Iron in PDB 7p0p: Naf-1 Bound to M1 Molecule
Protein crystallography data
The structure of Naf-1 Bound to M1 Molecule, PDB code: 7p0p
was solved by
O.Livnah,
Y.Eisenberg-Domovich,
H.B.Marjault,
R.Nechushtai,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.21 /
1.74
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
43.573,
47.589,
125.948,
90,
90,
90
|
R / Rfree (%)
|
20.4 /
25.4
|
Iron Binding Sites:
The binding sites of Iron atom in the Naf-1 Bound to M1 Molecule
(pdb code 7p0p). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Naf-1 Bound to M1 Molecule, PDB code: 7p0p:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 7p0p
Go back to
Iron Binding Sites List in 7p0p
Iron binding site 1 out
of 8 in the Naf-1 Bound to M1 Molecule
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe200
b:22.8
occ:1.00
|
FE1
|
A:FES200
|
0.0
|
22.8
|
1.0
|
S2
|
A:FES200
|
2.2
|
22.4
|
1.0
|
S1
|
A:FES200
|
2.2
|
25.1
|
1.0
|
SG
|
A:CYS101
|
2.3
|
25.2
|
1.0
|
SG
|
A:CYS99
|
2.4
|
23.2
|
1.0
|
FE2
|
A:FES200
|
2.7
|
23.5
|
1.0
|
CB
|
A:CYS101
|
3.3
|
27.8
|
1.0
|
CB
|
A:CYS99
|
3.4
|
23.6
|
1.0
|
N
|
A:CYS101
|
3.6
|
25.4
|
1.0
|
CA
|
A:CYS99
|
3.7
|
21.9
|
1.0
|
N
|
A:ARG100
|
3.9
|
20.1
|
1.0
|
CA
|
A:CYS101
|
3.9
|
26.1
|
1.0
|
CB
|
A:HIS114
|
4.0
|
24.0
|
1.0
|
N
|
A:HIS114
|
4.1
|
22.4
|
1.0
|
C
|
A:CYS99
|
4.2
|
19.8
|
1.0
|
N
|
A:SER104
|
4.3
|
25.8
|
1.0
|
ND1
|
A:HIS114
|
4.4
|
24.1
|
1.0
|
N
|
A:TRP102
|
4.4
|
25.8
|
1.0
|
CA
|
A:HIS114
|
4.4
|
24.0
|
1.0
|
C
|
A:CYS101
|
4.4
|
26.2
|
1.0
|
CB
|
A:SER104
|
4.5
|
26.5
|
1.0
|
N
|
A:ARG103
|
4.6
|
25.1
|
1.0
|
C
|
A:ARG100
|
4.6
|
23.1
|
1.0
|
SG
|
A:CYS110
|
4.7
|
24.7
|
1.0
|
CG
|
A:HIS114
|
4.7
|
22.0
|
1.0
|
CA
|
A:CYS110
|
4.8
|
25.6
|
1.0
|
CA
|
A:SER104
|
4.8
|
27.5
|
1.0
|
CB
|
A:CYS110
|
4.9
|
23.4
|
1.0
|
CA
|
A:ARG100
|
5.0
|
20.8
|
1.0
|
|
Iron binding site 2 out
of 8 in 7p0p
Go back to
Iron Binding Sites List in 7p0p
Iron binding site 2 out
of 8 in the Naf-1 Bound to M1 Molecule
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe200
b:23.5
occ:1.00
|
FE2
|
A:FES200
|
0.0
|
23.5
|
1.0
|
S1
|
A:FES200
|
2.2
|
25.1
|
1.0
|
ND1
|
A:HIS114
|
2.2
|
24.1
|
1.0
|
SG
|
A:CYS110
|
2.3
|
24.7
|
1.0
|
S2
|
A:FES200
|
2.3
|
22.4
|
1.0
|
FE1
|
A:FES200
|
2.7
|
22.8
|
1.0
|
CE1
|
A:HIS114
|
3.2
|
22.5
|
1.0
|
CG
|
A:HIS114
|
3.2
|
22.0
|
1.0
|
CB
|
A:CYS110
|
3.3
|
23.4
|
1.0
|
CB
|
A:HIS114
|
3.5
|
24.0
|
1.0
|
CA
|
A:CYS110
|
3.8
|
25.6
|
1.0
|
N
|
A:HIS114
|
3.9
|
22.4
|
1.0
|
N
|
A:GLY112
|
4.0
|
26.9
|
1.0
|
CB
|
A:PRO127
|
4.2
|
22.6
|
1.0
|
CD
|
A:PRO127
|
4.3
|
23.1
|
1.0
|
NE2
|
A:HIS114
|
4.3
|
23.2
|
1.0
|
CA
|
A:GLY112
|
4.3
|
25.2
|
1.0
|
N
|
A:ASP111
|
4.3
|
26.9
|
1.0
|
CD2
|
A:HIS114
|
4.3
|
21.6
|
1.0
|
CA
|
A:HIS114
|
4.3
|
24.0
|
1.0
|
N
|
A:SER113
|
4.4
|
24.5
|
1.0
|
CG
|
A:PRO127
|
4.4
|
22.6
|
1.0
|
C
|
A:CYS110
|
4.4
|
26.0
|
1.0
|
C
|
A:GLY112
|
4.5
|
24.1
|
1.0
|
SG
|
A:CYS101
|
4.5
|
25.2
|
1.0
|
CA
|
A:CYS99
|
4.6
|
21.9
|
1.0
|
SG
|
A:CYS99
|
4.6
|
23.2
|
1.0
|
N
|
A:PRO127
|
4.6
|
22.4
|
1.0
|
CB
|
A:CYS99
|
4.7
|
23.6
|
1.0
|
CA
|
A:PRO127
|
4.8
|
23.4
|
1.0
|
C
|
A:SER113
|
5.0
|
22.2
|
1.0
|
|
Iron binding site 3 out
of 8 in 7p0p
Go back to
Iron Binding Sites List in 7p0p
Iron binding site 3 out
of 8 in the Naf-1 Bound to M1 Molecule
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe200
b:23.9
occ:1.00
|
FE1
|
B:FES200
|
0.0
|
23.9
|
1.0
|
S1
|
B:FES200
|
2.2
|
24.7
|
1.0
|
S2
|
B:FES200
|
2.2
|
23.2
|
1.0
|
SG
|
B:CYS101
|
2.3
|
24.8
|
1.0
|
SG
|
B:CYS99
|
2.4
|
22.7
|
1.0
|
FE2
|
B:FES200
|
2.7
|
23.6
|
1.0
|
CB
|
B:CYS99
|
3.3
|
25.6
|
1.0
|
CB
|
B:CYS101
|
3.3
|
23.6
|
1.0
|
N
|
B:CYS101
|
3.6
|
21.6
|
1.0
|
CA
|
B:CYS99
|
3.6
|
24.8
|
1.0
|
N
|
B:ARG100
|
3.9
|
22.0
|
1.0
|
CA
|
B:CYS101
|
3.9
|
23.6
|
1.0
|
CB
|
B:HIS114
|
4.1
|
22.6
|
1.0
|
C
|
B:CYS99
|
4.2
|
23.0
|
1.0
|
ND1
|
B:HIS114
|
4.2
|
22.0
|
1.0
|
N
|
B:HIS114
|
4.3
|
23.9
|
1.0
|
N
|
B:TRP102
|
4.4
|
25.0
|
1.0
|
C
|
B:CYS101
|
4.4
|
23.7
|
1.0
|
CB
|
B:SER104
|
4.5
|
26.3
|
1.0
|
N
|
B:SER104
|
4.5
|
26.8
|
1.0
|
CA
|
B:HIS114
|
4.6
|
23.9
|
1.0
|
SG
|
B:CYS110
|
4.6
|
25.3
|
1.0
|
N
|
B:ARG103
|
4.6
|
26.3
|
1.0
|
CG
|
B:HIS114
|
4.7
|
23.4
|
1.0
|
C
|
B:ARG100
|
4.7
|
22.9
|
1.0
|
CA
|
B:CYS110
|
4.8
|
25.6
|
1.0
|
CB
|
B:CYS110
|
4.8
|
27.5
|
1.0
|
CA
|
B:SER104
|
4.9
|
27.5
|
1.0
|
CA
|
B:ARG100
|
5.0
|
22.2
|
1.0
|
N
|
B:CYS99
|
5.0
|
24.2
|
1.0
|
|
Iron binding site 4 out
of 8 in 7p0p
Go back to
Iron Binding Sites List in 7p0p
Iron binding site 4 out
of 8 in the Naf-1 Bound to M1 Molecule
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe200
b:23.6
occ:1.00
|
FE2
|
B:FES200
|
0.0
|
23.6
|
1.0
|
ND1
|
B:HIS114
|
2.2
|
22.0
|
1.0
|
S1
|
B:FES200
|
2.2
|
24.7
|
1.0
|
S2
|
B:FES200
|
2.2
|
23.2
|
1.0
|
SG
|
B:CYS110
|
2.3
|
25.3
|
1.0
|
FE1
|
B:FES200
|
2.7
|
23.9
|
1.0
|
CE1
|
B:HIS114
|
3.0
|
21.0
|
1.0
|
CB
|
B:CYS110
|
3.3
|
27.5
|
1.0
|
CG
|
B:HIS114
|
3.3
|
23.4
|
1.0
|
CB
|
B:HIS114
|
3.7
|
22.6
|
1.0
|
CA
|
B:CYS110
|
3.8
|
25.6
|
1.0
|
N
|
B:GLY112
|
4.0
|
25.9
|
1.0
|
N
|
B:HIS114
|
4.0
|
23.9
|
1.0
|
NE2
|
B:HIS114
|
4.2
|
22.4
|
1.0
|
CA
|
B:GLY112
|
4.2
|
25.1
|
1.0
|
CD
|
B:PRO127
|
4.3
|
23.5
|
1.0
|
CB
|
B:PRO127
|
4.3
|
21.6
|
1.0
|
CD2
|
B:HIS114
|
4.3
|
24.2
|
1.0
|
N
|
B:ASP111
|
4.4
|
27.8
|
1.0
|
C
|
B:CYS110
|
4.4
|
26.2
|
1.0
|
SG
|
B:CYS101
|
4.5
|
24.8
|
1.0
|
CA
|
B:HIS114
|
4.5
|
23.9
|
1.0
|
N
|
B:SER113
|
4.5
|
22.1
|
1.0
|
CG
|
B:PRO127
|
4.6
|
22.3
|
1.0
|
CA
|
B:CYS99
|
4.6
|
24.8
|
1.0
|
C
|
B:GLY112
|
4.6
|
24.3
|
1.0
|
N
|
B:PRO127
|
4.6
|
22.5
|
1.0
|
SG
|
B:CYS99
|
4.7
|
22.7
|
1.0
|
CB
|
B:CYS99
|
4.7
|
25.6
|
1.0
|
CA
|
B:PRO127
|
4.8
|
20.9
|
1.0
|
|
Iron binding site 5 out
of 8 in 7p0p
Go back to
Iron Binding Sites List in 7p0p
Iron binding site 5 out
of 8 in the Naf-1 Bound to M1 Molecule
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe200
b:23.4
occ:1.00
|
FE1
|
C:FES200
|
0.0
|
23.4
|
1.0
|
S2
|
C:FES200
|
2.2
|
23.0
|
1.0
|
S1
|
C:FES200
|
2.2
|
25.5
|
1.0
|
SG
|
C:CYS101
|
2.3
|
23.8
|
1.0
|
SG
|
C:CYS99
|
2.4
|
23.5
|
1.0
|
FE2
|
C:FES200
|
2.7
|
23.2
|
1.0
|
CB
|
C:CYS101
|
3.4
|
22.8
|
1.0
|
CB
|
C:CYS99
|
3.4
|
22.4
|
1.0
|
N
|
C:CYS101
|
3.6
|
22.2
|
1.0
|
CA
|
C:CYS99
|
3.7
|
22.2
|
1.0
|
N
|
C:ARG100
|
3.9
|
20.1
|
1.0
|
CA
|
C:CYS101
|
4.0
|
22.4
|
1.0
|
CB
|
C:HIS114
|
4.0
|
23.9
|
1.0
|
C
|
C:CYS99
|
4.2
|
21.0
|
1.0
|
N
|
C:HIS114
|
4.3
|
22.2
|
1.0
|
ND1
|
C:HIS114
|
4.3
|
26.0
|
1.0
|
N
|
C:TRP102
|
4.3
|
24.4
|
1.0
|
N
|
C:SER104
|
4.4
|
26.4
|
1.0
|
C
|
C:CYS101
|
4.5
|
23.1
|
1.0
|
CB
|
C:SER104
|
4.5
|
25.2
|
1.0
|
CA
|
C:HIS114
|
4.6
|
25.2
|
1.0
|
N
|
C:ARG103
|
4.6
|
25.8
|
1.0
|
C
|
C:ARG100
|
4.6
|
22.1
|
1.0
|
SG
|
C:CYS110
|
4.6
|
26.4
|
1.0
|
CG
|
C:HIS114
|
4.7
|
26.0
|
1.0
|
CA
|
C:SER104
|
4.9
|
26.9
|
1.0
|
CA
|
C:CYS110
|
4.9
|
25.7
|
1.0
|
CA
|
C:ARG100
|
4.9
|
22.7
|
1.0
|
CB
|
C:CYS110
|
5.0
|
26.4
|
1.0
|
N
|
C:CYS99
|
5.0
|
21.7
|
1.0
|
|
Iron binding site 6 out
of 8 in 7p0p
Go back to
Iron Binding Sites List in 7p0p
Iron binding site 6 out
of 8 in the Naf-1 Bound to M1 Molecule
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe200
b:23.2
occ:1.00
|
FE2
|
C:FES200
|
0.0
|
23.2
|
1.0
|
ND1
|
C:HIS114
|
2.2
|
26.0
|
1.0
|
S1
|
C:FES200
|
2.2
|
25.5
|
1.0
|
S2
|
C:FES200
|
2.3
|
23.0
|
1.0
|
SG
|
C:CYS110
|
2.3
|
26.4
|
1.0
|
FE1
|
C:FES200
|
2.7
|
23.4
|
1.0
|
CE1
|
C:HIS114
|
3.1
|
26.4
|
1.0
|
CG
|
C:HIS114
|
3.2
|
26.0
|
1.0
|
CB
|
C:CYS110
|
3.4
|
26.4
|
1.0
|
CB
|
C:HIS114
|
3.6
|
23.9
|
1.0
|
CA
|
C:CYS110
|
3.9
|
25.7
|
1.0
|
N
|
C:GLY112
|
4.0
|
25.9
|
1.0
|
N
|
C:HIS114
|
4.0
|
22.2
|
1.0
|
CD
|
C:PRO127
|
4.1
|
23.5
|
1.0
|
NE2
|
C:HIS114
|
4.2
|
24.5
|
1.0
|
CA
|
C:GLY112
|
4.3
|
26.1
|
1.0
|
CD2
|
C:HIS114
|
4.3
|
24.1
|
1.0
|
N
|
C:ASP111
|
4.4
|
26.2
|
1.0
|
CB
|
C:PRO127
|
4.4
|
21.0
|
1.0
|
SG
|
C:CYS101
|
4.4
|
23.8
|
1.0
|
CA
|
C:HIS114
|
4.4
|
25.2
|
1.0
|
CG
|
C:PRO127
|
4.5
|
23.0
|
1.0
|
C
|
C:CYS110
|
4.5
|
26.2
|
1.0
|
N
|
C:SER113
|
4.5
|
24.0
|
1.0
|
C
|
C:GLY112
|
4.6
|
26.1
|
1.0
|
CA
|
C:CYS99
|
4.6
|
22.2
|
1.0
|
N
|
C:PRO127
|
4.6
|
24.7
|
1.0
|
SG
|
C:CYS99
|
4.7
|
23.5
|
1.0
|
CB
|
C:CYS99
|
4.8
|
22.4
|
1.0
|
CA
|
C:PRO127
|
4.9
|
21.7
|
1.0
|
|
Iron binding site 7 out
of 8 in 7p0p
Go back to
Iron Binding Sites List in 7p0p
Iron binding site 7 out
of 8 in the Naf-1 Bound to M1 Molecule
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:22.3
occ:1.00
|
FE1
|
D:FES201
|
0.0
|
22.3
|
1.0
|
S1
|
D:FES201
|
2.2
|
23.1
|
1.0
|
S2
|
D:FES201
|
2.2
|
23.1
|
1.0
|
SG
|
D:CYS101
|
2.4
|
23.4
|
1.0
|
SG
|
D:CYS99
|
2.4
|
22.6
|
1.0
|
FE2
|
D:FES201
|
2.7
|
23.4
|
1.0
|
CB
|
D:CYS99
|
3.4
|
20.6
|
1.0
|
CB
|
D:CYS101
|
3.5
|
24.0
|
1.0
|
N
|
D:CYS101
|
3.6
|
20.7
|
1.0
|
CA
|
D:CYS99
|
3.7
|
21.4
|
1.0
|
N
|
D:ARG100
|
4.0
|
19.6
|
1.0
|
CA
|
D:CYS101
|
4.0
|
22.4
|
1.0
|
CB
|
D:HIS114
|
4.0
|
25.4
|
1.0
|
N
|
D:HIS114
|
4.0
|
25.0
|
1.0
|
C
|
D:CYS99
|
4.3
|
19.7
|
1.0
|
N
|
D:SER104
|
4.4
|
20.3
|
1.0
|
ND1
|
D:HIS114
|
4.4
|
23.3
|
1.0
|
CB
|
D:SER104
|
4.4
|
21.4
|
1.0
|
N
|
D:TRP102
|
4.4
|
21.8
|
1.0
|
CA
|
D:HIS114
|
4.4
|
25.1
|
1.0
|
C
|
D:CYS101
|
4.5
|
24.4
|
1.0
|
N
|
D:ARG103
|
4.6
|
22.6
|
1.0
|
SG
|
D:CYS110
|
4.6
|
24.4
|
1.0
|
C
|
D:ARG100
|
4.7
|
21.5
|
1.0
|
CG
|
D:HIS114
|
4.7
|
23.9
|
1.0
|
CB
|
D:CYS110
|
4.7
|
22.6
|
1.0
|
CA
|
D:SER104
|
4.8
|
21.8
|
1.0
|
CA
|
D:CYS110
|
4.8
|
24.5
|
1.0
|
C
|
D:SER113
|
4.9
|
23.2
|
1.0
|
CA
|
D:ARG100
|
5.0
|
20.8
|
1.0
|
|
Iron binding site 8 out
of 8 in 7p0p
Go back to
Iron Binding Sites List in 7p0p
Iron binding site 8 out
of 8 in the Naf-1 Bound to M1 Molecule
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Naf-1 Bound to M1 Molecule within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:23.4
occ:1.00
|
FE2
|
D:FES201
|
0.0
|
23.4
|
1.0
|
S2
|
D:FES201
|
2.2
|
23.1
|
1.0
|
S1
|
D:FES201
|
2.2
|
23.1
|
1.0
|
SG
|
D:CYS110
|
2.2
|
24.4
|
1.0
|
ND1
|
D:HIS114
|
2.2
|
23.3
|
1.0
|
FE1
|
D:FES201
|
2.7
|
22.3
|
1.0
|
CE1
|
D:HIS114
|
3.2
|
23.2
|
1.0
|
CG
|
D:HIS114
|
3.2
|
23.9
|
1.0
|
CB
|
D:CYS110
|
3.2
|
22.6
|
1.0
|
CB
|
D:HIS114
|
3.5
|
25.4
|
1.0
|
CA
|
D:CYS110
|
3.9
|
24.5
|
1.0
|
N
|
D:HIS114
|
3.9
|
25.0
|
1.0
|
N
|
D:GLY112
|
4.0
|
23.4
|
1.0
|
CB
|
D:PRO127
|
4.2
|
22.7
|
1.0
|
NE2
|
D:HIS114
|
4.3
|
22.3
|
1.0
|
CD
|
D:PRO127
|
4.3
|
22.2
|
1.0
|
CA
|
D:GLY112
|
4.3
|
22.0
|
1.0
|
CD2
|
D:HIS114
|
4.3
|
24.9
|
1.0
|
N
|
D:ASP111
|
4.3
|
22.9
|
1.0
|
CA
|
D:HIS114
|
4.3
|
25.1
|
1.0
|
N
|
D:SER113
|
4.4
|
22.3
|
1.0
|
C
|
D:CYS110
|
4.4
|
23.9
|
1.0
|
C
|
D:GLY112
|
4.5
|
21.6
|
1.0
|
SG
|
D:CYS101
|
4.5
|
23.4
|
1.0
|
CG
|
D:PRO127
|
4.5
|
22.2
|
1.0
|
N
|
D:PRO127
|
4.6
|
22.7
|
1.0
|
CA
|
D:CYS99
|
4.6
|
21.4
|
1.0
|
SG
|
D:CYS99
|
4.7
|
22.6
|
1.0
|
CA
|
D:PRO127
|
4.8
|
23.5
|
1.0
|
CB
|
D:CYS99
|
4.9
|
20.6
|
1.0
|
C
|
D:SER113
|
5.0
|
23.2
|
1.0
|
|
Reference:
H.B.Marjault,
O.Karmi,
K.Zuo,
D.Michaeli,
Y.Eisenberg-Domovich,
G.Rossetti,
B.De Chassey,
J.Vonderscher,
I.Cabantchik,
P.Carloni,
R.Mittler,
O.Livnah,
E.Meldrum,
R.Nechushtai.
An Anti-Diabetic Drug Targets Neet (Cisd) Proteins Through Destabilization of Their [2FE-2S] Clusters. Commun Biol V. 5 437 2022.
ISSN: ESSN 2399-3642
PubMed: 35538231
DOI: 10.1038/S42003-022-03393-X
Page generated: Thu Aug 8 14:51:49 2024
|