Osmium in PDB 5wse: Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os) Substituted Form I
Protein crystallography data
The structure of Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os) Substituted Form I, PDB code: 5wse
was solved by
N.Fujieda,
T.Nakano,
Y.Taniguchi,
H.Ichihashi,
Y.Nishikawa,
G.Kurisu,
S.Itoh,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
1.12
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
35.396,
48.878,
62.597,
69.07,
87.95,
78.89
|
R / Rfree (%)
|
15.1 /
18
|
Osmium Binding Sites:
The binding sites of Osmium atom in the Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os) Substituted Form I
(pdb code 5wse). This binding sites where shown within
5.0 Angstroms radius around Osmium atom.
In total 4 binding sites of Osmium where determined in the
Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os) Substituted Form I, PDB code: 5wse:
Jump to Osmium binding site number:
1;
2;
3;
4;
Osmium binding site 1 out
of 4 in 5wse
Go back to
Osmium Binding Sites List in 5wse
Osmium binding site 1 out
of 4 in the Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os) Substituted Form I
Mono view
Stereo pair view
|
A full contact list of Osmium with other atoms in the Os binding
site number 1 of Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os) Substituted Form I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Os201
b:9.2
occ:0.94
|
O
|
A:HOH310
|
1.8
|
10.5
|
1.0
|
O
|
A:HOH313
|
1.8
|
10.9
|
1.0
|
O
|
A:HOH352
|
1.9
|
11.1
|
1.0
|
NE2
|
A:HIS58
|
2.1
|
10.9
|
1.0
|
NE2
|
A:HIS92
|
2.1
|
9.3
|
1.0
|
NE2
|
A:HIS52
|
2.1
|
10.2
|
1.0
|
CE1
|
A:HIS92
|
3.0
|
9.1
|
1.0
|
CE1
|
A:HIS52
|
3.1
|
10.9
|
1.0
|
CE1
|
A:HIS58
|
3.1
|
12.0
|
1.0
|
CD2
|
A:HIS58
|
3.1
|
10.9
|
1.0
|
CD2
|
A:HIS52
|
3.1
|
10.0
|
1.0
|
CD2
|
A:HIS92
|
3.2
|
8.6
|
1.0
|
ND1
|
A:HIS92
|
4.2
|
9.2
|
1.0
|
O
|
A:HOH342
|
4.2
|
16.9
|
1.0
|
ND1
|
A:HIS58
|
4.2
|
11.0
|
1.0
|
ND1
|
A:HIS52
|
4.2
|
10.4
|
1.0
|
CD2
|
A:HIS54
|
4.2
|
14.1
|
1.0
|
CG
|
A:HIS58
|
4.2
|
9.8
|
1.0
|
O
|
A:HOH366
|
4.2
|
13.9
|
1.0
|
CG
|
A:HIS52
|
4.2
|
10.5
|
1.0
|
CG
|
A:HIS92
|
4.3
|
8.6
|
1.0
|
O
|
A:HOH364
|
4.3
|
20.1
|
0.5
|
O
|
A:HOH318
|
4.5
|
26.9
|
1.0
|
NE2
|
A:HIS54
|
5.0
|
15.8
|
1.0
|
|
Osmium binding site 2 out
of 4 in 5wse
Go back to
Osmium Binding Sites List in 5wse
Osmium binding site 2 out
of 4 in the Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os) Substituted Form I
Mono view
Stereo pair view
|
A full contact list of Osmium with other atoms in the Os binding
site number 2 of Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os) Substituted Form I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Os201
b:10.0
occ:0.92
|
O
|
B:HOH309
|
1.7
|
11.5
|
1.0
|
O
|
B:HOH308
|
1.8
|
11.1
|
1.0
|
O
|
B:HOH355
|
1.9
|
11.4
|
1.0
|
NE2
|
B:HIS58
|
2.1
|
11.3
|
1.0
|
NE2
|
B:HIS52
|
2.1
|
11.1
|
1.0
|
NE2
|
B:HIS92
|
2.1
|
10.1
|
1.0
|
CE1
|
B:HIS52
|
3.0
|
12.5
|
1.0
|
CE1
|
B:HIS92
|
3.0
|
10.4
|
1.0
|
CE1
|
B:HIS58
|
3.1
|
12.2
|
1.0
|
CD2
|
B:HIS58
|
3.1
|
10.3
|
1.0
|
CD2
|
B:HIS52
|
3.1
|
11.1
|
1.0
|
CD2
|
B:HIS92
|
3.2
|
10.1
|
1.0
|
O
|
B:HOH365
|
4.1
|
17.8
|
1.0
|
ND1
|
B:HIS52
|
4.2
|
13.3
|
1.0
|
ND1
|
B:HIS92
|
4.2
|
10.6
|
1.0
|
ND1
|
B:HIS58
|
4.2
|
12.7
|
1.0
|
CD2
|
B:HIS54
|
4.2
|
15.6
|
1.0
|
CG
|
B:HIS58
|
4.2
|
10.3
|
1.0
|
CG
|
B:HIS52
|
4.2
|
12.5
|
1.0
|
O
|
B:HOH362
|
4.2
|
15.4
|
1.0
|
CG
|
B:HIS92
|
4.3
|
10.4
|
1.0
|
O
|
B:HOH356
|
4.7
|
33.1
|
1.0
|
NE2
|
B:HIS54
|
5.0
|
16.7
|
1.0
|
|
Osmium binding site 3 out
of 4 in 5wse
Go back to
Osmium Binding Sites List in 5wse
Osmium binding site 3 out
of 4 in the Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os) Substituted Form I
Mono view
Stereo pair view
|
A full contact list of Osmium with other atoms in the Os binding
site number 3 of Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os) Substituted Form I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Os201
b:10.7
occ:0.94
|
O
|
C:HOH312
|
1.7
|
11.9
|
1.0
|
O
|
C:HOH324
|
1.8
|
11.6
|
1.0
|
O
|
C:HOH348
|
1.9
|
12.8
|
1.0
|
NE2
|
C:HIS52
|
2.1
|
12.7
|
1.0
|
NE2
|
C:HIS58
|
2.1
|
10.8
|
1.0
|
NE2
|
C:HIS92
|
2.1
|
11.5
|
1.0
|
CE1
|
C:HIS58
|
3.0
|
11.6
|
1.0
|
CE1
|
C:HIS52
|
3.0
|
12.6
|
1.0
|
CE1
|
C:HIS92
|
3.0
|
11.6
|
1.0
|
CD2
|
C:HIS58
|
3.1
|
11.0
|
1.0
|
CD2
|
C:HIS52
|
3.1
|
12.7
|
1.0
|
CD2
|
C:HIS92
|
3.1
|
11.9
|
1.0
|
O
|
C:HOH374
|
4.1
|
25.6
|
0.5
|
O
|
C:HOH361
|
4.1
|
19.4
|
1.0
|
ND1
|
C:HIS58
|
4.1
|
12.0
|
1.0
|
O
|
C:HOH343
|
4.2
|
14.8
|
1.0
|
ND1
|
C:HIS52
|
4.2
|
12.2
|
1.0
|
ND1
|
C:HIS92
|
4.2
|
11.8
|
1.0
|
CG
|
C:HIS58
|
4.2
|
10.9
|
1.0
|
CG
|
C:HIS52
|
4.2
|
11.9
|
1.0
|
CG
|
C:HIS92
|
4.3
|
12.0
|
1.0
|
CD2
|
C:HIS54
|
4.3
|
21.1
|
1.0
|
O
|
C:HOH333
|
4.5
|
36.7
|
1.0
|
|
Osmium binding site 4 out
of 4 in 5wse
Go back to
Osmium Binding Sites List in 5wse
Osmium binding site 4 out
of 4 in the Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os) Substituted Form I
Mono view
Stereo pair view
|
A full contact list of Osmium with other atoms in the Os binding
site number 4 of Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os) Substituted Form I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Os201
b:11.9
occ:0.93
|
O
|
D:HOH311
|
1.7
|
13.8
|
1.0
|
O
|
D:HOH317
|
1.7
|
13.2
|
1.0
|
O
|
D:HOH362
|
2.0
|
13.9
|
1.0
|
NE2
|
D:HIS58
|
2.1
|
12.0
|
1.0
|
NE2
|
D:HIS52
|
2.1
|
14.5
|
1.0
|
NE2
|
D:HIS92
|
2.1
|
11.7
|
1.0
|
CE1
|
D:HIS58
|
3.0
|
15.0
|
1.0
|
CE1
|
D:HIS92
|
3.0
|
12.5
|
1.0
|
CE1
|
D:HIS52
|
3.1
|
13.9
|
1.0
|
CD2
|
D:HIS58
|
3.1
|
12.0
|
1.0
|
CD2
|
D:HIS52
|
3.1
|
13.4
|
1.0
|
CD2
|
D:HIS92
|
3.1
|
11.2
|
1.0
|
ND1
|
D:HIS58
|
4.1
|
14.0
|
1.0
|
CD2
|
D:HIS54
|
4.1
|
20.0
|
1.0
|
O
|
D:HOH372
|
4.2
|
36.1
|
1.0
|
ND1
|
D:HIS92
|
4.2
|
12.2
|
1.0
|
ND1
|
D:HIS52
|
4.2
|
13.9
|
1.0
|
O
|
D:HOH348
|
4.2
|
25.9
|
1.0
|
CG
|
D:HIS58
|
4.2
|
11.5
|
1.0
|
O
|
D:HOH355
|
4.2
|
17.6
|
1.0
|
CG
|
D:HIS52
|
4.2
|
13.5
|
1.0
|
CG
|
D:HIS92
|
4.3
|
10.3
|
1.0
|
O
|
D:HOH338
|
4.4
|
29.1
|
1.0
|
NE2
|
D:HIS54
|
5.0
|
23.7
|
1.0
|
|
Reference:
N.Fujieda,
T.Nakano,
Y.Taniguchi,
H.Ichihashi,
H.Sugimoto,
Y.Morimoto,
Y.Nishikawa,
G.Kurisu,
S.Itoh.
A Well-Defined Osmium-Cupin Complex: Hyperstable Artificial Osmium Peroxygenase J. Am. Chem. Soc. 2017.
ISSN: ESSN 1520-5126
PubMed: 28340294
DOI: 10.1021/JACS.7B00675
Page generated: Thu Oct 10 09:56:58 2024
|