Iron in PDB 1oj6: Human Brain Neuroglobin Three-Dimensional Structure
Protein crystallography data
The structure of Human Brain Neuroglobin Three-Dimensional Structure, PDB code: 1oj6
was solved by
A.Pesce,
S.Dewilde,
M.Nardini,
L.Moens,
P.Ascenzi,
T.Hankeln,
T.Burmester,
M.Bolognesi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.00 /
1.95
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.598,
94.927,
67.563,
90.00,
94.38,
90.00
|
R / Rfree (%)
|
17.8 /
23.3
|
Iron Binding Sites:
The binding sites of Iron atom in the Human Brain Neuroglobin Three-Dimensional Structure
(pdb code 1oj6). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Human Brain Neuroglobin Three-Dimensional Structure, PDB code: 1oj6:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1oj6
Go back to
Iron Binding Sites List in 1oj6
Iron binding site 1 out
of 4 in the Human Brain Neuroglobin Three-Dimensional Structure
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Human Brain Neuroglobin Three-Dimensional Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1150
b:3.6
occ:1.00
|
FE
|
A:HEM1150
|
0.0
|
3.6
|
1.0
|
NC
|
A:HEM1150
|
2.0
|
13.6
|
1.0
|
NA
|
A:HEM1150
|
2.0
|
26.8
|
1.0
|
NB
|
A:HEM1150
|
2.1
|
18.8
|
1.0
|
NE2
|
A:HIS96
|
2.1
|
17.3
|
1.0
|
ND
|
A:HEM1150
|
2.1
|
19.7
|
1.0
|
NE2
|
A:HIS64
|
2.1
|
12.5
|
1.0
|
CD2
|
A:HIS96
|
3.0
|
16.4
|
1.0
|
C1C
|
A:HEM1150
|
3.0
|
16.4
|
1.0
|
C4C
|
A:HEM1150
|
3.0
|
15.7
|
1.0
|
C1A
|
A:HEM1150
|
3.0
|
25.6
|
1.0
|
C4A
|
A:HEM1150
|
3.0
|
17.9
|
1.0
|
C4B
|
A:HEM1150
|
3.1
|
13.3
|
1.0
|
C1B
|
A:HEM1150
|
3.1
|
17.7
|
1.0
|
C4D
|
A:HEM1150
|
3.1
|
14.9
|
1.0
|
C1D
|
A:HEM1150
|
3.1
|
11.1
|
1.0
|
CE1
|
A:HIS64
|
3.1
|
18.3
|
1.0
|
CD2
|
A:HIS64
|
3.1
|
17.5
|
1.0
|
CE1
|
A:HIS96
|
3.1
|
19.9
|
1.0
|
CHC
|
A:HEM1150
|
3.4
|
19.7
|
1.0
|
CHD
|
A:HEM1150
|
3.4
|
17.6
|
1.0
|
CHA
|
A:HEM1150
|
3.4
|
18.6
|
1.0
|
CHB
|
A:HEM1150
|
3.4
|
14.6
|
1.0
|
CG
|
A:HIS96
|
4.2
|
13.2
|
1.0
|
C3C
|
A:HEM1150
|
4.2
|
20.1
|
1.0
|
C2C
|
A:HEM1150
|
4.2
|
21.2
|
1.0
|
ND1
|
A:HIS96
|
4.2
|
18.3
|
1.0
|
ND1
|
A:HIS64
|
4.2
|
11.4
|
1.0
|
C2A
|
A:HEM1150
|
4.3
|
26.2
|
1.0
|
C3A
|
A:HEM1150
|
4.3
|
22.8
|
1.0
|
CG
|
A:HIS64
|
4.3
|
18.5
|
1.0
|
C3B
|
A:HEM1150
|
4.3
|
22.7
|
1.0
|
C2B
|
A:HEM1150
|
4.3
|
26.5
|
1.0
|
C3D
|
A:HEM1150
|
4.3
|
21.0
|
1.0
|
C2D
|
A:HEM1150
|
4.3
|
16.9
|
1.0
|
CG2
|
A:VAL68
|
4.8
|
13.7
|
1.0
|
|
Iron binding site 2 out
of 4 in 1oj6
Go back to
Iron Binding Sites List in 1oj6
Iron binding site 2 out
of 4 in the Human Brain Neuroglobin Three-Dimensional Structure
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Human Brain Neuroglobin Three-Dimensional Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1152
b:2.0
occ:1.00
|
FE
|
B:HEM1152
|
0.0
|
2.0
|
1.0
|
NC
|
B:HEM1152
|
2.0
|
15.2
|
1.0
|
ND
|
B:HEM1152
|
2.0
|
12.1
|
1.0
|
NE2
|
B:HIS96
|
2.0
|
14.6
|
1.0
|
NA
|
B:HEM1152
|
2.1
|
23.5
|
1.0
|
NB
|
B:HEM1152
|
2.1
|
26.8
|
1.0
|
NE2
|
B:HIS64
|
2.2
|
15.2
|
1.0
|
CD2
|
B:HIS96
|
2.9
|
19.3
|
1.0
|
C4C
|
B:HEM1152
|
2.9
|
18.1
|
1.0
|
C1D
|
B:HEM1152
|
3.0
|
18.7
|
1.0
|
C1C
|
B:HEM1152
|
3.0
|
13.6
|
1.0
|
C4D
|
B:HEM1152
|
3.0
|
15.9
|
1.0
|
C1A
|
B:HEM1152
|
3.1
|
17.1
|
1.0
|
CE1
|
B:HIS96
|
3.1
|
22.9
|
1.0
|
C4B
|
B:HEM1152
|
3.1
|
13.0
|
1.0
|
C4A
|
B:HEM1152
|
3.1
|
19.1
|
1.0
|
CE1
|
B:HIS64
|
3.1
|
17.4
|
1.0
|
C1B
|
B:HEM1152
|
3.1
|
15.9
|
1.0
|
CD2
|
B:HIS64
|
3.2
|
15.1
|
1.0
|
CHD
|
B:HEM1152
|
3.3
|
13.6
|
1.0
|
CHA
|
B:HEM1152
|
3.4
|
11.1
|
1.0
|
CHC
|
B:HEM1152
|
3.4
|
12.3
|
1.0
|
CHB
|
B:HEM1152
|
3.5
|
14.9
|
1.0
|
CG
|
B:HIS96
|
4.1
|
18.4
|
1.0
|
ND1
|
B:HIS96
|
4.1
|
14.7
|
1.0
|
C3C
|
B:HEM1152
|
4.2
|
15.9
|
1.0
|
C2C
|
B:HEM1152
|
4.2
|
14.9
|
1.0
|
C2D
|
B:HEM1152
|
4.2
|
15.3
|
1.0
|
C3D
|
B:HEM1152
|
4.2
|
14.5
|
1.0
|
ND1
|
B:HIS64
|
4.3
|
17.4
|
1.0
|
CG
|
B:HIS64
|
4.3
|
15.5
|
1.0
|
C2A
|
B:HEM1152
|
4.3
|
20.1
|
1.0
|
C3B
|
B:HEM1152
|
4.3
|
18.2
|
1.0
|
C3A
|
B:HEM1152
|
4.3
|
17.9
|
1.0
|
C2B
|
B:HEM1152
|
4.3
|
20.2
|
1.0
|
CG2
|
B:VAL68
|
4.9
|
11.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 1oj6
Go back to
Iron Binding Sites List in 1oj6
Iron binding site 3 out
of 4 in the Human Brain Neuroglobin Three-Dimensional Structure
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Human Brain Neuroglobin Three-Dimensional Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1152
b:2.0
occ:1.00
|
FE
|
C:HEM1152
|
0.0
|
2.0
|
1.0
|
ND
|
C:HEM1152
|
2.0
|
16.0
|
1.0
|
NC
|
C:HEM1152
|
2.0
|
15.1
|
1.0
|
NE2
|
C:HIS64
|
2.1
|
13.3
|
1.0
|
NA
|
C:HEM1152
|
2.1
|
17.2
|
1.0
|
NB
|
C:HEM1152
|
2.1
|
19.4
|
1.0
|
NE2
|
C:HIS96
|
2.1
|
16.4
|
1.0
|
C4C
|
C:HEM1152
|
3.0
|
15.1
|
1.0
|
C1D
|
C:HEM1152
|
3.0
|
22.4
|
1.0
|
CD2
|
C:HIS96
|
3.0
|
18.0
|
1.0
|
C4D
|
C:HEM1152
|
3.0
|
16.1
|
1.0
|
CD2
|
C:HIS64
|
3.0
|
19.0
|
1.0
|
C1C
|
C:HEM1152
|
3.0
|
13.9
|
1.0
|
C1A
|
C:HEM1152
|
3.1
|
15.0
|
1.0
|
CE1
|
C:HIS64
|
3.1
|
16.8
|
1.0
|
C4B
|
C:HEM1152
|
3.1
|
17.5
|
1.0
|
C1B
|
C:HEM1152
|
3.1
|
5.5
|
1.0
|
C4A
|
C:HEM1152
|
3.1
|
11.2
|
1.0
|
CE1
|
C:HIS96
|
3.2
|
19.4
|
1.0
|
CHD
|
C:HEM1152
|
3.3
|
21.2
|
1.0
|
CHA
|
C:HEM1152
|
3.4
|
15.3
|
1.0
|
CHC
|
C:HEM1152
|
3.4
|
17.3
|
1.0
|
CHB
|
C:HEM1152
|
3.5
|
11.2
|
1.0
|
CG
|
C:HIS96
|
4.2
|
18.9
|
1.0
|
ND1
|
C:HIS64
|
4.2
|
12.7
|
1.0
|
CG
|
C:HIS64
|
4.2
|
14.3
|
1.0
|
C3C
|
C:HEM1152
|
4.2
|
11.4
|
1.0
|
C2D
|
C:HEM1152
|
4.2
|
12.9
|
1.0
|
ND1
|
C:HIS96
|
4.2
|
19.0
|
1.0
|
C2C
|
C:HEM1152
|
4.2
|
18.0
|
1.0
|
C3D
|
C:HEM1152
|
4.2
|
15.1
|
1.0
|
C3B
|
C:HEM1152
|
4.3
|
19.7
|
1.0
|
C2A
|
C:HEM1152
|
4.3
|
16.9
|
1.0
|
C2B
|
C:HEM1152
|
4.3
|
10.9
|
1.0
|
C3A
|
C:HEM1152
|
4.3
|
21.0
|
1.0
|
CG2
|
C:VAL68
|
5.0
|
14.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 1oj6
Go back to
Iron Binding Sites List in 1oj6
Iron binding site 4 out
of 4 in the Human Brain Neuroglobin Three-Dimensional Structure
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Human Brain Neuroglobin Three-Dimensional Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1151
b:2.3
occ:1.00
|
FE
|
D:HEM1151
|
0.0
|
2.3
|
1.0
|
NA
|
D:HEM1151
|
1.9
|
20.0
|
1.0
|
NC
|
D:HEM1151
|
2.0
|
20.6
|
1.0
|
NE2
|
D:HIS96
|
2.0
|
17.8
|
1.0
|
ND
|
D:HEM1151
|
2.1
|
17.6
|
1.0
|
NE2
|
D:HIS64
|
2.1
|
19.4
|
1.0
|
NB
|
D:HEM1151
|
2.1
|
26.4
|
1.0
|
C1A
|
D:HEM1151
|
3.0
|
16.3
|
1.0
|
CD2
|
D:HIS96
|
3.0
|
19.9
|
1.0
|
C4A
|
D:HEM1151
|
3.0
|
21.1
|
1.0
|
C4C
|
D:HEM1151
|
3.0
|
22.7
|
1.0
|
CE1
|
D:HIS96
|
3.0
|
21.4
|
1.0
|
CE1
|
D:HIS64
|
3.0
|
17.6
|
1.0
|
C4D
|
D:HEM1151
|
3.0
|
17.9
|
1.0
|
C1C
|
D:HEM1151
|
3.1
|
17.2
|
1.0
|
C1D
|
D:HEM1151
|
3.1
|
19.5
|
1.0
|
CD2
|
D:HIS64
|
3.1
|
23.1
|
1.0
|
C4B
|
D:HEM1151
|
3.1
|
12.6
|
1.0
|
C1B
|
D:HEM1151
|
3.1
|
19.3
|
1.0
|
CHA
|
D:HEM1151
|
3.4
|
18.7
|
1.0
|
CHD
|
D:HEM1151
|
3.4
|
17.7
|
1.0
|
CHB
|
D:HEM1151
|
3.4
|
14.4
|
1.0
|
CHC
|
D:HEM1151
|
3.5
|
11.9
|
1.0
|
ND1
|
D:HIS96
|
4.1
|
21.7
|
1.0
|
CG
|
D:HIS96
|
4.1
|
19.9
|
1.0
|
ND1
|
D:HIS64
|
4.2
|
18.3
|
1.0
|
C2A
|
D:HEM1151
|
4.2
|
23.2
|
1.0
|
C3A
|
D:HEM1151
|
4.2
|
23.9
|
1.0
|
CG
|
D:HIS64
|
4.2
|
20.3
|
1.0
|
C3C
|
D:HEM1151
|
4.2
|
19.2
|
1.0
|
C2C
|
D:HEM1151
|
4.3
|
18.3
|
1.0
|
C3D
|
D:HEM1151
|
4.3
|
17.1
|
1.0
|
C2D
|
D:HEM1151
|
4.3
|
24.6
|
1.0
|
C3B
|
D:HEM1151
|
4.3
|
26.6
|
1.0
|
C2B
|
D:HEM1151
|
4.3
|
21.3
|
1.0
|
CG2
|
D:VAL68
|
5.0
|
19.2
|
1.0
|
|
Reference:
A.Pesce,
S.Dewilde,
M.Nardini,
L.Moens,
P.Ascenzi,
T.Hankeln,
T.Burmester,
M.Bolognesi.
Human Brain Neuroglobin Structure Reveals A Distinct Mode of Controlling Oxygen Affinity Structure V. 11 1087 2003.
ISSN: ISSN 0969-2126
PubMed: 12962627
DOI: 10.1016/S0969-2126(03)00166-7
Page generated: Sat Aug 3 12:31:43 2024
|