Osmium in PDB 5wsf: Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os)- Substituted Form II
Protein crystallography data
The structure of Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os)- Substituted Form II, PDB code: 5wsf
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 /
1.11
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
35.488,
49.014,
64.431,
65.45,
83.58,
78.79
|
R / Rfree (%)
|
14.7 /
18.3
|
Osmium Binding Sites:
The binding sites of Osmium atom in the Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os)- Substituted Form II
(pdb code 5wsf). 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 II, PDB code: 5wsf:
Jump to Osmium binding site number:
1;
2;
3;
4;
Osmium binding site 1 out
of 4 in 5wsf
Go back to
Osmium Binding Sites List in 5wsf
Osmium binding site 1 out
of 4 in the Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os)- Substituted Form II
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 II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Os201
b:11.2
occ:0.94
|
O
|
A:HOH319
|
1.9
|
13.9
|
1.0
|
O
|
A:HOH336
|
1.9
|
15.4
|
1.0
|
NE2
|
A:HIS54
|
2.1
|
12.8
|
0.6
|
NE2
|
A:HIS92
|
2.1
|
11.1
|
1.0
|
NE2
|
A:HIS58
|
2.1
|
10.9
|
1.0
|
NE2
|
A:HIS52
|
2.1
|
15.2
|
1.0
|
CE1
|
A:HIS54
|
3.0
|
12.1
|
0.6
|
CE1
|
A:HIS92
|
3.0
|
11.3
|
1.0
|
CE1
|
A:HIS58
|
3.1
|
12.6
|
1.0
|
CD2
|
A:HIS58
|
3.1
|
12.1
|
1.0
|
CE1
|
A:HIS52
|
3.1
|
14.4
|
1.0
|
CD2
|
A:HIS92
|
3.1
|
10.5
|
1.0
|
CD2
|
A:HIS52
|
3.1
|
14.8
|
1.0
|
CD2
|
A:HIS54
|
3.1
|
13.6
|
0.6
|
O
|
A:HOH370
|
3.5
|
31.5
|
1.0
|
CD2
|
A:HIS54
|
4.1
|
13.8
|
0.4
|
ND1
|
A:HIS92
|
4.2
|
10.4
|
1.0
|
ND1
|
A:HIS54
|
4.2
|
13.6
|
0.6
|
ND1
|
A:HIS58
|
4.2
|
12.7
|
1.0
|
ND1
|
A:HIS52
|
4.2
|
14.4
|
1.0
|
CG
|
A:HIS92
|
4.2
|
10.2
|
1.0
|
CG
|
A:HIS58
|
4.2
|
10.5
|
1.0
|
CG
|
A:HIS54
|
4.3
|
12.8
|
0.6
|
CG
|
A:HIS52
|
4.3
|
13.8
|
1.0
|
O
|
A:HOH376
|
4.3
|
18.6
|
1.0
|
NE2
|
A:HIS54
|
4.9
|
14.8
|
0.4
|
|
Osmium binding site 2 out
of 4 in 5wsf
Go back to
Osmium Binding Sites List in 5wsf
Osmium binding site 2 out
of 4 in the Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os)- Substituted Form II
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 II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Os201
b:12.7
occ:0.92
|
O
|
B:HOH317
|
1.8
|
14.4
|
1.0
|
O
|
B:HOH348
|
2.0
|
16.1
|
1.0
|
NE2
|
B:HIS58
|
2.1
|
13.1
|
1.0
|
NE2
|
B:HIS52
|
2.1
|
16.9
|
1.0
|
NE2
|
B:HIS54
|
2.1
|
13.6
|
0.6
|
NE2
|
B:HIS92
|
2.1
|
12.4
|
1.0
|
CE1
|
B:HIS92
|
3.0
|
12.3
|
1.0
|
CE1
|
B:HIS52
|
3.1
|
16.3
|
1.0
|
CE1
|
B:HIS54
|
3.1
|
13.7
|
0.6
|
CE1
|
B:HIS58
|
3.1
|
13.2
|
1.0
|
CD2
|
B:HIS58
|
3.1
|
12.7
|
1.0
|
CD2
|
B:HIS52
|
3.1
|
17.1
|
1.0
|
CD2
|
B:HIS54
|
3.1
|
16.1
|
0.6
|
CD2
|
B:HIS92
|
3.2
|
12.3
|
1.0
|
O
|
B:HOH342
|
3.3
|
30.1
|
1.0
|
CD2
|
B:HIS54
|
4.0
|
18.6
|
0.4
|
ND1
|
B:HIS92
|
4.2
|
13.1
|
1.0
|
ND1
|
B:HIS52
|
4.2
|
19.1
|
1.0
|
ND1
|
B:HIS54
|
4.2
|
15.2
|
0.6
|
ND1
|
B:HIS58
|
4.2
|
12.9
|
1.0
|
CG
|
B:HIS58
|
4.2
|
11.1
|
1.0
|
O
|
B:HOH346
|
4.2
|
40.6
|
1.0
|
CG
|
B:HIS52
|
4.2
|
18.2
|
1.0
|
CG
|
B:HIS54
|
4.3
|
14.4
|
0.6
|
CG
|
B:HIS92
|
4.3
|
13.1
|
1.0
|
O
|
B:HOH375
|
4.4
|
23.5
|
1.0
|
NE2
|
B:HIS54
|
4.7
|
24.4
|
0.4
|
O
|
B:HOH368
|
4.8
|
34.3
|
1.0
|
|
Osmium binding site 3 out
of 4 in 5wsf
Go back to
Osmium Binding Sites List in 5wsf
Osmium binding site 3 out
of 4 in the Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os)- Substituted Form II
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 II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Os201
b:13.2
occ:0.95
|
O
|
C:HOH315
|
1.8
|
16.0
|
1.0
|
O
|
C:HOH361
|
2.0
|
18.6
|
1.0
|
NE2
|
C:HIS58
|
2.1
|
13.7
|
1.0
|
NE2
|
C:HIS54
|
2.1
|
16.2
|
1.0
|
NE2
|
C:HIS52
|
2.1
|
19.1
|
1.0
|
NE2
|
C:HIS92
|
2.1
|
15.9
|
1.0
|
CE1
|
C:HIS54
|
3.0
|
18.7
|
1.0
|
CE1
|
C:HIS58
|
3.1
|
14.6
|
1.0
|
CE1
|
C:HIS92
|
3.1
|
13.9
|
1.0
|
CD2
|
C:HIS52
|
3.1
|
18.2
|
1.0
|
CD2
|
C:HIS58
|
3.1
|
13.4
|
1.0
|
CE1
|
C:HIS52
|
3.1
|
19.3
|
1.0
|
CD2
|
C:HIS92
|
3.1
|
14.2
|
1.0
|
CD2
|
C:HIS54
|
3.2
|
20.5
|
1.0
|
O
|
C:HOH385
|
3.4
|
32.2
|
0.5
|
O
|
C:HOH375
|
4.0
|
29.8
|
1.0
|
O
|
C:HOH344
|
4.1
|
20.9
|
1.0
|
ND1
|
C:HIS54
|
4.2
|
20.4
|
1.0
|
ND1
|
C:HIS58
|
4.2
|
13.8
|
1.0
|
ND1
|
C:HIS92
|
4.2
|
13.6
|
1.0
|
ND1
|
C:HIS52
|
4.2
|
19.8
|
1.0
|
CG
|
C:HIS58
|
4.2
|
12.4
|
1.0
|
CG
|
C:HIS52
|
4.3
|
17.9
|
1.0
|
CG
|
C:HIS92
|
4.3
|
14.9
|
1.0
|
CG
|
C:HIS54
|
4.3
|
19.3
|
1.0
|
O
|
C:HOH385
|
4.9
|
31.4
|
0.5
|
|
Osmium binding site 4 out
of 4 in 5wsf
Go back to
Osmium Binding Sites List in 5wsf
Osmium binding site 4 out
of 4 in the Crystal Structure of A Cupin Protein (TM1459) in Osmium (Os)- Substituted Form II
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 II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Os201
b:13.3
occ:0.93
|
O
|
D:HOH323
|
1.9
|
15.2
|
1.0
|
O
|
D:HOH343
|
2.0
|
17.0
|
1.0
|
NE2
|
D:HIS54
|
2.1
|
16.2
|
1.0
|
NE2
|
D:HIS58
|
2.1
|
13.7
|
1.0
|
NE2
|
D:HIS92
|
2.1
|
12.8
|
1.0
|
NE2
|
D:HIS52
|
2.1
|
18.5
|
1.0
|
CE1
|
D:HIS54
|
3.0
|
17.9
|
1.0
|
CE1
|
D:HIS58
|
3.0
|
15.2
|
1.0
|
CE1
|
D:HIS92
|
3.1
|
13.1
|
1.0
|
CD2
|
D:HIS58
|
3.1
|
14.1
|
1.0
|
CD2
|
D:HIS52
|
3.1
|
17.2
|
1.0
|
CE1
|
D:HIS52
|
3.1
|
20.4
|
1.0
|
CD2
|
D:HIS92
|
3.1
|
11.6
|
1.0
|
CD2
|
D:HIS54
|
3.1
|
20.1
|
1.0
|
O
|
D:HOH391
|
4.0
|
36.0
|
1.0
|
O
|
D:HOH381
|
4.0
|
37.3
|
1.0
|
ND1
|
D:HIS54
|
4.2
|
18.8
|
1.0
|
ND1
|
D:HIS58
|
4.2
|
14.2
|
1.0
|
ND1
|
D:HIS92
|
4.2
|
12.4
|
1.0
|
CG
|
D:HIS58
|
4.2
|
12.4
|
1.0
|
ND1
|
D:HIS52
|
4.2
|
20.3
|
1.0
|
O
|
D:HOH361
|
4.2
|
20.2
|
1.0
|
CG
|
D:HIS54
|
4.2
|
19.5
|
1.0
|
CG
|
D:HIS92
|
4.2
|
11.1
|
1.0
|
CG
|
D:HIS52
|
4.3
|
16.8
|
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 09:57:05 2024
|