802
|
4.4
|
15.0
|
1.0
|
CG
|
A:HIS541
|
4.5
|
14.9
|
1.0
|
CHD
|
A:HEM802
|
4.6
|
15.0
|
1.0
|
CG
|
A:GLU494
|
4.6
|
22.2
|
0.5
|
C1C
|
A:HEM802
|
4.7
|
15.0
|
1.0
|
CG
|
A:GLU494
|
4.8
|
22.2
|
0.5
|
NB
|
A:HEM802
|
4.8
|
15.0
|
1.0
|
NA
|
A:HEM802
|
4.8
|
15.0
|
1.0
|
C4D
|
A:HEM802
|
4.8
|
15.0
|
1.0
|
O
|
A:GLY538
|
4.9
|
17.4
|
1.0
|
OE1
|
A:GLU563
|
4.9
|
19.5
|
1.0
|
|
Iron binding site 4 out
of 6 in 8zgp
Go back to
Iron Binding Sites List in 8zgp
Iron binding site 4 out
of 6 in the Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis
 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 Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe801
b:16.5
occ:1.00
|
FE
|
B:HEM801
|
0.0
|
16.5
|
1.0
|
ND
|
B:HEM801
|
2.0
|
16.5
|
1.0
|
NA
|
B:HEM801
|
2.0
|
16.5
|
1.0
|
NB
|
B:HEM801
|
2.1
|
16.5
|
1.0
|
NC
|
B:HEM801
|
2.1
|
16.5
|
1.0
|
NE2
|
B:HIS335
|
2.2
|
17.1
|
1.0
|
NE2
|
B:HIS635
|
2.4
|
14.0
|
1.0
|
C1D
|
B:HEM801
|
3.0
|
16.5
|
1.0
|
C4D
|
B:HEM801
|
3.0
|
16.5
|
1.0
|
C1A
|
B:HEM801
|
3.0
|
16.5
|
1.0
|
C4A
|
B:HEM801
|
3.0
|
16.5
|
1.0
|
C1B
|
B:HEM801
|
3.0
|
16.5
|
1.0
|
C4C
|
B:HEM801
|
3.1
|
16.5
|
1.0
|
CD2
|
B:HIS635
|
3.1
|
14.0
|
1.0
|
C1C
|
B:HEM801
|
3.1
|
16.5
|
1.0
|
C4B
|
B:HEM801
|
3.1
|
16.5
|
1.0
|
CD2
|
B:HIS335
|
3.1
|
17.1
|
1.0
|
CE1
|
B:HIS335
|
3.2
|
17.1
|
1.0
|
CHB
|
B:HEM801
|
3.4
|
16.5
|
1.0
|
CHA
|
B:HEM801
|
3.4
|
16.5
|
1.0
|
CHD
|
B:HEM801
|
3.4
|
16.5
|
1.0
|
CE1
|
B:HIS635
|
3.4
|
14.0
|
1.0
|
CHC
|
B:HEM801
|
3.5
|
16.5
|
1.0
|
C3D
|
B:HEM801
|
4.2
|
16.5
|
1.0
|
C2D
|
B:HEM801
|
4.2
|
16.5
|
1.0
|
CG
|
B:HIS635
|
4.2
|
14.0
|
1.0
|
C2A
|
B:HEM801
|
4.2
|
16.5
|
1.0
|
C3A
|
B:HEM801
|
4.2
|
16.5
|
1.0
|
CG
|
B:HIS335
|
4.3
|
17.1
|
1.0
|
C2B
|
B:HEM801
|
4.3
|
16.5
|
1.0
|
C3C
|
B:HEM801
|
4.3
|
16.5
|
1.0
|
ND1
|
B:HIS335
|
4.3
|
17.1
|
1.0
|
C2C
|
B:HEM801
|
4.3
|
16.5
|
1.0
|
C3B
|
B:HEM801
|
4.3
|
16.5
|
1.0
|
ND1
|
B:HIS635
|
4.4
|
14.0
|
1.0
|
NH2
|
B:ARG724
|
4.5
|
24.1
|
1.0
|
NE2
|
B:GLN294
|
4.9
|
17.6
|
1.0
|
O
|
B:HOH935
|
4.9
|
30.0
|
1.0
|
|
Iron binding site 5 out
of 6 in 8zgp
Go back to
Iron Binding Sites List in 8zgp
Iron binding site 5 out
of 6 in the Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis
 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 Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe802
b:15.0
occ:1.00
|
FE
|
B:HEM802
|
0.0
|
15.0
|
1.0
|
NC
|
B:HEM802
|
2.0
|
15.0
|
1.0
|
NA
|
B:HEM802
|
2.0
|
15.0
|
1.0
|
NB
|
B:HEM802
|
2.1
|
15.0
|
1.0
|
ND
|
B:HEM802
|
2.1
|
15.0
|
1.0
|
NE2
|
B:HIS633
|
2.5
|
13.3
|
1.0
|
O
|
B:HOH905
|
2.5
|
30.0
|
1.0
|
C4C
|
B:HEM802
|
3.0
|
15.0
|
1.0
|
C1C
|
B:HEM802
|
3.1
|
15.0
|
1.0
|
C4A
|
B:HEM802
|
3.1
|
15.0
|
1.0
|
C1D
|
B:HEM802
|
3.1
|
15.0
|
1.0
|
C1A
|
B:HEM802
|
3.1
|
15.0
|
1.0
|
C4B
|
B:HEM802
|
3.1
|
15.0
|
1.0
|
C1B
|
B:HEM802
|
3.1
|
15.0
|
1.0
|
C4D
|
B:HEM802
|
3.1
|
15.0
|
1.0
|
CD2
|
B:HIS633
|
3.2
|
13.3
|
1.0
|
CHD
|
B:HEM802
|
3.4
|
15.0
|
1.0
|
CHC
|
B:HEM802
|
3.4
|
15.0
|
1.0
|
CHB
|
B:HEM802
|
3.4
|
15.0
|
1.0
|
CHA
|
B:HEM802
|
3.5
|
15.0
|
1.0
|
CE1
|
B:HIS633
|
3.6
|
13.3
|
1.0
|
FE
|
B:FE803
|
3.9
|
22.2
|
1.0
|
C3C
|
B:HEM802
|
4.3
|
15.0
|
1.0
|
C2C
|
B:HEM802
|
4.3
|
15.0
|
1.0
|
C2A
|
B:HEM802
|
4.3
|
15.0
|
1.0
|
C2D
|
B:HEM802
|
4.3
|
15.0
|
1.0
|
C3A
|
B:HEM802
|
4.3
|
15.0
|
1.0
|
C3B
|
B:HEM802
|
4.3
|
15.0
|
1.0
|
C2B
|
B:HEM802
|
4.3
|
15.0
|
1.0
|
C3D
|
B:HEM802
|
4.3
|
15.0
|
1.0
|
OE1
|
B:GLU494
|
4.3
|
22.2
|
0.5
|
OE2
|
B:GLU494
|
4.3
|
22.2
|
0.5
|
OE2
|
B:GLU494
|
4.4
|
22.2
|
0.5
|
CD
|
B:GLU494
|
4.4
|
22.2
|
0.5
|
CG
|
B:HIS633
|
4.5
|
13.3
|
1.0
|
OE1
|
B:GLU494
|
4.5
|
22.2
|
0.5
|
CE1
|
B:HIS542
|
4.5
|
15.3
|
1.0
|
CD
|
B:GLU494
|
4.5
|
22.2
|
0.5
|
ND1
|
B:HIS633
|
4.6
|
13.3
|
1.0
|
NE2
|
B:HIS542
|
4.8
|
15.3
|
1.0
|
NE2
|
B:HIS541
|
4.8
|
14.9
|
1.0
|
|
Iron binding site 6 out
of 6 in 8zgp
Go back to
Iron Binding Sites List in 8zgp
Iron binding site 6 out
of 6 in the Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis
 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 Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe803
b:22.2
occ:1.00
|
O
|
B:HOH905
|
2.1
|
30.0
|
1.0
|
ND1
|
B:HIS490
|
2.1
|
18.2
|
1.0
|
NE2
|
B:HIS542
|
2.1
|
15.3
|
1.0
|
NE2
|
B:HIS541
|
2.3
|
14.9
|
1.0
|
OE1
|
B:GLU494
|
2.4
|
22.2
|
0.5
|
OE1
|
B:GLU494
|
2.6
|
22.2
|
0.5
|
CE1
|
B:HIS490
|
2.9
|
18.2
|
1.0
|
CE1
|
B:HIS542
|
3.1
|
15.3
|
1.0
|
CE1
|
B:HIS541
|
3.1
|
14.9
|
1.0
|
CD2
|
B:HIS542
|
3.1
|
15.3
|
1.0
|
CD
|
B:GLU494
|
3.2
|
22.2
|
0.5
|
CG
|
B:HIS490
|
3.2
|
18.2
|
1.0
|
OE2
|
B:GLU494
|
3.2
|
22.2
|
0.5
|
CD2
|
B:HIS541
|
3.4
|
14.9
|
1.0
|
CB
|
B:HIS490
|
3.6
|
18.2
|
1.0
|
CD
|
B:GLU494
|
3.7
|
22.2
|
0.5
|
FE
|
B:HEM802
|
3.9
|
15.0
|
1.0
|
NC
|
B:HEM802
|
4.1
|
15.0
|
1.0
|
NE2
|
B:HIS490
|
4.1
|
18.2
|
1.0
|
ND1
|
B:HIS542
|
4.2
|
15.3
|
1.0
|
CG
|
B:HIS542
|
4.2
|
15.3
|
1.0
|
CD2
|
B:HIS490
|
4.2
|
18.2
|
1.0
|
ND
|
B:HEM802
|
4.3
|
15.0
|
1.0
|
ND1
|
B:HIS541
|
4.3
|
14.9
|
1.0
|
OE2
|
B:GLU494
|
4.3
|
22.2
|
0.5
|
CA
|
B:HIS490
|
4.4
|
18.2
|
1.0
|
C1D
|
B:HEM802
|
4.4
|
15.0
|
1.0
|
C4C
|
B:HEM802
|
4.4
|
15.0
|
1.0
|
CG
|
B:HIS541
|
4.5
|
14.9
|
1.0
|
CHD
|
B:HEM802
|
4.6
|
15.0
|
1.0
|
CG
|
B:GLU494
|
4.6
|
22.2
|
0.5
|
C1C
|
B:HEM802
|
4.7
|
15.0
|
1.0
|
CG
|
B:GLU494
|
4.8
|
22.2
|
0.5
|
NB
|
B:HEM802
|
4.8
|
15.0
|
1.0
|
NA
|
B:HEM802
|
4.8
|
15.0
|
1.0
|
C4D
|
B:HEM802
|
4.8
|
15.0
|
1.0
|
O
|
B:GLY538
|
4.9
|
17.4
|
1.0
|
OE1
|
B:GLU563
|
4.9
|
19.5
|
1.0
|
|
Reference:
C.C.Gopalasingam,
Y.Shiro,
T.Tosha.
Cryoem Structure of Dimeric Quinol Dependent Nitric Oxide Reductase From Neisseria Meningitidis To Be Published.
Page generated: Fri Aug 8 01:57:05 2025
|