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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

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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 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

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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 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

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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 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

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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 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: Wed Dec 16 02:01:42 2020

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