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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

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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

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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

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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

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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: Wed Dec 16 02:01:36 2020

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