Iron in PDB 1tjo: Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States
Protein crystallography data
The structure of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States, PDB code: 1tjo
was solved by
K.Zeth,
S.Offermann,
L.O.Essen,
D.Oesterhelt,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
15.00 /
1.60
|
Space group
|
P 3 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.110,
91.110,
150.040,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.5 /
21
|
Other elements in 1tjo:
The structure of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States
(pdb code 1tjo). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States, PDB code: 1tjo:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 1tjo
Go back to
Iron Binding Sites List in 1tjo
Iron binding site 1 out
of 6 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1302
b:24.0
occ:0.50
|
OE1
|
A:GLU83
|
1.9
|
30.2
|
1.0
|
O
|
A:HOH1547
|
1.9
|
33.6
|
1.0
|
OD2
|
A:ASP79
|
2.1
|
25.8
|
1.0
|
NE2
|
B:HIS52
|
2.2
|
22.6
|
1.0
|
O
|
A:HOH1477
|
2.2
|
37.5
|
1.0
|
OD1
|
A:ASP79
|
2.4
|
24.0
|
1.0
|
CG
|
A:ASP79
|
2.7
|
23.4
|
1.0
|
CD
|
A:GLU83
|
3.0
|
30.4
|
1.0
|
CE1
|
B:HIS52
|
3.2
|
23.1
|
1.0
|
CD2
|
B:HIS52
|
3.2
|
22.7
|
1.0
|
OE2
|
A:GLU83
|
3.6
|
32.3
|
1.0
|
O
|
B:HOH1547
|
3.9
|
49.9
|
1.0
|
O
|
A:HOH1455
|
4.1
|
46.5
|
1.0
|
CG
|
A:GLU83
|
4.1
|
23.6
|
1.0
|
CB
|
A:ASP79
|
4.2
|
18.6
|
1.0
|
ND1
|
B:HIS52
|
4.3
|
21.5
|
1.0
|
CG
|
B:HIS52
|
4.3
|
19.5
|
1.0
|
CE1
|
B:HIS64
|
4.4
|
28.1
|
1.0
|
O
|
A:HOH1514
|
4.4
|
40.5
|
1.0
|
NE2
|
B:HIS64
|
4.4
|
29.8
|
1.0
|
CD1
|
B:TRP53
|
4.5
|
21.9
|
1.0
|
NZ
|
B:LYS49
|
4.5
|
31.7
|
1.0
|
NE1
|
B:TRP53
|
4.5
|
22.4
|
1.0
|
O
|
B:HOH1557
|
4.8
|
53.3
|
1.0
|
O
|
B:HOH1446
|
4.9
|
39.3
|
1.0
|
|
Iron binding site 2 out
of 6 in 1tjo
Go back to
Iron Binding Sites List in 1tjo
Iron binding site 2 out
of 6 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1306
b:30.8
occ:1.00
|
O
|
C:HOH1642
|
2.1
|
29.7
|
1.0
|
OE2
|
A:GLU154
|
2.1
|
25.3
|
1.0
|
O
|
A:HOH1546
|
2.1
|
27.1
|
1.0
|
OE2
|
C:GLU154
|
2.1
|
25.9
|
1.0
|
O
|
C:HOH1678
|
2.1
|
28.2
|
1.0
|
O
|
A:HOH1569
|
2.9
|
23.9
|
1.0
|
O
|
C:HOH1706
|
2.9
|
24.0
|
1.0
|
CD
|
A:GLU154
|
3.1
|
28.2
|
1.0
|
CD
|
C:GLU154
|
3.1
|
28.6
|
1.0
|
OE1
|
C:GLU154
|
3.3
|
31.1
|
1.0
|
OE1
|
A:GLU154
|
3.3
|
31.4
|
1.0
|
O
|
C:HOH1712
|
4.1
|
41.2
|
1.0
|
O
|
A:HOH1444
|
4.1
|
34.1
|
1.0
|
O
|
C:HOH1518
|
4.1
|
30.8
|
1.0
|
O
|
C:HOH1713
|
4.2
|
51.0
|
1.0
|
CE1
|
C:HIS150
|
4.3
|
27.8
|
1.0
|
O
|
C:HOH1714
|
4.3
|
52.1
|
1.0
|
CE1
|
A:HIS150
|
4.3
|
23.7
|
1.0
|
NE2
|
A:HIS150
|
4.4
|
26.8
|
1.0
|
CG
|
C:GLU154
|
4.5
|
25.7
|
1.0
|
CG
|
A:GLU154
|
4.5
|
23.8
|
1.0
|
NE2
|
C:HIS150
|
4.5
|
28.8
|
1.0
|
O
|
A:HOH1505
|
4.6
|
40.0
|
1.0
|
O
|
C:HOH1677
|
4.7
|
39.6
|
1.0
|
O
|
C:HOH1622
|
4.7
|
42.1
|
1.0
|
O
|
C:HOH1627
|
4.8
|
47.1
|
1.0
|
O
|
C:HOH1715
|
5.0
|
64.9
|
1.0
|
|
Iron binding site 3 out
of 6 in 1tjo
Go back to
Iron Binding Sites List in 1tjo
Iron binding site 3 out
of 6 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1301
b:25.0
occ:0.50
|
OE1
|
B:GLU83
|
1.9
|
30.3
|
1.0
|
O
|
B:HOH1589
|
2.0
|
31.9
|
1.0
|
OD2
|
B:ASP79
|
2.1
|
27.5
|
1.0
|
NE2
|
A:HIS52
|
2.2
|
21.7
|
1.0
|
O
|
B:HOH1421
|
2.3
|
33.4
|
1.0
|
OD1
|
B:ASP79
|
2.4
|
24.2
|
1.0
|
CG
|
B:ASP79
|
2.7
|
24.3
|
1.0
|
CD
|
B:GLU83
|
3.0
|
31.2
|
1.0
|
CE1
|
A:HIS52
|
3.2
|
25.0
|
1.0
|
CD2
|
A:HIS52
|
3.2
|
21.7
|
1.0
|
OE2
|
B:GLU83
|
3.5
|
35.9
|
1.0
|
O
|
A:HOH1548
|
3.7
|
53.1
|
1.0
|
CG
|
B:GLU83
|
4.1
|
23.8
|
1.0
|
CB
|
B:ASP79
|
4.1
|
20.5
|
1.0
|
O
|
B:HOH1457
|
4.2
|
49.9
|
1.0
|
O
|
B:HOH1588
|
4.2
|
61.9
|
1.0
|
O
|
B:HOH1596
|
4.2
|
49.5
|
1.0
|
ND1
|
A:HIS52
|
4.3
|
20.4
|
1.0
|
CG
|
A:HIS52
|
4.3
|
20.2
|
1.0
|
CE1
|
A:HIS64
|
4.4
|
26.6
|
1.0
|
NE2
|
A:HIS64
|
4.5
|
30.9
|
1.0
|
CD1
|
A:TRP53
|
4.5
|
19.5
|
1.0
|
NE1
|
A:TRP53
|
4.5
|
19.4
|
1.0
|
NZ
|
A:LYS49
|
4.6
|
31.0
|
1.0
|
O
|
B:HOH1595
|
4.6
|
63.6
|
1.0
|
O
|
B:HOH1581
|
4.6
|
52.8
|
1.0
|
O
|
B:HOH1492
|
4.8
|
41.1
|
1.0
|
O
|
A:HOH1563
|
5.0
|
52.9
|
1.0
|
|
Iron binding site 4 out
of 6 in 1tjo
Go back to
Iron Binding Sites List in 1tjo
Iron binding site 4 out
of 6 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1305
b:30.1
occ:0.33
|
OE2
|
B:GLU154
|
2.0
|
26.5
|
1.0
|
O
|
B:HOH1479
|
2.3
|
31.1
|
1.0
|
O
|
B:HOH1610
|
3.0
|
26.3
|
1.0
|
CD
|
B:GLU154
|
3.0
|
29.9
|
1.0
|
OE1
|
B:GLU154
|
3.2
|
31.2
|
1.0
|
O
|
B:HOH1413
|
4.2
|
34.0
|
1.0
|
CE1
|
B:HIS150
|
4.2
|
24.1
|
1.0
|
O
|
B:HOH1591
|
4.3
|
46.5
|
1.0
|
CG
|
B:GLU154
|
4.4
|
25.4
|
1.0
|
NE2
|
B:HIS150
|
4.5
|
28.3
|
1.0
|
O
|
B:HOH1519
|
4.7
|
39.1
|
1.0
|
O
|
B:HOH1535
|
4.7
|
43.7
|
1.0
|
|
Iron binding site 5 out
of 6 in 1tjo
Go back to
Iron Binding Sites List in 1tjo
Iron binding site 5 out
of 6 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1304
b:25.7
occ:0.50
|
O
|
C:HOH1645
|
2.0
|
34.9
|
1.0
|
OE1
|
C:GLU83
|
2.0
|
27.7
|
1.0
|
OD2
|
C:ASP79
|
2.1
|
27.1
|
1.0
|
O
|
C:HOH1540
|
2.2
|
35.1
|
1.0
|
NE2
|
D:HIS52
|
2.2
|
22.9
|
1.0
|
OD1
|
C:ASP79
|
2.4
|
23.1
|
1.0
|
CG
|
C:ASP79
|
2.6
|
25.5
|
1.0
|
CD
|
C:GLU83
|
3.1
|
31.5
|
1.0
|
CE1
|
D:HIS52
|
3.1
|
22.6
|
1.0
|
CD2
|
D:HIS52
|
3.2
|
24.6
|
1.0
|
OE2
|
C:GLU83
|
3.6
|
33.5
|
1.0
|
O
|
C:HOH1596
|
3.8
|
48.9
|
1.0
|
CB
|
C:ASP79
|
4.1
|
20.8
|
1.0
|
CG
|
C:GLU83
|
4.2
|
23.6
|
1.0
|
ND1
|
D:HIS52
|
4.3
|
22.2
|
1.0
|
O
|
C:HOH1585
|
4.3
|
47.7
|
1.0
|
CG
|
D:HIS52
|
4.3
|
20.0
|
1.0
|
NZ
|
D:LYS49
|
4.4
|
30.2
|
1.0
|
CE1
|
D:HIS64
|
4.4
|
29.1
|
1.0
|
NE1
|
D:TRP53
|
4.5
|
21.1
|
1.0
|
O
|
C:HOH1552
|
4.5
|
49.2
|
1.0
|
CD1
|
D:TRP53
|
4.5
|
21.0
|
1.0
|
NE2
|
D:HIS64
|
4.5
|
30.8
|
1.0
|
O
|
C:HOH1629
|
4.6
|
58.2
|
1.0
|
O
|
D:HOH1642
|
4.8
|
51.9
|
1.0
|
O
|
C:ASP79
|
5.0
|
19.9
|
1.0
|
|
Iron binding site 6 out
of 6 in 1tjo
Go back to
Iron Binding Sites List in 1tjo
Iron binding site 6 out
of 6 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1303
b:24.9
occ:0.50
|
OE1
|
D:GLU83
|
1.9
|
28.9
|
1.0
|
O
|
D:HOH1648
|
1.9
|
36.7
|
1.0
|
OD2
|
D:ASP79
|
2.2
|
28.6
|
1.0
|
NE2
|
C:HIS52
|
2.2
|
23.9
|
1.0
|
O
|
C:HOH1628
|
2.3
|
33.6
|
1.0
|
OD1
|
D:ASP79
|
2.4
|
25.1
|
1.0
|
CG
|
D:ASP79
|
2.6
|
25.4
|
1.0
|
CD
|
D:GLU83
|
3.0
|
31.8
|
1.0
|
CE1
|
C:HIS52
|
3.1
|
24.0
|
1.0
|
CD2
|
C:HIS52
|
3.2
|
22.3
|
1.0
|
OE2
|
D:GLU83
|
3.6
|
36.0
|
1.0
|
O
|
C:HOH1623
|
3.8
|
51.6
|
1.0
|
O
|
D:HOH1569
|
4.0
|
42.1
|
1.0
|
CB
|
D:ASP79
|
4.1
|
21.4
|
1.0
|
CG
|
D:GLU83
|
4.2
|
22.8
|
1.0
|
ND1
|
C:HIS52
|
4.3
|
22.0
|
1.0
|
CG
|
C:HIS52
|
4.3
|
19.1
|
1.0
|
CE1
|
C:HIS64
|
4.4
|
27.2
|
1.0
|
O
|
C:HOH1634
|
4.4
|
47.1
|
1.0
|
NZ
|
C:LYS49
|
4.4
|
32.4
|
1.0
|
O
|
D:HOH1665
|
4.5
|
59.5
|
1.0
|
NE2
|
C:HIS64
|
4.5
|
31.0
|
1.0
|
NE1
|
C:TRP53
|
4.5
|
21.0
|
1.0
|
CD1
|
C:TRP53
|
4.5
|
22.0
|
1.0
|
O
|
C:HOH1687
|
4.7
|
46.7
|
1.0
|
O
|
C:HOH1613
|
4.9
|
40.2
|
1.0
|
O
|
D:ASP79
|
5.0
|
21.8
|
1.0
|
|
Reference:
K.Zeth,
S.Offermann,
L.O.Essen,
D.Oesterhelt.
Iron-Oxo Clusters Biomineralizing on Protein Surfaces: Structural Analysis of Halobacterium Salinarum Dpsa in Its Low- and High-Iron States. Proc.Natl.Acad.Sci.Usa V. 101 13780 2004.
ISSN: ISSN 0027-8424
PubMed: 15365182
DOI: 10.1073/PNAS.0401821101
Page generated: Sat Aug 3 15:16:16 2024
|