Iron in PDB 1nf4: X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure)
Protein crystallography data
The structure of X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure), PDB code: 1nf4
was solved by
S.Macedo,
C.V.Romao,
E.Mitchell,
P.M.Matias,
M.Y.Liu,
A.V.Xavier,
J.Legall,
M.Teixeira,
P.Lindley,
M.A.Carrondo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.05
|
Space group
|
P 21 3 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
225.680,
225.680,
225.680,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.1 /
27
|
Iron Binding Sites:
Iron binding site 1 out
of 48 in 1nf4
Go back to
Iron Binding Sites List in 1nf4
Iron binding site 1 out
of 48 in the X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe200
b:31.9
occ:1.00
|
OE2
|
A:GLU132
|
2.1
|
27.5
|
1.0
|
OE1
|
A:GLU56
|
2.1
|
25.8
|
1.0
|
OE2
|
A:GLU23
|
2.2
|
22.4
|
1.0
|
ND1
|
A:HIS59
|
2.2
|
17.2
|
1.0
|
OE1
|
A:GLU23
|
2.3
|
22.8
|
1.0
|
O
|
A:HOH1094
|
2.4
|
28.6
|
1.0
|
CD
|
A:GLU23
|
2.6
|
21.5
|
1.0
|
CD
|
A:GLU132
|
3.0
|
25.4
|
1.0
|
CE1
|
A:HIS59
|
3.1
|
17.9
|
1.0
|
CD
|
A:GLU56
|
3.1
|
25.4
|
1.0
|
OE1
|
A:GLU132
|
3.2
|
26.3
|
1.0
|
CG
|
A:HIS59
|
3.3
|
16.8
|
1.0
|
CB
|
A:HIS59
|
3.7
|
16.7
|
1.0
|
OE2
|
A:GLU56
|
3.7
|
29.4
|
1.0
|
FE
|
A:FE2201
|
4.0
|
34.8
|
1.0
|
CG
|
A:GLU23
|
4.1
|
18.8
|
1.0
|
CA
|
A:GLU56
|
4.1
|
18.8
|
1.0
|
CG
|
A:GLU56
|
4.2
|
20.5
|
1.0
|
NE2
|
A:HIS59
|
4.3
|
18.2
|
1.0
|
CB
|
A:GLU56
|
4.3
|
19.9
|
1.0
|
OH
|
A:TYR106
|
4.3
|
21.1
|
1.0
|
CG
|
A:GLU132
|
4.4
|
22.3
|
1.0
|
CD2
|
A:HIS59
|
4.4
|
17.2
|
1.0
|
CG2
|
A:ILE128
|
4.5
|
18.8
|
1.0
|
CE2
|
A:TYR106
|
4.6
|
21.7
|
1.0
|
CB
|
A:GLU23
|
4.9
|
18.1
|
1.0
|
O
|
A:GLU56
|
4.9
|
18.7
|
1.0
|
N
|
A:GLU56
|
4.9
|
19.0
|
1.0
|
CZ
|
A:TYR106
|
5.0
|
22.1
|
1.0
|
|
Iron binding site 2 out
of 48 in 1nf4
Go back to
Iron Binding Sites List in 1nf4
Iron binding site 2 out
of 48 in the X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:34.8
occ:1.00
|
OE1
|
A:GLU132
|
2.0
|
26.3
|
1.0
|
OE2
|
A:GLU56
|
2.1
|
29.4
|
1.0
|
OE2
|
A:GLU99
|
2.2
|
25.9
|
1.0
|
ND1
|
A:HIS135
|
2.3
|
18.8
|
1.0
|
OE1
|
A:GLU99
|
2.5
|
27.2
|
1.0
|
CD
|
A:GLU99
|
2.7
|
24.3
|
1.0
|
CD
|
A:GLU56
|
3.0
|
25.4
|
1.0
|
OE1
|
A:GLU56
|
3.2
|
25.8
|
1.0
|
CE1
|
A:HIS135
|
3.2
|
19.4
|
1.0
|
CD
|
A:GLU132
|
3.2
|
25.4
|
1.0
|
CG
|
A:HIS135
|
3.3
|
18.7
|
1.0
|
CB
|
A:HIS135
|
3.6
|
18.4
|
1.0
|
O
|
A:HOH1094
|
3.8
|
28.6
|
1.0
|
OE2
|
A:GLU132
|
3.8
|
27.5
|
1.0
|
FE
|
A:FE2200
|
4.0
|
31.9
|
1.0
|
CG
|
A:GLU99
|
4.2
|
22.5
|
1.0
|
CA
|
A:GLU132
|
4.2
|
20.8
|
1.0
|
NE2
|
A:HIS135
|
4.3
|
19.9
|
1.0
|
CG
|
A:GLU132
|
4.3
|
22.3
|
1.0
|
CB
|
A:GLU132
|
4.4
|
20.9
|
1.0
|
CD2
|
A:HIS135
|
4.4
|
18.9
|
1.0
|
CG
|
A:GLU56
|
4.4
|
20.5
|
1.0
|
OH
|
A:TYR30
|
4.5
|
25.0
|
1.0
|
CE1
|
A:TYR30
|
4.5
|
21.5
|
1.0
|
CG2
|
A:ILE52
|
4.6
|
16.1
|
1.0
|
O
|
A:GLU132
|
4.9
|
21.2
|
1.0
|
CZ
|
A:TYR30
|
5.0
|
22.7
|
1.0
|
|
Iron binding site 3 out
of 48 in 1nf4
Go back to
Iron Binding Sites List in 1nf4
Iron binding site 3 out
of 48 in the X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1007
b:19.2
occ:0.50
|
FE
|
A:FEC1007
|
0.0
|
19.2
|
0.5
|
FE
|
A:FEC1007
|
0.0
|
14.3
|
0.5
|
ND
|
A:FEC1007
|
1.6
|
9.4
|
0.5
|
NA
|
A:FEC1007
|
1.8
|
15.4
|
0.5
|
NB
|
A:FEC1007
|
1.9
|
20.0
|
0.5
|
NB
|
A:FEC1007
|
2.0
|
12.5
|
0.5
|
ND
|
A:FEC1007
|
2.0
|
19.7
|
0.5
|
NC
|
A:FEC1007
|
2.1
|
21.1
|
0.5
|
NC
|
A:FEC1007
|
2.2
|
25.2
|
0.5
|
NA
|
A:FEC1007
|
2.3
|
20.1
|
0.5
|
SD
|
A:MET57
|
2.4
|
19.2
|
1.0
|
SD
|
B:MET57
|
2.4
|
16.6
|
1.0
|
C4D
|
A:FEC1007
|
3.0
|
19.4
|
0.5
|
C4C
|
A:FEC1007
|
3.0
|
20.4
|
0.5
|
C4C
|
A:FEC1007
|
3.0
|
19.8
|
0.5
|
C1A
|
A:FEC1007
|
3.0
|
18.4
|
0.5
|
C1D
|
A:FEC1007
|
3.0
|
19.1
|
0.5
|
C4B
|
A:FEC1007
|
3.0
|
19.8
|
0.5
|
C1C
|
A:FEC1007
|
3.0
|
21.2
|
0.5
|
C4A
|
A:FEC1007
|
3.0
|
20.0
|
0.5
|
C1D
|
A:FEC1007
|
3.0
|
19.6
|
0.5
|
C1B
|
A:FEC1007
|
3.0
|
19.6
|
0.5
|
C4B
|
A:FEC1007
|
3.0
|
20.1
|
0.5
|
C1A
|
A:FEC1007
|
3.0
|
19.4
|
0.5
|
C1B
|
A:FEC1007
|
3.1
|
19.6
|
0.5
|
C4A
|
A:FEC1007
|
3.1
|
19.6
|
0.5
|
C4D
|
A:FEC1007
|
3.1
|
19.7
|
0.5
|
C1C
|
A:FEC1007
|
3.1
|
21.2
|
0.5
|
CE
|
B:MET57
|
3.4
|
15.9
|
1.0
|
CHC
|
A:FEC1007
|
3.4
|
20.4
|
0.5
|
CHC
|
A:FEC1007
|
3.4
|
20.5
|
0.5
|
CHA
|
A:FEC1007
|
3.4
|
19.5
|
0.5
|
CHB
|
A:FEC1007
|
3.4
|
19.3
|
0.5
|
CHD
|
A:FEC1007
|
3.4
|
19.9
|
0.5
|
CHB
|
A:FEC1007
|
3.4
|
19.6
|
0.5
|
CHD
|
A:FEC1007
|
3.4
|
19.4
|
0.5
|
CE
|
A:MET57
|
3.4
|
14.8
|
1.0
|
CHA
|
A:FEC1007
|
3.4
|
19.2
|
0.5
|
CG
|
B:MET57
|
3.5
|
16.9
|
1.0
|
CG
|
A:MET57
|
3.5
|
16.6
|
1.0
|
CB
|
A:MET57
|
4.2
|
16.5
|
1.0
|
CB
|
B:MET57
|
4.2
|
16.7
|
1.0
|
C3D
|
A:FEC1007
|
4.2
|
20.4
|
0.5
|
C2C
|
A:FEC1007
|
4.2
|
22.7
|
0.5
|
C3C
|
A:FEC1007
|
4.2
|
20.8
|
0.5
|
C2D
|
A:FEC1007
|
4.2
|
19.2
|
0.5
|
C3C
|
A:FEC1007
|
4.3
|
19.8
|
0.5
|
C3B
|
A:FEC1007
|
4.3
|
19.8
|
0.5
|
C2B
|
A:FEC1007
|
4.3
|
19.2
|
0.5
|
C2A
|
A:FEC1007
|
4.3
|
18.5
|
0.5
|
C3A
|
A:FEC1007
|
4.3
|
20.1
|
0.5
|
C3A
|
A:FEC1007
|
4.3
|
19.0
|
0.5
|
C2A
|
A:FEC1007
|
4.3
|
19.6
|
0.5
|
C2B
|
A:FEC1007
|
4.3
|
18.9
|
0.5
|
C2C
|
A:FEC1007
|
4.3
|
22.4
|
0.5
|
C2D
|
A:FEC1007
|
4.3
|
19.6
|
0.5
|
C3B
|
A:FEC1007
|
4.3
|
19.7
|
0.5
|
C3D
|
A:FEC1007
|
4.3
|
19.9
|
0.5
|
|
Iron binding site 4 out
of 48 in 1nf4
Go back to
Iron Binding Sites List in 1nf4
Iron binding site 4 out
of 48 in the X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1007
b:14.3
occ:0.50
|
FE
|
A:FEC1007
|
0.0
|
14.3
|
0.5
|
FE
|
A:FEC1007
|
0.0
|
19.2
|
0.5
|
ND
|
A:FEC1007
|
1.6
|
9.4
|
0.5
|
NA
|
A:FEC1007
|
1.8
|
15.4
|
0.5
|
NB
|
A:FEC1007
|
1.9
|
20.0
|
0.5
|
NB
|
A:FEC1007
|
1.9
|
12.5
|
0.5
|
ND
|
A:FEC1007
|
2.0
|
19.7
|
0.5
|
NC
|
A:FEC1007
|
2.1
|
21.1
|
0.5
|
NC
|
A:FEC1007
|
2.2
|
25.2
|
0.5
|
NA
|
A:FEC1007
|
2.3
|
20.1
|
0.5
|
SD
|
A:MET57
|
2.4
|
19.2
|
1.0
|
SD
|
B:MET57
|
2.4
|
16.6
|
1.0
|
C4C
|
A:FEC1007
|
3.0
|
20.4
|
0.5
|
C4B
|
A:FEC1007
|
3.0
|
20.1
|
0.5
|
C4C
|
A:FEC1007
|
3.0
|
19.8
|
0.5
|
C1C
|
A:FEC1007
|
3.0
|
21.2
|
0.5
|
C1D
|
A:FEC1007
|
3.0
|
19.6
|
0.5
|
C4D
|
A:FEC1007
|
3.0
|
19.4
|
0.5
|
C1B
|
A:FEC1007
|
3.0
|
19.6
|
0.5
|
C1A
|
A:FEC1007
|
3.0
|
18.4
|
0.5
|
C4B
|
A:FEC1007
|
3.0
|
19.8
|
0.5
|
C4A
|
A:FEC1007
|
3.0
|
19.6
|
0.5
|
C1D
|
A:FEC1007
|
3.1
|
19.1
|
0.5
|
C1C
|
A:FEC1007
|
3.1
|
21.2
|
0.5
|
C4D
|
A:FEC1007
|
3.1
|
19.7
|
0.5
|
C1B
|
A:FEC1007
|
3.1
|
19.6
|
0.5
|
C1A
|
A:FEC1007
|
3.1
|
19.4
|
0.5
|
C4A
|
A:FEC1007
|
3.1
|
20.0
|
0.5
|
CHC
|
A:FEC1007
|
3.4
|
20.4
|
0.5
|
CHC
|
A:FEC1007
|
3.4
|
20.5
|
0.5
|
CHB
|
A:FEC1007
|
3.4
|
19.3
|
0.5
|
CHD
|
A:FEC1007
|
3.4
|
19.9
|
0.5
|
CE
|
B:MET57
|
3.4
|
15.9
|
1.0
|
CHA
|
A:FEC1007
|
3.4
|
19.5
|
0.5
|
CE
|
A:MET57
|
3.4
|
14.8
|
1.0
|
CHD
|
A:FEC1007
|
3.4
|
19.4
|
0.5
|
CHB
|
A:FEC1007
|
3.4
|
19.6
|
0.5
|
CHA
|
A:FEC1007
|
3.5
|
19.2
|
0.5
|
CG
|
B:MET57
|
3.5
|
16.9
|
1.0
|
CG
|
A:MET57
|
3.5
|
16.6
|
1.0
|
CB
|
A:MET57
|
4.2
|
16.5
|
1.0
|
CB
|
B:MET57
|
4.2
|
16.7
|
1.0
|
C2C
|
A:FEC1007
|
4.2
|
22.7
|
0.5
|
C3C
|
A:FEC1007
|
4.2
|
20.8
|
0.5
|
C3C
|
A:FEC1007
|
4.3
|
19.8
|
0.5
|
C2B
|
A:FEC1007
|
4.3
|
18.9
|
0.5
|
C3D
|
A:FEC1007
|
4.3
|
20.4
|
0.5
|
C3B
|
A:FEC1007
|
4.3
|
19.7
|
0.5
|
C2D
|
A:FEC1007
|
4.3
|
19.6
|
0.5
|
C3B
|
A:FEC1007
|
4.3
|
19.8
|
0.5
|
C2D
|
A:FEC1007
|
4.3
|
19.2
|
0.5
|
C2C
|
A:FEC1007
|
4.3
|
22.4
|
0.5
|
C2A
|
A:FEC1007
|
4.3
|
18.5
|
0.5
|
C3A
|
A:FEC1007
|
4.3
|
19.0
|
0.5
|
C2B
|
A:FEC1007
|
4.3
|
19.2
|
0.5
|
C3D
|
A:FEC1007
|
4.3
|
19.9
|
0.5
|
C3A
|
A:FEC1007
|
4.3
|
20.1
|
0.5
|
C2A
|
A:FEC1007
|
4.3
|
19.6
|
0.5
|
|
Iron binding site 5 out
of 48 in 1nf4
Go back to
Iron Binding Sites List in 1nf4
Iron binding site 5 out
of 48 in the X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe200
b:29.9
occ:1.00
|
OE2
|
B:GLU132
|
2.1
|
26.7
|
1.0
|
OE1
|
B:GLU56
|
2.1
|
25.3
|
1.0
|
ND1
|
B:HIS59
|
2.2
|
16.4
|
1.0
|
OE2
|
B:GLU23
|
2.2
|
21.8
|
1.0
|
OE1
|
B:GLU23
|
2.2
|
22.2
|
1.0
|
O
|
B:HOH1190
|
2.5
|
31.7
|
1.0
|
CD
|
B:GLU23
|
2.5
|
21.2
|
1.0
|
CD
|
B:GLU132
|
3.0
|
25.4
|
1.0
|
CE1
|
B:HIS59
|
3.1
|
17.5
|
1.0
|
CD
|
B:GLU56
|
3.1
|
24.3
|
1.0
|
CG
|
B:HIS59
|
3.3
|
15.7
|
1.0
|
OE1
|
B:GLU132
|
3.3
|
25.9
|
1.0
|
CB
|
B:HIS59
|
3.6
|
16.4
|
1.0
|
OE2
|
B:GLU56
|
3.7
|
29.0
|
1.0
|
CA
|
B:GLU56
|
4.0
|
18.0
|
1.0
|
CG
|
B:GLU23
|
4.1
|
18.5
|
1.0
|
FE
|
B:FE2201
|
4.1
|
31.9
|
1.0
|
CB
|
B:GLU56
|
4.2
|
19.1
|
1.0
|
CG
|
B:GLU56
|
4.2
|
19.5
|
1.0
|
O
|
B:HOH1208
|
4.3
|
35.5
|
1.0
|
NE2
|
B:HIS59
|
4.3
|
17.8
|
1.0
|
CD2
|
B:HIS59
|
4.4
|
16.4
|
1.0
|
CG
|
B:GLU132
|
4.4
|
22.4
|
1.0
|
OH
|
B:TYR106
|
4.4
|
21.0
|
1.0
|
CG2
|
B:ILE128
|
4.5
|
18.6
|
1.0
|
CE2
|
B:TYR106
|
4.7
|
21.3
|
1.0
|
N
|
B:GLU56
|
4.8
|
18.3
|
1.0
|
O
|
B:GLU56
|
4.9
|
17.8
|
1.0
|
CB
|
B:GLU23
|
4.9
|
17.6
|
1.0
|
|
Iron binding site 6 out
of 48 in 1nf4
Go back to
Iron Binding Sites List in 1nf4
Iron binding site 6 out
of 48 in the X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:31.9
occ:1.00
|
OE1
|
B:GLU132
|
2.0
|
25.9
|
1.0
|
OE2
|
B:GLU56
|
2.1
|
29.0
|
1.0
|
OE2
|
B:GLU99
|
2.2
|
24.7
|
1.0
|
ND1
|
B:HIS135
|
2.3
|
18.0
|
1.0
|
OE1
|
B:GLU99
|
2.5
|
25.5
|
1.0
|
CD
|
B:GLU99
|
2.6
|
23.4
|
1.0
|
O
|
B:HOH1208
|
2.9
|
35.5
|
1.0
|
CD
|
B:GLU56
|
3.1
|
24.3
|
1.0
|
CD
|
B:GLU132
|
3.2
|
25.4
|
1.0
|
CE1
|
B:HIS135
|
3.2
|
18.8
|
1.0
|
CG
|
B:HIS135
|
3.3
|
18.5
|
1.0
|
OE1
|
B:GLU56
|
3.3
|
25.3
|
1.0
|
CB
|
B:HIS135
|
3.5
|
18.0
|
1.0
|
OE2
|
B:GLU132
|
3.8
|
26.7
|
1.0
|
O
|
B:HOH1190
|
4.0
|
31.7
|
1.0
|
FE
|
B:FE2200
|
4.1
|
29.9
|
1.0
|
CG
|
B:GLU99
|
4.1
|
21.6
|
1.0
|
CA
|
B:GLU132
|
4.2
|
20.6
|
1.0
|
CG
|
B:GLU132
|
4.3
|
22.4
|
1.0
|
CB
|
B:GLU132
|
4.3
|
19.7
|
1.0
|
NE2
|
B:HIS135
|
4.4
|
18.4
|
1.0
|
CD2
|
B:HIS135
|
4.4
|
18.0
|
1.0
|
CG
|
B:GLU56
|
4.4
|
19.5
|
1.0
|
CE1
|
B:TYR30
|
4.5
|
21.0
|
1.0
|
OH
|
B:TYR30
|
4.6
|
23.9
|
1.0
|
CG2
|
B:ILE52
|
4.7
|
16.4
|
1.0
|
O
|
B:GLU132
|
4.8
|
20.2
|
1.0
|
|
Iron binding site 7 out
of 48 in 1nf4
Go back to
Iron Binding Sites List in 1nf4
Iron binding site 7 out
of 48 in the X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe200
b:31.9
occ:1.00
|
OE2
|
C:GLU132
|
2.0
|
26.8
|
1.0
|
OE1
|
C:GLU56
|
2.1
|
26.3
|
1.0
|
ND1
|
C:HIS59
|
2.2
|
17.5
|
1.0
|
OE2
|
C:GLU23
|
2.2
|
23.1
|
1.0
|
OE1
|
C:GLU23
|
2.3
|
22.4
|
1.0
|
O
|
C:HOH1250
|
2.4
|
35.5
|
1.0
|
CD
|
C:GLU23
|
2.6
|
22.2
|
1.0
|
CD
|
C:GLU132
|
3.0
|
25.5
|
1.0
|
CE1
|
C:HIS59
|
3.1
|
18.6
|
1.0
|
CD
|
C:GLU56
|
3.1
|
25.8
|
1.0
|
OE1
|
C:GLU132
|
3.2
|
25.8
|
1.0
|
CG
|
C:HIS59
|
3.3
|
16.6
|
1.0
|
OE2
|
C:GLU56
|
3.7
|
29.6
|
1.0
|
CB
|
C:HIS59
|
3.7
|
16.9
|
1.0
|
FE
|
C:FE2201
|
4.0
|
36.3
|
1.0
|
CG
|
C:GLU23
|
4.1
|
18.9
|
1.0
|
O
|
C:HOH9509
|
4.2
|
30.9
|
1.0
|
CA
|
C:GLU56
|
4.2
|
18.9
|
1.0
|
NE2
|
C:HIS59
|
4.2
|
19.1
|
1.0
|
CG
|
C:GLU56
|
4.3
|
20.4
|
1.0
|
CB
|
C:GLU56
|
4.3
|
19.3
|
1.0
|
CD2
|
C:HIS59
|
4.4
|
17.8
|
1.0
|
CG
|
C:GLU132
|
4.4
|
22.2
|
1.0
|
OH
|
C:TYR106
|
4.4
|
21.2
|
1.0
|
CG2
|
C:ILE128
|
4.6
|
18.2
|
1.0
|
CE2
|
C:TYR106
|
4.6
|
20.7
|
1.0
|
CB
|
C:GLU23
|
4.9
|
18.0
|
1.0
|
N
|
C:GLU56
|
5.0
|
19.0
|
1.0
|
O
|
C:GLU56
|
5.0
|
19.7
|
1.0
|
|
Iron binding site 8 out
of 48 in 1nf4
Go back to
Iron Binding Sites List in 1nf4
Iron binding site 8 out
of 48 in the X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:36.3
occ:1.00
|
OE1
|
C:GLU132
|
2.0
|
25.8
|
1.0
|
OE2
|
C:GLU56
|
2.1
|
29.6
|
1.0
|
OE2
|
C:GLU99
|
2.2
|
25.3
|
1.0
|
ND1
|
C:HIS135
|
2.3
|
18.5
|
1.0
|
OE1
|
C:GLU99
|
2.5
|
27.5
|
1.0
|
CD
|
C:GLU99
|
2.6
|
24.3
|
1.0
|
CD
|
C:GLU56
|
3.1
|
25.8
|
1.0
|
CD
|
C:GLU132
|
3.2
|
25.5
|
1.0
|
CE1
|
C:HIS135
|
3.2
|
19.5
|
1.0
|
CG
|
C:HIS135
|
3.3
|
18.6
|
1.0
|
OE1
|
C:GLU56
|
3.3
|
26.3
|
1.0
|
O
|
C:HOH1250
|
3.5
|
35.5
|
1.0
|
CB
|
C:HIS135
|
3.5
|
18.8
|
1.0
|
OE2
|
C:GLU132
|
3.8
|
26.8
|
1.0
|
FE
|
C:FE2200
|
4.0
|
31.9
|
1.0
|
CG
|
C:GLU99
|
4.1
|
22.0
|
1.0
|
CA
|
C:GLU132
|
4.2
|
20.3
|
1.0
|
CB
|
C:GLU132
|
4.3
|
20.6
|
1.0
|
CG
|
C:GLU132
|
4.3
|
22.2
|
1.0
|
NE2
|
C:HIS135
|
4.4
|
20.1
|
1.0
|
CD2
|
C:HIS135
|
4.4
|
18.9
|
1.0
|
CG
|
C:GLU56
|
4.4
|
20.4
|
1.0
|
CE1
|
C:TYR30
|
4.6
|
21.8
|
1.0
|
OH
|
C:TYR30
|
4.6
|
25.2
|
1.0
|
CG2
|
C:ILE52
|
4.7
|
16.4
|
1.0
|
O
|
C:GLU132
|
4.9
|
22.9
|
1.0
|
CE1
|
C:HIS59
|
5.0
|
18.6
|
1.0
|
|
Iron binding site 9 out
of 48 in 1nf4
Go back to
Iron Binding Sites List in 1nf4
Iron binding site 9 out
of 48 in the X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1207
b:19.5
occ:0.51
|
FE
|
C:FEC1207
|
0.0
|
19.5
|
0.5
|
FE
|
C:FEC1207
|
0.2
|
20.0
|
0.5
|
NC
|
C:FEC1207
|
0.8
|
35.8
|
0.5
|
NB
|
C:FEC1207
|
1.6
|
24.2
|
0.5
|
NB
|
C:FEC1207
|
1.9
|
20.2
|
0.5
|
ND
|
C:FEC1207
|
2.0
|
20.3
|
0.5
|
NC
|
C:FEC1207
|
2.1
|
21.5
|
0.5
|
NA
|
C:FEC1207
|
2.2
|
12.4
|
0.5
|
NA
|
C:FEC1207
|
2.3
|
20.9
|
0.5
|
SD
|
D:MET57
|
2.4
|
19.9
|
1.0
|
SD
|
C:MET57
|
2.4
|
20.5
|
1.0
|
ND
|
C:FEC1207
|
2.6
|
22.3
|
0.5
|
C1B
|
C:FEC1207
|
2.8
|
20.3
|
0.5
|
C4A
|
C:FEC1207
|
2.9
|
20.4
|
0.5
|
C4B
|
C:FEC1207
|
2.9
|
20.9
|
0.5
|
C1A
|
C:FEC1207
|
3.0
|
19.5
|
0.5
|
C1D
|
C:FEC1207
|
3.0
|
20.0
|
0.5
|
C4D
|
C:FEC1207
|
3.0
|
20.1
|
0.5
|
C4B
|
C:FEC1207
|
3.0
|
20.1
|
0.5
|
C1C
|
C:FEC1207
|
3.0
|
21.7
|
0.5
|
C4A
|
C:FEC1207
|
3.0
|
20.4
|
0.5
|
C4C
|
C:FEC1207
|
3.0
|
20.6
|
0.5
|
C1A
|
C:FEC1207
|
3.0
|
19.4
|
0.5
|
C1B
|
C:FEC1207
|
3.0
|
19.6
|
0.5
|
C1C
|
C:FEC1207
|
3.1
|
22.5
|
0.5
|
C4D
|
C:FEC1207
|
3.2
|
20.9
|
0.5
|
CHB
|
C:FEC1207
|
3.2
|
20.1
|
0.5
|
C4C
|
C:FEC1207
|
3.2
|
20.3
|
0.5
|
C1D
|
C:FEC1207
|
3.2
|
19.7
|
0.5
|
CHC
|
C:FEC1207
|
3.4
|
20.9
|
0.5
|
CHC
|
C:FEC1207
|
3.4
|
21.3
|
0.5
|
CHD
|
C:FEC1207
|
3.4
|
20.1
|
0.5
|
CHA
|
C:FEC1207
|
3.4
|
19.6
|
0.5
|
CHB
|
C:FEC1207
|
3.4
|
19.8
|
0.5
|
CG
|
D:MET57
|
3.4
|
17.5
|
1.0
|
CE
|
C:MET57
|
3.4
|
14.6
|
1.0
|
CE
|
D:MET57
|
3.4
|
14.5
|
1.0
|
CHA
|
C:FEC1207
|
3.5
|
20.6
|
0.5
|
CG
|
C:MET57
|
3.6
|
17.5
|
1.0
|
CHD
|
C:FEC1207
|
3.6
|
19.7
|
0.5
|
C2B
|
C:FEC1207
|
4.1
|
20.4
|
0.5
|
C3A
|
C:FEC1207
|
4.1
|
21.1
|
0.5
|
C3B
|
C:FEC1207
|
4.1
|
20.7
|
0.5
|
C2A
|
C:FEC1207
|
4.1
|
20.2
|
0.5
|
CB
|
D:MET57
|
4.2
|
16.0
|
1.0
|
C2D
|
C:FEC1207
|
4.3
|
19.8
|
0.5
|
C3A
|
C:FEC1207
|
4.3
|
20.3
|
0.5
|
CB
|
C:MET57
|
4.3
|
16.6
|
1.0
|
C3D
|
C:FEC1207
|
4.3
|
20.0
|
0.5
|
C2C
|
C:FEC1207
|
4.3
|
22.7
|
0.5
|
C2A
|
C:FEC1207
|
4.3
|
19.4
|
0.5
|
C3C
|
C:FEC1207
|
4.3
|
20.9
|
0.5
|
C3B
|
C:FEC1207
|
4.3
|
20.1
|
0.5
|
C2B
|
C:FEC1207
|
4.3
|
19.4
|
0.5
|
C2C
|
C:FEC1207
|
4.4
|
23.3
|
0.5
|
C3D
|
C:FEC1207
|
4.4
|
20.8
|
0.5
|
C3C
|
C:FEC1207
|
4.4
|
21.3
|
0.5
|
C2D
|
C:FEC1207
|
4.5
|
20.0
|
0.5
|
|
Iron binding site 10 out
of 48 in 1nf4
Go back to
Iron Binding Sites List in 1nf4
Iron binding site 10 out
of 48 in the X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure)
Mono view
Stereo pair view
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A full contact list of Iron with other atoms in the Fe binding
site number 10 of X-Ray Structure of the Desulfovibrio Desulfuricans Bacterioferritin: the Diiron Site in Different States (Reduced Structure) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1207
b:20.0
occ:0.49
|
FE
|
C:FEC1207
|
0.0
|
20.0
|
0.5
|
FE
|
C:FEC1207
|
0.2
|
19.5
|
0.5
|
NC
|
C:FEC1207
|
0.7
|
35.8
|
0.5
|
NB
|
C:FEC1207
|
1.7
|
20.2
|
0.5
|
NB
|
C:FEC1207
|
1.8
|
24.2
|
0.5
|
NC
|
C:FEC1207
|
2.2
|
21.5
|
0.5
|
ND
|
C:FEC1207
|
2.2
|
20.3
|
0.5
|
NA
|
C:FEC1207
|
2.2
|
20.9
|
0.5
|
SD
|
D:MET57
|
2.4
|
19.9
|
1.0
|
SD
|
C:MET57
|
2.4
|
20.5
|
1.0
|
NA
|
C:FEC1207
|
2.4
|
12.4
|
0.5
|
ND
|
C:FEC1207
|
2.4
|
22.3
|
0.5
|
C1B
|
C:FEC1207
|
2.8
|
19.6
|
0.5
|
C4B
|
C:FEC1207
|
2.8
|
20.1
|
0.5
|
C4A
|
C:FEC1207
|
2.9
|
20.4
|
0.5
|
C1C
|
C:FEC1207
|
3.0
|
21.7
|
0.5
|
C1B
|
C:FEC1207
|
3.0
|
20.3
|
0.5
|
C4C
|
C:FEC1207
|
3.0
|
20.3
|
0.5
|
C4B
|
C:FEC1207
|
3.0
|
20.9
|
0.5
|
C1A
|
C:FEC1207
|
3.0
|
19.5
|
0.5
|
C4A
|
C:FEC1207
|
3.0
|
20.4
|
0.5
|
C1D
|
C:FEC1207
|
3.0
|
19.7
|
0.5
|
C4D
|
C:FEC1207
|
3.0
|
20.9
|
0.5
|
C1C
|
C:FEC1207
|
3.0
|
22.5
|
0.5
|
C1A
|
C:FEC1207
|
3.1
|
19.4
|
0.5
|
C4C
|
C:FEC1207
|
3.2
|
20.6
|
0.5
|
C4D
|
C:FEC1207
|
3.2
|
20.1
|
0.5
|
C1D
|
C:FEC1207
|
3.2
|
20.0
|
0.5
|
CHC
|
C:FEC1207
|
3.2
|
20.9
|
0.5
|
CHB
|
C:FEC1207
|
3.3
|
19.8
|
0.5
|
CE
|
D:MET57
|
3.4
|
14.5
|
1.0
|
CHB
|
C:FEC1207
|
3.4
|
20.1
|
0.5
|
CHC
|
C:FEC1207
|
3.4
|
21.3
|
0.5
|
CHD
|
C:FEC1207
|
3.4
|
19.7
|
0.5
|
CHA
|
C:FEC1207
|
3.4
|
20.6
|
0.5
|
CG
|
D:MET57
|
3.5
|
17.5
|
1.0
|
CG
|
C:MET57
|
3.5
|
17.5
|
1.0
|
CE
|
C:MET57
|
3.5
|
14.6
|
1.0
|
CHA
|
C:FEC1207
|
3.5
|
19.6
|
0.5
|
CHD
|
C:FEC1207
|
3.6
|
20.1
|
0.5
|
C2B
|
C:FEC1207
|
4.1
|
19.4
|
0.5
|
C3B
|
C:FEC1207
|
4.1
|
20.1
|
0.5
|
CB
|
C:MET57
|
4.1
|
16.6
|
1.0
|
C3A
|
C:FEC1207
|
4.2
|
20.3
|
0.5
|
C2B
|
C:FEC1207
|
4.3
|
20.4
|
0.5
|
C3A
|
C:FEC1207
|
4.3
|
21.1
|
0.5
|
C2A
|
C:FEC1207
|
4.3
|
20.2
|
0.5
|
C3C
|
C:FEC1207
|
4.3
|
21.3
|
0.5
|
C2C
|
C:FEC1207
|
4.3
|
23.3
|
0.5
|
C2C
|
C:FEC1207
|
4.3
|
22.7
|
0.5
|
C3B
|
C:FEC1207
|
4.3
|
20.7
|
0.5
|
C2A
|
C:FEC1207
|
4.3
|
19.4
|
0.5
|
C3D
|
C:FEC1207
|
4.3
|
20.8
|
0.5
|
C2D
|
C:FEC1207
|
4.3
|
20.0
|
0.5
|
CB
|
D:MET57
|
4.3
|
16.0
|
1.0
|
C3C
|
C:FEC1207
|
4.3
|
20.9
|
0.5
|
C3D
|
C:FEC1207
|
4.5
|
20.0
|
0.5
|
C2D
|
C:FEC1207
|
4.5
|
19.8
|
0.5
|
|
Reference:
S.Macedo,
C.V.Romao,
E.Mitchell,
P.M.Matias,
M.Y.Liu,
A.V.Xavier,
J.Legall,
M.Teixeira,
P.Lindley,
M.A.Carrondo.
The Nature of the Di-Iron Site in the Bacterioferritin From Desulfovibrio Desulfuricans Nat.Struct.Biol. V. 10 285 2003.
ISSN: ISSN 1072-8368
PubMed: 12627224
DOI: 10.1038/NSB909
Page generated: Sat Aug 3 11:34:55 2024
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