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Iron in PDB 5ve5: Crystal Structure of Persulfide Dioxygenase Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans in Complex with Glutathione

Enzymatic activity of Crystal Structure of Persulfide Dioxygenase Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans in Complex with Glutathione

All present enzymatic activity of Crystal Structure of Persulfide Dioxygenase Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans in Complex with Glutathione:
1.13.11.18; 2.8.1.1;

Protein crystallography data

The structure of Crystal Structure of Persulfide Dioxygenase Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans in Complex with Glutathione, PDB code: 5ve5 was solved by N.Motl, M.A.Skiba, J.L.Smith, R.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.66 / 2.35
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 83.503, 83.503, 547.609, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 25.2

Other elements in 5ve5:

The structure of Crystal Structure of Persulfide Dioxygenase Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans in Complex with Glutathione also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Persulfide Dioxygenase Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans in Complex with Glutathione (pdb code 5ve5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of Persulfide Dioxygenase Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans in Complex with Glutathione, PDB code: 5ve5:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 5ve5

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Iron binding site 1 out of 3 in the Crystal Structure of Persulfide Dioxygenase Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans in Complex with Glutathione


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Persulfide Dioxygenase Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans in Complex with Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:61.2
occ:1.00
 OD2 A:ASP133 2.1 63.7 1.0
O A:HOH545 2.2 51.7 1.0
O A:HOH511 2.2 61.5 1.0
NE2 A:HIS114 2.4 54.8 1.0
NE2 A:HIS58 2.4 52.2 1.0
SG2 A:GSH402 2.8 82.8 1.0
CG A:ASP133 3.2 60.4 1.0
CD2 A:HIS114 3.2 54.2 1.0
CE1 A:HIS58 3.3 53.7 1.0
CE1 A:HIS114 3.4 57.1 1.0
CD2 A:HIS58 3.4 56.9 1.0
CB2 A:GSH402 3.7 68.7 1.0
CB A:ASP133 3.7 51.9 1.0
OD1 A:ASP133 4.2 69.0 1.0
OD2 A:ASP62 4.2 69.1 1.0
CE1 A:HIS174 4.4 53.2 1.0
CG A:HIS114 4.4 59.4 1.0
ND1 A:HIS58 4.4 55.8 1.0
ND1 A:HIS60 4.5 50.6 1.0
ND1 A:HIS114 4.5 58.0 1.0
CG A:HIS58 4.5 57.6 1.0
N A:ALA61 4.5 53.6 1.0
CA A:HIS60 4.7 55.1 1.0
ND1 A:HIS174 4.9 52.4 1.0
CA2 A:GSH402 5.0 72.6 1.0

Iron binding site 2 out of 3 in 5ve5

Go back to Iron Binding Sites List in 5ve5
Iron binding site 2 out of 3 in the Crystal Structure of Persulfide Dioxygenase Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans in Complex with Glutathione


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Persulfide Dioxygenase Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans in Complex with Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:68.3
occ:1.00
 NE2 B:HIS58 2.1 62.7 1.0
O B:HOH503 2.2 50.6 1.0
OD1 B:ASP133 2.2 76.1 1.0
O B:HOH541 2.3 79.5 1.0
NE2 B:HIS114 2.4 66.0 1.0
SG2 B:GSH402 2.7 77.8 1.0
CD2 B:HIS58 3.1 54.1 1.0
CE1 B:HIS58 3.1 52.6 1.0
CD2 B:HIS114 3.2 65.1 1.0
CG B:ASP133 3.3 55.7 1.0
CE1 B:HIS114 3.4 56.6 1.0
CB B:ASP133 3.7 54.2 1.0
CB2 B:GSH402 3.9 94.3 1.0
ND1 B:HIS58 4.2 58.4 1.0
CG B:HIS58 4.2 53.5 1.0
ND1 B:HIS60 4.3 53.4 1.0
OD2 B:ASP133 4.3 61.7 1.0
CG B:HIS114 4.4 62.2 1.0
CE1 B:HIS174 4.4 56.3 1.0
N B:ALA61 4.4 64.8 1.0
ND1 B:HIS114 4.4 66.3 1.0
OD1 B:ASP62 4.5 62.8 1.0
CA B:HIS60 4.5 61.5 1.0
CA2 B:GSH402 4.9 0.6 1.0
ND1 B:HIS174 5.0 58.2 1.0
O B:VAL59 5.0 68.8 1.0

Iron binding site 3 out of 3 in 5ve5

Go back to Iron Binding Sites List in 5ve5
Iron binding site 3 out of 3 in the Crystal Structure of Persulfide Dioxygenase Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans in Complex with Glutathione


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Persulfide Dioxygenase Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans in Complex with Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:80.3
occ:1.00
 NE2 C:HIS114 2.1 1.0 1.0
O C:HOH526 2.1 84.5 1.0
OD2 C:ASP133 2.2 0.7 1.0
O C:HOH501 2.2 63.4 1.0
NE2 C:HIS58 2.4 87.2 1.0
SG2 C:GSH402 2.9 98.4 1.0
CD2 C:HIS114 3.0 0.2 1.0
CE1 C:HIS114 3.0 0.3 1.0
CG C:ASP133 3.2 98.7 1.0
CE1 C:HIS58 3.2 87.8 1.0
CD2 C:HIS58 3.5 90.2 1.0
CB C:ASP133 3.7 86.0 1.0
CB2 C:GSH402 4.1 96.7 1.0
ND1 C:HIS114 4.1 0.4 1.0
CG C:HIS114 4.1 0.8 1.0
OD1 C:ASP133 4.3 94.0 1.0
CE1 C:HIS174 4.3 80.2 1.0
OD1 C:ASP62 4.3 0.4 1.0
ND1 C:HIS58 4.4 87.0 1.0
CG C:HIS58 4.5 85.9 1.0
N C:ALA61 4.6 89.6 1.0
ND1 C:HIS60 4.6 0.7 1.0
CA C:HIS60 4.8 99.9 1.0
ND1 C:HIS174 4.9 78.4 1.0
CA2 C:GSH402 4.9 90.2 1.0

Reference:

N.Motl, M.A.Skiba, O.Kabil, J.L.Smith, R.Banerjee. Structural and Biochemical Analyses Indicate That A Bacterial Persulfide Dioxygenase-Rhodanese Fusion Protein Functions in Sulfur Assimilation. J. Biol. Chem. V. 292 14026 2017.
ISSN: ESSN 1083-351X
PubMed: 28684420
DOI: 10.1074/JBC.M117.790170
Page generated: Tue Aug 6 10:26:27 2024

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