Iron in PDB 5jca: Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus
Enzymatic activity of Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus
All present enzymatic activity of Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus:
1.6.1.4;
Protein crystallography data
The structure of Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus, PDB code: 5jca
was solved by
O.A.Zadvornyy,
G.J.Schut,
D.M.Nguyen,
J.H.Artz,
M.Tokmina-Lukaszewska,
G.Lipscomb,
M.W.Adams,
J.W.Peters,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.53 /
1.50
|
|
Space group
|
P 32 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
179.681,
179.681,
80.672,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
13.9 /
15.3
|
Other elements in 5jca:
The structure of Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus
(pdb code 5jca). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the
Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus, PDB code: 5jca:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 10 in 5jca
Go back to
Iron Binding Sites List in 5jca
Iron binding site 1 out
of 10 in the Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Fe501
b:11.6
occ:1.00
|
FE1
|
L:SF4501
|
0.0
|
11.6
|
1.0
|
|
OE1
|
L:GLU126
|
1.8
|
15.3
|
1.0
|
|
S3
|
L:SF4501
|
2.1
|
10.0
|
1.0
|
|
S4
|
L:SF4501
|
2.1
|
10.9
|
1.0
|
|
S2
|
L:SF4501
|
2.1
|
11.1
|
1.0
|
|
CD
|
L:GLU126
|
2.8
|
15.4
|
1.0
|
|
FE2
|
L:SF4501
|
3.0
|
10.6
|
1.0
|
|
FE4
|
L:SF4501
|
3.0
|
11.0
|
1.0
|
|
FE3
|
L:SF4501
|
3.0
|
11.3
|
1.0
|
|
OE2
|
L:GLU126
|
3.2
|
14.7
|
1.0
|
|
HD12
|
L:ILE60
|
3.2
|
14.4
|
1.0
|
|
S1
|
L:SF4501
|
3.7
|
10.2
|
1.0
|
|
HG1
|
L:THR97
|
3.8
|
13.7
|
1.0
|
|
CD1
|
L:ILE60
|
4.0
|
12.0
|
1.0
|
|
OG1
|
L:THR97
|
4.0
|
11.4
|
1.0
|
|
HB2
|
L:GLU126
|
4.0
|
12.6
|
1.0
|
|
HD13
|
L:ILE60
|
4.0
|
14.4
|
1.0
|
|
HB
|
L:THR97
|
4.1
|
13.3
|
1.0
|
|
CG
|
L:GLU126
|
4.1
|
10.4
|
1.0
|
|
HB3
|
L:GLU126
|
4.1
|
12.6
|
1.0
|
|
HD11
|
L:ILE60
|
4.1
|
14.4
|
1.0
|
|
HG22
|
L:ILE122
|
4.1
|
14.2
|
1.0
|
|
HA2
|
L:GLY123
|
4.2
|
13.1
|
1.0
|
|
HA2
|
L:GLY98
|
4.2
|
11.8
|
1.0
|
|
HD22
|
L:ASN91
|
4.3
|
12.9
|
1.0
|
|
CB
|
L:GLU126
|
4.3
|
10.5
|
1.0
|
|
CB
|
L:THR97
|
4.6
|
11.1
|
1.0
|
|
HG2
|
L:GLU126
|
4.6
|
12.5
|
1.0
|
|
HG3
|
L:GLU126
|
4.7
|
12.5
|
1.0
|
|
N
|
L:GLY98
|
4.8
|
10.0
|
1.0
|
|
HD21
|
L:ASN91
|
4.8
|
12.9
|
1.0
|
|
C
|
L:THR97
|
4.8
|
10.0
|
1.0
|
|
ND2
|
L:ASN91
|
4.8
|
10.8
|
1.0
|
|
HE21
|
L:GLN103
|
4.8
|
12.8
|
1.0
|
|
SG
|
L:CYS101
|
4.9
|
9.9
|
1.0
|
|
CA
|
L:GLY98
|
4.9
|
9.8
|
1.0
|
|
HG21
|
L:ILE122
|
4.9
|
14.2
|
1.0
|
|
H
|
L:GLY98
|
4.9
|
12.0
|
1.0
|
|
O
|
L:THR97
|
5.0
|
10.3
|
1.0
|
|
CG2
|
L:ILE122
|
5.0
|
11.8
|
1.0
|
|
HB2
|
L:CYS101
|
5.0
|
13.1
|
1.0
|
|
SG
|
L:CYS107
|
5.0
|
11.8
|
1.0
|
|
Iron binding site 2 out
of 10 in 5jca
Go back to
Iron Binding Sites List in 5jca
Iron binding site 2 out
of 10 in the Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Fe501
b:10.6
occ:1.00
|
FE2
|
L:SF4501
|
0.0
|
10.6
|
1.0
|
|
S4
|
L:SF4501
|
2.1
|
10.9
|
1.0
|
|
S1
|
L:SF4501
|
2.1
|
10.2
|
1.0
|
|
S3
|
L:SF4501
|
2.1
|
10.0
|
1.0
|
|
SG
|
L:CYS101
|
2.2
|
9.9
|
1.0
|
|
HB2
|
L:CYS101
|
3.0
|
13.1
|
1.0
|
|
FE1
|
L:SF4501
|
3.0
|
11.6
|
1.0
|
|
FE4
|
L:SF4501
|
3.0
|
11.0
|
1.0
|
|
FE3
|
L:SF4501
|
3.0
|
11.3
|
1.0
|
|
CB
|
L:CYS101
|
3.0
|
10.9
|
1.0
|
|
HB3
|
L:CYS101
|
3.2
|
13.1
|
1.0
|
|
HB
|
L:THR97
|
3.2
|
13.3
|
1.0
|
|
HE21
|
L:GLN106
|
3.4
|
14.0
|
1.0
|
|
HE22
|
L:GLN106
|
3.5
|
14.0
|
1.0
|
|
S2
|
L:SF4501
|
3.7
|
11.1
|
1.0
|
|
NE2
|
L:GLN106
|
3.8
|
11.7
|
1.0
|
|
HG12
|
L:ILE453
|
3.9
|
12.1
|
1.0
|
|
HG21
|
L:ILE453
|
4.0
|
11.8
|
1.0
|
|
HB
|
L:ILE453
|
4.0
|
10.2
|
1.0
|
|
HG3
|
L:GLN103
|
4.1
|
14.6
|
1.0
|
|
CB
|
L:THR97
|
4.2
|
11.1
|
1.0
|
|
HD2
|
L:PRO57
|
4.2
|
14.3
|
1.0
|
|
O
|
L:THR97
|
4.3
|
10.3
|
1.0
|
|
HE21
|
L:GLN103
|
4.3
|
12.8
|
1.0
|
|
HD13
|
L:ILE453
|
4.4
|
14.6
|
1.0
|
|
HG1
|
L:THR97
|
4.4
|
13.7
|
1.0
|
|
OE1
|
L:GLU126
|
4.5
|
15.3
|
1.0
|
|
CA
|
L:CYS101
|
4.5
|
9.8
|
1.0
|
|
OG1
|
L:THR97
|
4.6
|
11.4
|
1.0
|
|
CB
|
L:ILE453
|
4.6
|
8.5
|
1.0
|
|
CG1
|
L:ILE453
|
4.6
|
10.1
|
1.0
|
|
C
|
L:THR97
|
4.7
|
10.0
|
1.0
|
|
CG2
|
L:ILE453
|
4.7
|
9.8
|
1.0
|
|
H
|
L:CYS101
|
4.7
|
11.5
|
1.0
|
|
HA
|
L:CYS101
|
4.8
|
11.8
|
1.0
|
|
SG
|
L:CYS107
|
4.9
|
11.8
|
1.0
|
|
HG21
|
L:THR97
|
4.9
|
14.4
|
1.0
|
|
CG
|
L:GLN103
|
4.9
|
12.2
|
1.0
|
|
CA
|
L:THR97
|
4.9
|
9.1
|
1.0
|
|
HB2
|
L:GLN106
|
5.0
|
12.6
|
1.0
|
|
HB3
|
L:GLN106
|
5.0
|
12.6
|
1.0
|
|
HD3
|
L:PRO57
|
5.0
|
14.3
|
1.0
|
|
SG
|
L:CYS56
|
5.0
|
10.8
|
1.0
|
|
HG22
|
L:ILE453
|
5.0
|
11.8
|
1.0
|
|
Iron binding site 3 out
of 10 in 5jca
Go back to
Iron Binding Sites List in 5jca
Iron binding site 3 out
of 10 in the Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Fe501
b:11.3
occ:1.00
|
FE3
|
L:SF4501
|
0.0
|
11.3
|
1.0
|
|
SG
|
L:CYS107
|
2.1
|
11.8
|
1.0
|
|
S2
|
L:SF4501
|
2.1
|
11.1
|
1.0
|
|
S1
|
L:SF4501
|
2.1
|
10.2
|
1.0
|
|
S4
|
L:SF4501
|
2.1
|
10.9
|
1.0
|
|
HB3
|
L:CYS107
|
2.9
|
13.2
|
1.0
|
|
FE4
|
L:SF4501
|
3.0
|
11.0
|
1.0
|
|
FE1
|
L:SF4501
|
3.0
|
11.6
|
1.0
|
|
FE2
|
L:SF4501
|
3.0
|
10.6
|
1.0
|
|
CB
|
L:CYS107
|
3.1
|
11.0
|
1.0
|
|
HG3
|
L:GLN103
|
3.5
|
14.6
|
1.0
|
|
H
|
L:CYS107
|
3.6
|
13.2
|
1.0
|
|
HB2
|
L:CYS107
|
3.6
|
13.2
|
1.0
|
|
HG22
|
L:ILE122
|
3.7
|
14.2
|
1.0
|
|
HG2
|
L:GLN103
|
3.7
|
14.6
|
1.0
|
|
S3
|
L:SF4501
|
3.7
|
10.0
|
1.0
|
|
HG21
|
L:ILE122
|
3.7
|
14.2
|
1.0
|
|
CG
|
L:GLN103
|
4.1
|
12.2
|
1.0
|
|
HB2
|
L:CYS56
|
4.1
|
13.6
|
1.0
|
|
CG2
|
L:ILE122
|
4.1
|
11.8
|
1.0
|
|
HD11
|
L:ILE62
|
4.3
|
15.7
|
1.0
|
|
HB
|
L:ILE122
|
4.3
|
14.0
|
1.0
|
|
N
|
L:CYS107
|
4.3
|
11.0
|
1.0
|
|
CA
|
L:CYS107
|
4.3
|
11.3
|
1.0
|
|
HE21
|
L:GLN106
|
4.4
|
14.0
|
1.0
|
|
HE21
|
L:GLN103
|
4.5
|
12.8
|
1.0
|
|
HA
|
L:CYS56
|
4.5
|
13.2
|
1.0
|
|
OE1
|
L:GLU126
|
4.6
|
15.3
|
1.0
|
|
HB2
|
L:CYS101
|
4.6
|
13.1
|
1.0
|
|
HA2
|
L:GLY123
|
4.6
|
13.1
|
1.0
|
|
HB2
|
L:GLN106
|
4.7
|
12.6
|
1.0
|
|
HB3
|
L:GLN103
|
4.7
|
14.9
|
1.0
|
|
HA
|
L:GLN103
|
4.7
|
14.6
|
1.0
|
|
HB3
|
L:CYS101
|
4.7
|
13.1
|
1.0
|
|
H
|
L:GLU108
|
4.7
|
14.8
|
1.0
|
|
HB3
|
L:GLN106
|
4.7
|
12.6
|
1.0
|
|
HG3
|
L:GLU108
|
4.8
|
15.3
|
1.0
|
|
CB
|
L:ILE122
|
4.8
|
11.7
|
1.0
|
|
CB
|
L:CYS56
|
4.8
|
11.3
|
1.0
|
|
SG
|
L:CYS56
|
4.9
|
10.8
|
1.0
|
|
HD13
|
L:ILE62
|
4.9
|
15.7
|
1.0
|
|
CB
|
L:GLN103
|
4.9
|
12.4
|
1.0
|
|
SG
|
L:CYS101
|
4.9
|
9.9
|
1.0
|
|
HA
|
L:CYS107
|
5.0
|
13.5
|
1.0
|
|
HG23
|
L:ILE122
|
5.0
|
14.2
|
1.0
|
|
CB
|
L:CYS101
|
5.0
|
10.9
|
1.0
|
|
H
|
L:GLY123
|
5.0
|
13.6
|
1.0
|
|
HD13
|
L:ILE122
|
5.0
|
15.4
|
1.0
|
|
Iron binding site 4 out
of 10 in 5jca
Go back to
Iron Binding Sites List in 5jca
Iron binding site 4 out
of 10 in the Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Fe501
b:11.0
occ:1.00
|
FE4
|
L:SF4501
|
0.0
|
11.0
|
1.0
|
|
S1
|
L:SF4501
|
2.1
|
10.2
|
1.0
|
|
S3
|
L:SF4501
|
2.1
|
10.0
|
1.0
|
|
S2
|
L:SF4501
|
2.1
|
11.1
|
1.0
|
|
SG
|
L:CYS56
|
2.2
|
10.8
|
1.0
|
|
HB2
|
L:CYS56
|
2.9
|
13.6
|
1.0
|
|
HD12
|
L:ILE60
|
2.9
|
14.4
|
1.0
|
|
FE1
|
L:SF4501
|
3.0
|
11.6
|
1.0
|
|
FE3
|
L:SF4501
|
3.0
|
11.3
|
1.0
|
|
FE2
|
L:SF4501
|
3.0
|
10.6
|
1.0
|
|
CB
|
L:CYS56
|
3.1
|
11.3
|
1.0
|
|
HA
|
L:CYS56
|
3.4
|
13.2
|
1.0
|
|
HD2
|
L:PRO57
|
3.7
|
14.3
|
1.0
|
|
S4
|
L:SF4501
|
3.7
|
10.9
|
1.0
|
|
CA
|
L:CYS56
|
3.8
|
11.0
|
1.0
|
|
CD1
|
L:ILE60
|
3.9
|
12.0
|
1.0
|
|
HB3
|
L:CYS56
|
3.9
|
13.6
|
1.0
|
|
HG12
|
L:ILE453
|
3.9
|
12.1
|
1.0
|
|
HB3
|
L:CYS107
|
4.0
|
13.2
|
1.0
|
|
HD11
|
L:ILE60
|
4.1
|
14.4
|
1.0
|
|
HB
|
L:ILE60
|
4.1
|
14.3
|
1.0
|
|
HG13
|
L:ILE60
|
4.1
|
13.3
|
1.0
|
|
HD11
|
L:ILE62
|
4.2
|
15.7
|
1.0
|
|
HG22
|
L:VAL58
|
4.3
|
12.7
|
1.0
|
|
CD
|
L:PRO57
|
4.4
|
11.9
|
1.0
|
|
HD3
|
L:PRO57
|
4.4
|
14.3
|
1.0
|
|
CG1
|
L:ILE60
|
4.5
|
11.1
|
1.0
|
|
H
|
L:VAL58
|
4.5
|
13.2
|
1.0
|
|
H
|
L:ILE60
|
4.5
|
13.2
|
1.0
|
|
HD13
|
L:ILE60
|
4.5
|
14.4
|
1.0
|
|
C
|
L:CYS56
|
4.5
|
10.9
|
1.0
|
|
N
|
L:PRO57
|
4.6
|
11.4
|
1.0
|
|
HD13
|
L:ILE453
|
4.7
|
14.6
|
1.0
|
|
HD11
|
L:ILE453
|
4.7
|
14.6
|
1.0
|
|
HE21
|
L:GLN106
|
4.7
|
14.0
|
1.0
|
|
OE1
|
L:GLU126
|
4.7
|
15.3
|
1.0
|
|
CB
|
L:ILE60
|
4.8
|
11.9
|
1.0
|
|
SG
|
L:CYS107
|
4.8
|
11.8
|
1.0
|
|
CG1
|
L:ILE453
|
4.8
|
10.1
|
1.0
|
|
CB
|
L:CYS107
|
4.8
|
11.0
|
1.0
|
|
CD1
|
L:ILE453
|
5.0
|
12.2
|
1.0
|
|
HG23
|
L:VAL58
|
5.0
|
12.7
|
1.0
|
|
SG
|
L:CYS101
|
5.0
|
9.9
|
1.0
|
|
Iron binding site 5 out
of 10 in 5jca
Go back to
Iron Binding Sites List in 5jca
Iron binding site 5 out
of 10 in the Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Fe502
b:14.7
occ:1.00
|
FE1
|
L:SF4502
|
0.0
|
14.7
|
1.0
|
|
S4
|
L:SF4502
|
2.1
|
14.9
|
1.0
|
|
S3
|
L:SF4502
|
2.1
|
13.8
|
1.0
|
|
S2
|
L:SF4502
|
2.1
|
14.5
|
1.0
|
|
SG
|
L:CYS45
|
2.2
|
19.8
|
1.0
|
|
FE3
|
L:SF4502
|
3.0
|
14.0
|
1.0
|
|
FE4
|
L:SF4502
|
3.0
|
14.0
|
1.0
|
|
FE2
|
L:SF4502
|
3.0
|
13.1
|
1.0
|
|
HB2
|
L:CYS45
|
3.1
|
20.2
|
1.0
|
|
H
|
L:CYS45
|
3.2
|
22.2
|
1.0
|
|
HG12
|
L:VAL112
|
3.2
|
24.3
|
1.0
|
|
CB
|
L:CYS45
|
3.3
|
16.8
|
1.0
|
|
HB2
|
L:LEU43
|
3.6
|
19.2
|
1.0
|
|
S1
|
L:SF4502
|
3.7
|
13.2
|
1.0
|
|
HD2
|
L:PRO51
|
3.8
|
17.5
|
1.0
|
|
HG11
|
L:VAL112
|
3.9
|
24.3
|
1.0
|
|
N
|
L:CYS45
|
3.9
|
18.5
|
1.0
|
|
CG1
|
L:VAL112
|
4.0
|
20.2
|
1.0
|
|
HB3
|
L:CYS45
|
4.0
|
20.2
|
1.0
|
|
H
|
L:LEU43
|
4.1
|
18.5
|
1.0
|
|
H
|
L:VAL112
|
4.1
|
17.5
|
1.0
|
|
CA
|
L:CYS45
|
4.3
|
17.7
|
1.0
|
|
H
|
L:GLN44
|
4.3
|
20.0
|
1.0
|
|
HB1
|
L:ALA50
|
4.4
|
23.0
|
1.0
|
|
HG13
|
L:VAL112
|
4.5
|
24.3
|
1.0
|
|
HD12
|
L:LEU43
|
4.5
|
20.3
|
1.0
|
|
CB
|
L:LEU43
|
4.6
|
16.0
|
1.0
|
|
N
|
L:GLN44
|
4.6
|
16.7
|
1.0
|
|
N
|
L:LEU43
|
4.8
|
15.4
|
1.0
|
|
CD
|
L:PRO51
|
4.8
|
14.6
|
1.0
|
|
HA
|
L:CYS45
|
4.8
|
21.2
|
1.0
|
|
HG2
|
L:PRO51
|
4.8
|
24.5
|
1.0
|
|
SG
|
L:CYS42
|
4.8
|
14.1
|
1.0
|
|
HA
|
L:ALA50
|
4.8
|
18.9
|
1.0
|
|
SG
|
L:CYS52
|
4.8
|
12.9
|
1.0
|
|
HB
|
L:VAL112
|
4.9
|
20.6
|
1.0
|
|
HA
|
L:CYS111
|
4.9
|
16.6
|
1.0
|
|
N
|
L:VAL112
|
4.9
|
14.6
|
1.0
|
|
HG23
|
L:VAL113
|
5.0
|
19.5
|
1.0
|
|
HG
|
L:LEU43
|
5.0
|
19.5
|
1.0
|
|
H
|
L:CYS52
|
5.0
|
15.4
|
1.0
|
|
C
|
L:LEU43
|
5.0
|
18.4
|
1.0
|
|
Iron binding site 6 out
of 10 in 5jca
Go back to
Iron Binding Sites List in 5jca
Iron binding site 6 out
of 10 in the Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Fe502
b:13.1
occ:1.00
|
FE2
|
L:SF4502
|
0.0
|
13.1
|
1.0
|
|
SG
|
L:CYS52
|
2.1
|
12.9
|
1.0
|
|
S4
|
L:SF4502
|
2.1
|
14.9
|
1.0
|
|
S3
|
L:SF4502
|
2.1
|
13.8
|
1.0
|
|
S1
|
L:SF4502
|
2.1
|
13.2
|
1.0
|
|
HB3
|
L:CYS52
|
2.8
|
15.2
|
1.0
|
|
FE3
|
L:SF4502
|
3.0
|
14.0
|
1.0
|
|
FE4
|
L:SF4502
|
3.0
|
14.0
|
1.0
|
|
FE1
|
L:SF4502
|
3.0
|
14.7
|
1.0
|
|
CB
|
L:CYS52
|
3.0
|
12.7
|
1.0
|
|
HD3
|
L:PRO63
|
3.4
|
15.7
|
1.0
|
|
H
|
L:CYS52
|
3.4
|
15.4
|
1.0
|
|
HB1
|
L:ALA50
|
3.5
|
23.0
|
1.0
|
|
HB2
|
L:CYS52
|
3.6
|
15.2
|
1.0
|
|
S2
|
L:SF4502
|
3.7
|
14.5
|
1.0
|
|
HG22
|
L:ILE62
|
4.0
|
15.2
|
1.0
|
|
HG21
|
L:ILE62
|
4.0
|
15.2
|
1.0
|
|
N
|
L:CYS52
|
4.1
|
12.8
|
1.0
|
|
HD11
|
L:ILE122
|
4.2
|
15.4
|
1.0
|
|
CA
|
L:CYS52
|
4.2
|
12.1
|
1.0
|
|
HB2
|
L:CYS45
|
4.3
|
20.2
|
1.0
|
|
CD
|
L:PRO63
|
4.4
|
13.1
|
1.0
|
|
HB
|
L:ILE62
|
4.4
|
13.9
|
1.0
|
|
HD2
|
L:PRO51
|
4.4
|
17.5
|
1.0
|
|
HA
|
L:CYS111
|
4.4
|
16.6
|
1.0
|
|
CG2
|
L:ILE62
|
4.4
|
12.7
|
1.0
|
|
CB
|
L:ALA50
|
4.5
|
19.2
|
1.0
|
|
HG3
|
L:PRO63
|
4.5
|
17.9
|
1.0
|
|
HB3
|
L:PRO63
|
4.6
|
18.4
|
1.0
|
|
H
|
L:ILE53
|
4.6
|
15.6
|
1.0
|
|
HB2
|
L:CYS111
|
4.7
|
16.2
|
1.0
|
|
HB2
|
L:ALA50
|
4.8
|
23.0
|
1.0
|
|
HA
|
L:CYS52
|
4.9
|
14.5
|
1.0
|
|
HG13
|
L:ILE53
|
4.9
|
16.1
|
1.0
|
|
SG
|
L:CYS42
|
4.9
|
14.1
|
1.0
|
|
HB3
|
L:ALA50
|
4.9
|
23.0
|
1.0
|
|
HD2
|
L:PRO63
|
4.9
|
15.7
|
1.0
|
|
H
|
L:CYS45
|
4.9
|
22.2
|
1.0
|
|
SG
|
L:CYS111
|
4.9
|
14.0
|
1.0
|
|
SG
|
L:CYS45
|
4.9
|
19.8
|
1.0
|
|
CG
|
L:PRO63
|
4.9
|
14.9
|
1.0
|
|
HD13
|
L:ILE122
|
4.9
|
15.4
|
1.0
|
|
CB
|
L:ILE62
|
5.0
|
11.6
|
1.0
|
|
CD1
|
L:ILE122
|
5.0
|
12.8
|
1.0
|
|
HG2
|
L:PRO51
|
5.0
|
24.5
|
1.0
|
|
Iron binding site 7 out
of 10 in 5jca
Go back to
Iron Binding Sites List in 5jca
Iron binding site 7 out
of 10 in the Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Fe502
b:14.0
occ:1.00
|
FE3
|
L:SF4502
|
0.0
|
14.0
|
1.0
|
|
S2
|
L:SF4502
|
2.1
|
14.5
|
1.0
|
|
S4
|
L:SF4502
|
2.1
|
14.9
|
1.0
|
|
S1
|
L:SF4502
|
2.1
|
13.2
|
1.0
|
|
SG
|
L:CYS42
|
2.2
|
14.1
|
1.0
|
|
FE1
|
L:SF4502
|
3.0
|
14.7
|
1.0
|
|
FE4
|
L:SF4502
|
3.0
|
14.0
|
1.0
|
|
FE2
|
L:SF4502
|
3.0
|
13.1
|
1.0
|
|
H
|
L:LEU43
|
3.2
|
18.5
|
1.0
|
|
HG13
|
L:ILE120
|
3.3
|
17.3
|
1.0
|
|
CB
|
L:CYS42
|
3.3
|
14.5
|
1.0
|
|
H
|
L:GLN44
|
3.3
|
20.0
|
1.0
|
|
HA
|
L:CYS42
|
3.3
|
18.8
|
1.0
|
|
HB2
|
L:CYS42
|
3.4
|
17.4
|
1.0
|
|
S3
|
L:SF4502
|
3.7
|
13.8
|
1.0
|
|
CA
|
L:CYS42
|
3.7
|
15.7
|
1.0
|
|
N
|
L:LEU43
|
3.8
|
15.4
|
1.0
|
|
H
|
L:CYS45
|
4.0
|
22.2
|
1.0
|
|
N
|
L:GLN44
|
4.1
|
16.7
|
1.0
|
|
CG1
|
L:ILE120
|
4.1
|
14.4
|
1.0
|
|
HB3
|
L:CYS42
|
4.1
|
17.4
|
1.0
|
|
C
|
L:CYS42
|
4.2
|
15.5
|
1.0
|
|
HG12
|
L:ILE120
|
4.2
|
17.3
|
1.0
|
|
HB3
|
L:PRO63
|
4.2
|
18.4
|
1.0
|
|
HD12
|
L:ILE66
|
4.2
|
18.4
|
1.0
|
|
HA
|
L:GLN44
|
4.4
|
21.6
|
1.0
|
|
HG21
|
L:ILE120
|
4.4
|
16.8
|
1.0
|
|
HB2
|
L:LEU43
|
4.6
|
19.2
|
1.0
|
|
HA
|
L:PRO63
|
4.6
|
17.6
|
1.0
|
|
HG22
|
L:ILE62
|
4.6
|
15.2
|
1.0
|
|
HD13
|
L:ILE66
|
4.6
|
18.4
|
1.0
|
|
HB
|
L:ILE120
|
4.6
|
16.5
|
1.0
|
|
HE21
|
L:GLN44
|
4.7
|
23.7
|
1.0
|
|
HD3
|
L:PRO63
|
4.7
|
15.7
|
1.0
|
|
CA
|
L:LEU43
|
4.8
|
16.3
|
1.0
|
|
CA
|
L:GLN44
|
4.8
|
18.0
|
1.0
|
|
C
|
L:LEU43
|
4.9
|
18.4
|
1.0
|
|
CD1
|
L:ILE66
|
4.9
|
15.3
|
1.0
|
|
N
|
L:CYS45
|
4.9
|
18.5
|
1.0
|
|
CB
|
L:ILE120
|
4.9
|
13.7
|
1.0
|
|
SG
|
L:CYS52
|
4.9
|
12.9
|
1.0
|
|
SG
|
L:CYS45
|
4.9
|
19.8
|
1.0
|
|
SG
|
L:CYS111
|
5.0
|
14.0
|
1.0
|
|
Iron binding site 8 out
of 10 in 5jca
Go back to
Iron Binding Sites List in 5jca
Iron binding site 8 out
of 10 in the Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Fe502
b:14.0
occ:1.00
|
FE4
|
L:SF4502
|
0.0
|
14.0
|
1.0
|
|
S3
|
L:SF4502
|
2.1
|
13.8
|
1.0
|
|
S2
|
L:SF4502
|
2.1
|
14.5
|
1.0
|
|
S1
|
L:SF4502
|
2.1
|
13.2
|
1.0
|
|
SG
|
L:CYS111
|
2.2
|
14.0
|
1.0
|
|
FE1
|
L:SF4502
|
3.0
|
14.7
|
1.0
|
|
FE3
|
L:SF4502
|
3.0
|
14.0
|
1.0
|
|
FE2
|
L:SF4502
|
3.0
|
13.1
|
1.0
|
|
HG12
|
L:ILE120
|
3.2
|
17.3
|
1.0
|
|
CB
|
L:CYS111
|
3.3
|
13.5
|
1.0
|
|
HA
|
L:CYS111
|
3.3
|
16.6
|
1.0
|
|
HB2
|
L:CYS111
|
3.3
|
16.2
|
1.0
|
|
H
|
L:VAL112
|
3.4
|
17.5
|
1.0
|
|
HG12
|
L:VAL112
|
3.5
|
24.3
|
1.0
|
|
HG13
|
L:ILE120
|
3.6
|
17.3
|
1.0
|
|
S4
|
L:SF4502
|
3.7
|
14.9
|
1.0
|
|
H
|
L:VAL113
|
3.7
|
18.6
|
1.0
|
|
CA
|
L:CYS111
|
3.7
|
13.8
|
1.0
|
|
HG23
|
L:VAL113
|
3.8
|
19.5
|
1.0
|
|
CG1
|
L:ILE120
|
3.8
|
14.4
|
1.0
|
|
HB
|
L:ILE120
|
3.8
|
16.5
|
1.0
|
|
N
|
L:VAL112
|
3.9
|
14.6
|
1.0
|
|
HB3
|
L:CYS52
|
3.9
|
15.2
|
1.0
|
|
HB3
|
L:CYS111
|
4.1
|
16.2
|
1.0
|
|
H
|
L:ILE120
|
4.2
|
17.0
|
1.0
|
|
C
|
L:CYS111
|
4.2
|
14.3
|
1.0
|
|
HD11
|
L:ILE122
|
4.2
|
15.4
|
1.0
|
|
CB
|
L:ILE120
|
4.4
|
13.7
|
1.0
|
|
CG1
|
L:VAL112
|
4.4
|
20.2
|
1.0
|
|
N
|
L:VAL113
|
4.6
|
15.5
|
1.0
|
|
HG13
|
L:VAL112
|
4.6
|
24.3
|
1.0
|
|
CG2
|
L:VAL113
|
4.6
|
16.2
|
1.0
|
|
HB
|
L:VAL113
|
4.6
|
19.0
|
1.0
|
|
H
|
L:LEU43
|
4.7
|
18.5
|
1.0
|
|
HG21
|
L:VAL113
|
4.7
|
19.5
|
1.0
|
|
HA
|
L:CYS42
|
4.7
|
18.8
|
1.0
|
|
CB
|
L:CYS52
|
4.8
|
12.7
|
1.0
|
|
SG
|
L:CYS52
|
4.8
|
12.9
|
1.0
|
|
N
|
L:ILE120
|
5.0
|
14.2
|
1.0
|
|
CA
|
L:VAL112
|
5.0
|
16.0
|
1.0
|
|
HG11
|
L:VAL112
|
5.0
|
24.3
|
1.0
|
|
Iron binding site 9 out
of 10 in 5jca
Go back to
Iron Binding Sites List in 5jca
Iron binding site 9 out
of 10 in the Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe302
b:10.8
occ:1.00
|
FE1
|
S:FES302
|
0.0
|
10.8
|
1.0
|
|
S2
|
S:FES302
|
2.2
|
10.3
|
1.0
|
|
S1
|
S:FES302
|
2.3
|
10.0
|
1.0
|
|
SG
|
S:CYS231
|
2.3
|
10.8
|
1.0
|
|
SG
|
S:CYS243
|
2.4
|
9.9
|
1.0
|
|
FE2
|
S:FES302
|
2.8
|
10.2
|
1.0
|
|
HB3
|
S:CYS243
|
3.1
|
11.0
|
1.0
|
|
HB3
|
S:CYS231
|
3.3
|
11.8
|
1.0
|
|
CB
|
S:CYS243
|
3.4
|
9.2
|
1.0
|
|
CB
|
S:CYS231
|
3.5
|
9.8
|
1.0
|
|
H
|
S:CYS231
|
3.5
|
12.7
|
1.0
|
|
H
|
S:CYS243
|
3.5
|
11.9
|
1.0
|
|
H
|
S:GLY226
|
3.6
|
11.9
|
1.0
|
|
HB3
|
S:PHE241
|
3.7
|
14.2
|
1.0
|
|
HA2
|
S:GLY224
|
3.7
|
12.6
|
1.0
|
|
H
|
S:GLY224
|
3.8
|
11.3
|
1.0
|
|
H
|
S:GLY229
|
4.0
|
13.4
|
1.0
|
|
HB2
|
S:CYS243
|
4.0
|
11.0
|
1.0
|
|
HG2
|
S:MET221
|
4.0
|
11.1
|
1.0
|
|
HB2
|
S:CYS231
|
4.1
|
11.8
|
1.0
|
|
HA2
|
S:GLY226
|
4.1
|
12.5
|
1.0
|
|
N
|
S:CYS231
|
4.3
|
10.6
|
1.0
|
|
N
|
S:CYS243
|
4.3
|
9.9
|
1.0
|
|
N
|
S:GLY226
|
4.3
|
9.9
|
1.0
|
|
CA
|
S:GLY224
|
4.4
|
10.5
|
1.0
|
|
CA
|
S:CYS243
|
4.4
|
10.6
|
1.0
|
|
N
|
S:GLY224
|
4.4
|
9.4
|
1.0
|
|
H
|
S:THR225
|
4.5
|
12.0
|
1.0
|
|
OD1
|
S:ASP223
|
4.5
|
10.9
|
1.0
|
|
CA
|
S:CYS231
|
4.5
|
10.1
|
1.0
|
|
H
|
S:ALA230
|
4.5
|
13.7
|
1.0
|
|
H
|
S:CYS228
|
4.6
|
13.2
|
1.0
|
|
HE2
|
S:MET221
|
4.6
|
12.0
|
1.0
|
|
HB3
|
S:ALA230
|
4.6
|
14.2
|
1.0
|
|
HD2
|
S:PHE241
|
4.6
|
15.3
|
1.0
|
|
HA
|
S:MET221
|
4.7
|
10.7
|
1.0
|
|
CB
|
S:PHE241
|
4.7
|
11.9
|
1.0
|
|
C
|
S:GLY224
|
4.7
|
11.0
|
1.0
|
|
CA
|
S:GLY226
|
4.7
|
10.4
|
1.0
|
|
N
|
S:THR225
|
4.7
|
10.0
|
1.0
|
|
N
|
S:GLY229
|
4.7
|
11.2
|
1.0
|
|
H
|
S:VAL222
|
4.7
|
11.3
|
1.0
|
|
SG
|
S:CYS228
|
4.8
|
11.3
|
1.0
|
|
HA2
|
S:GLY229
|
4.8
|
12.3
|
1.0
|
|
N
|
S:ALA230
|
4.9
|
11.4
|
1.0
|
|
HG22
|
S:VAL244
|
4.9
|
16.3
|
1.0
|
|
CG
|
S:MET221
|
4.9
|
9.2
|
1.0
|
|
HB3
|
S:MET221
|
4.9
|
9.5
|
1.0
|
|
H
|
S:VAL244
|
4.9
|
12.9
|
1.0
|
|
H
|
S:MET227
|
5.0
|
11.4
|
1.0
|
|
Iron binding site 10 out
of 10 in 5jca
Go back to
Iron Binding Sites List in 5jca
Iron binding site 10 out
of 10 in the Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Nadp(H) Bound Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe302
b:10.2
occ:1.00
|
FE2
|
S:FES302
|
0.0
|
10.2
|
1.0
|
|
OD1
|
S:ASP223
|
2.1
|
10.9
|
1.0
|
|
S1
|
S:FES302
|
2.3
|
10.0
|
1.0
|
|
S2
|
S:FES302
|
2.3
|
10.3
|
1.0
|
|
SG
|
S:CYS228
|
2.3
|
11.3
|
1.0
|
|
FE1
|
S:FES302
|
2.8
|
10.8
|
1.0
|
|
H
|
S:CYS228
|
3.1
|
13.2
|
1.0
|
|
CG
|
S:ASP223
|
3.1
|
10.5
|
1.0
|
|
H
|
S:GLY224
|
3.2
|
11.3
|
1.0
|
|
H
|
S:ASP223
|
3.3
|
10.8
|
1.0
|
|
H
|
S:GLY229
|
3.3
|
13.4
|
1.0
|
|
H
|
S:ALA230
|
3.5
|
13.7
|
1.0
|
|
CB
|
S:CYS228
|
3.5
|
10.2
|
1.0
|
|
OD2
|
S:ASP223
|
3.6
|
10.5
|
1.0
|
|
HB3
|
S:CYS228
|
3.6
|
12.2
|
1.0
|
|
N
|
S:CYS228
|
3.6
|
11.0
|
1.0
|
|
H
|
S:MET227
|
3.7
|
11.4
|
1.0
|
|
H
|
S:VAL222
|
3.8
|
11.3
|
1.0
|
|
N
|
S:GLY229
|
3.9
|
11.2
|
1.0
|
|
HB3
|
S:ALA230
|
3.9
|
14.2
|
1.0
|
|
H
|
S:GLY226
|
3.9
|
11.9
|
1.0
|
|
CA
|
S:CYS228
|
3.9
|
11.4
|
1.0
|
|
N
|
S:ASP223
|
4.0
|
9.0
|
1.0
|
|
N
|
S:GLY224
|
4.0
|
9.4
|
1.0
|
|
HB
|
S:VAL222
|
4.1
|
12.9
|
1.0
|
|
H
|
S:THR225
|
4.2
|
12.0
|
1.0
|
|
N
|
S:MET227
|
4.2
|
9.5
|
1.0
|
|
N
|
S:ALA230
|
4.2
|
11.4
|
1.0
|
|
C
|
S:CYS228
|
4.2
|
11.8
|
1.0
|
|
H
|
S:CYS231
|
4.3
|
12.7
|
1.0
|
|
HB2
|
S:CYS228
|
4.3
|
12.2
|
1.0
|
|
CB
|
S:ASP223
|
4.3
|
10.7
|
1.0
|
|
O
|
S:HOH701
|
4.4
|
17.1
|
1.0
|
|
HB2
|
S:MET227
|
4.5
|
14.3
|
1.0
|
|
HB2
|
S:ALA230
|
4.5
|
14.2
|
1.0
|
|
SG
|
S:CYS243
|
4.5
|
9.9
|
1.0
|
|
CB
|
S:ALA230
|
4.6
|
11.9
|
1.0
|
|
C
|
S:MET227
|
4.6
|
13.9
|
1.0
|
|
CA
|
S:ASP223
|
4.6
|
9.1
|
1.0
|
|
N
|
S:GLY226
|
4.6
|
9.9
|
1.0
|
|
HA2
|
S:GLY224
|
4.6
|
12.6
|
1.0
|
|
N
|
S:VAL222
|
4.6
|
9.4
|
1.0
|
|
HB3
|
S:ASP223
|
4.6
|
12.8
|
1.0
|
|
SG
|
S:CYS231
|
4.7
|
10.8
|
1.0
|
|
C
|
S:ASP223
|
4.8
|
9.0
|
1.0
|
|
HA2
|
S:GLY226
|
4.8
|
12.5
|
1.0
|
|
C
|
S:GLY226
|
4.8
|
9.4
|
1.0
|
|
CA
|
S:GLY224
|
4.8
|
10.5
|
1.0
|
|
HA
|
S:CYS228
|
4.8
|
13.7
|
1.0
|
|
CA
|
S:MET227
|
4.9
|
10.6
|
1.0
|
|
CA
|
S:GLY229
|
4.9
|
10.3
|
1.0
|
|
N
|
S:THR225
|
4.9
|
10.0
|
1.0
|
|
HA
|
S:MET221
|
4.9
|
10.7
|
1.0
|
|
HB3
|
S:CYS231
|
4.9
|
11.8
|
1.0
|
|
CB
|
S:VAL222
|
5.0
|
10.8
|
1.0
|
|
C
|
S:VAL222
|
5.0
|
9.3
|
1.0
|
|
CA
|
S:GLY226
|
5.0
|
10.4
|
1.0
|
|
C
|
S:GLY229
|
5.0
|
11.4
|
1.0
|
|
CA
|
S:ALA230
|
5.0
|
10.7
|
1.0
|
|
Reference:
C.E.Lubner,
D.P.Jennings,
D.W.Mulder,
G.J.Schut,
O.A.Zadvornyy,
J.P.Hoben,
M.Tokmina-Lukaszewska,
L.Berry,
D.M.Nguyen,
G.L.Lipscomb,
B.Bothner,
A.K.Jones,
A.F.Miller,
P.W.King,
M.W.W.Adams,
J.W.Peters.
Mechanistic Insights Into Energy Conservation By Flavin-Based Electron Bifurcation. Nat. Chem. Biol. V. 13 655 2017.
ISSN: ESSN 1552-4469
PubMed: 28394885
DOI: 10.1038/NCHEMBIO.2348
Page generated: Tue Aug 6 02:25:35 2024
|
