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Iron in PDB 5ve4: Crystal Structure of Persulfide Dioxygenase-Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans

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

All present enzymatic activity of Crystal Structure of Persulfide Dioxygenase-Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans:
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, PDB code: 5ve4 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) 46.88 / 2.65
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 84.504, 84.504, 549.379, 90.00, 90.00, 120.00
R / Rfree (%) 23.2 / 26.7

Other elements in 5ve4:

The structure of Crystal Structure of Persulfide Dioxygenase-Rhodanese Fusion Protein with Rhodanese Domain Inactivating Mutation (C314S) From Burkholderia Phytofirmans 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 (pdb code 5ve4). 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, PDB code: 5ve4:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 5ve4

Go back to Iron Binding Sites List in 5ve4
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:0.5
occ:1.00
 O A:HOH504 1.8 21.2 1.0
OD2 A:ASP133 1.9 60.6 1.0
O A:HOH506 2.0 53.7 1.0
O A:HOH515 2.1 22.6 1.0
NE2 A:HIS58 2.1 65.8 1.0
NE2 A:HIS114 2.2 64.0 1.0
CG A:ASP133 3.0 58.5 1.0
CD2 A:HIS114 3.0 62.6 1.0
CE1 A:HIS58 3.1 60.5 1.0
CD2 A:HIS58 3.1 70.0 1.0
CE1 A:HIS114 3.2 64.4 1.0
CB A:ASP133 3.5 57.6 1.0
OD1 A:ASP133 4.0 57.5 1.0
CG A:HIS114 4.1 62.1 1.0
ND1 A:HIS58 4.2 60.2 1.0
ND1 A:HIS114 4.2 63.2 1.0
CG A:HIS58 4.2 62.4 1.0
OD2 A:ASP62 4.5 66.5 1.0
ND1 A:HIS60 4.5 60.4 1.0
CE1 A:HIS174 4.6 61.0 1.0
CA A:HIS60 4.9 66.8 1.0
CA A:ASP133 5.0 55.3 1.0
N A:ALA61 5.0 71.3 1.0

Iron binding site 2 out of 3 in 5ve4

Go back to Iron Binding Sites List in 5ve4
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:95.2
occ:1.00
 O B:HOH501 1.9 32.6 1.0
OD1 B:ASP133 2.0 63.0 1.0
O B:HOH506 2.0 30.9 1.0
O B:HOH533 2.2 30.4 1.0
NE2 B:HIS114 2.2 65.9 1.0
NE2 B:HIS58 2.5 58.9 1.0
CG B:ASP133 3.1 60.5 1.0
CD2 B:HIS114 3.2 64.2 1.0
CE1 B:HIS114 3.2 66.9 1.0
CE1 B:HIS58 3.4 57.1 1.0
CD2 B:HIS58 3.5 60.0 1.0
CB B:ASP133 3.8 59.4 1.0
OD2 B:ASP133 4.1 59.9 1.0
OD1 B:ASP62 4.2 62.0 1.0
CE1 B:HIS174 4.2 63.0 1.0
ND1 B:HIS114 4.3 65.8 1.0
CG B:HIS114 4.3 64.1 1.0
ND1 B:HIS58 4.5 57.1 1.0
N B:ALA61 4.5 66.1 1.0
CG B:HIS58 4.6 58.9 1.0
ND1 B:HIS60 4.7 57.4 1.0
NE2 B:HIS174 4.8 65.3 1.0
CA B:HIS60 4.8 62.6 1.0
ND1 B:HIS174 4.9 72.8 1.0

Iron binding site 3 out of 3 in 5ve4

Go back to Iron Binding Sites List in 5ve4
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:0.3
occ:1.00
 O C:HOH501 1.9 0.5 1.0
O C:HOH503 2.0 0.5 1.0
OD2 C:ASP133 2.1 0.4 1.0
O C:HOH514 2.1 0.9 1.0
NE2 C:HIS114 2.1 97.8 1.0
NE2 C:HIS58 2.2 93.1 1.0
CD2 C:HIS114 3.1 98.2 1.0
CD2 C:HIS58 3.1 96.6 1.0
CE1 C:HIS114 3.1 99.2 1.0
CE1 C:HIS58 3.2 89.9 1.0
CG C:ASP133 3.2 0.9 1.0
CB C:ASP133 3.9 88.2 1.0
OD1 C:ASP133 4.2 84.0 1.0
CG C:HIS114 4.2 99.5 1.0
ND1 C:HIS114 4.2 0.2 1.0
CG C:HIS58 4.3 95.5 1.0
ND1 C:HIS58 4.3 91.3 1.0
OD1 C:ASP62 4.4 91.4 1.0
ND1 C:HIS60 4.6 90.2 1.0
N C:ALA61 4.6 0.1 1.0
CE1 C:HIS174 4.7 85.6 1.0
CA C:HIS60 4.7 98.6 1.0
O C:VAL59 4.9 0.8 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: Wed Aug 6 02:08:57 2025

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