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Chlorine 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:

Iron (Fe) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5ve4

Go back to Chlorine Binding Sites List in 5ve4
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl402

b:62.8
occ:1.00
 OG A:SER314 2.9 71.3 1.0
NE A:ARG319 3.1 73.3 1.0
N A:ARG319 3.4 71.2 1.0
N A:GLY318 3.5 70.0 1.0
CB A:SER314 3.6 70.6 1.0
N A:ALA316 3.6 67.3 1.0
CG A:ARG319 3.6 83.9 1.0
N A:ARG315 3.7 69.3 1.0
NH2 A:ARG319 3.8 74.7 1.0
N A:GLY317 3.8 67.2 1.0
CZ A:ARG319 3.9 74.6 1.0
CB A:ARG319 3.9 83.6 1.0
CD A:ARG319 4.0 73.4 1.0
CA A:GLY318 4.1 69.4 1.0
CB A:ARG315 4.1 69.4 1.0
C A:GLY318 4.3 70.4 1.0
CA A:ARG315 4.3 68.7 1.0
CA A:ARG319 4.3 72.5 1.0
CA A:ALA316 4.4 66.7 1.0
C A:ARG315 4.4 67.5 1.0
C A:SER314 4.5 69.4 1.0
C A:ALA316 4.5 66.7 1.0
C A:GLY317 4.5 68.3 1.0
CA A:SER314 4.6 70.6 1.0
CA A:GLY317 4.6 67.5 1.0
CB A:ALA316 4.7 70.4 1.0

Chlorine binding site 2 out of 3 in 5ve4

Go back to Chlorine Binding Sites List in 5ve4
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl402

b:68.6
occ:1.00
 OG B:SER314 2.6 97.4 1.0
N B:GLY318 2.9 88.0 1.0
N B:ARG319 3.1 94.7 1.0
N B:GLY317 3.3 87.2 1.0
CB B:SER314 3.4 0.7 1.0
N B:ALA316 3.4 93.2 1.0
CD2 C:LEU198 3.6 91.2 1.0
CA B:GLY318 3.6 88.9 1.0
N B:ARG315 3.7 97.1 1.0
OD1 C:ASP202 3.7 0.6 1.0
CG C:ASP202 3.8 0.1 1.0
NE B:ARG319 3.8 0.9 1.0
C B:GLY317 3.9 84.9 1.0
CG B:ARG319 3.9 0.9 1.0
C B:GLY318 3.9 91.6 1.0
C B:ALA316 4.0 87.1 1.0
CB B:ARG319 4.0 0.7 1.0
CA B:GLY317 4.0 84.6 1.0
CA B:ALA316 4.1 90.4 1.0
CA B:ARG319 4.1 97.8 1.0
OD2 C:ASP202 4.1 0.8 1.0
CB C:ASP202 4.2 99.5 1.0
C B:ARG315 4.3 94.3 1.0
C B:SER314 4.3 94.8 1.0
CA B:ARG315 4.3 97.7 1.0
CB B:ARG315 4.4 0.3 1.0
CB B:ALA316 4.4 92.2 1.0
CA B:SER314 4.4 95.3 1.0
CD B:ARG319 4.5 0.0 1.0
N B:SER320 4.6 93.1 1.0
CZ B:ARG319 4.7 0.5 1.0
NH2 B:ARG319 4.7 0.7 1.0
C B:ARG319 4.9 96.4 1.0
O B:ALA316 4.9 84.8 1.0

Chlorine binding site 3 out of 3 in 5ve4

Go back to Chlorine Binding Sites List in 5ve4
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl402

b:43.5
occ:1.00
 OG C:SER314 2.8 56.6 1.0
N C:GLY318 3.1 58.5 1.0
OD1 B:ASP202 3.2 71.8 1.0
CG B:ASP202 3.3 70.7 1.0
N C:ARG319 3.4 60.3 1.0
N C:ALA316 3.4 57.1 1.0
CB C:SER314 3.5 57.1 1.0
N C:GLY317 3.5 56.4 1.0
CD2 B:LEU198 3.5 64.4 1.0
N C:ARG315 3.6 57.2 1.0
OD2 B:ASP202 3.6 70.6 1.0
NE C:ARG319 3.8 62.4 1.0
CA C:GLY318 3.8 60.4 1.0
CB B:ASP202 3.9 69.7 1.0
CG C:ARG319 4.0 62.8 1.0
C C:GLY318 4.1 61.0 1.0
C C:ALA316 4.1 57.0 1.0
C C:GLY317 4.1 58.1 1.0
CB C:ARG315 4.2 59.4 1.0
CB C:ARG319 4.2 61.6 1.0
CA C:ALA316 4.2 57.4 1.0
CA C:ARG315 4.2 57.8 1.0
CA C:GLY317 4.2 56.8 1.0
C C:ARG315 4.3 57.2 1.0
C C:SER314 4.3 56.5 1.0
CA C:ARG319 4.3 61.4 1.0
NH2 C:ARG319 4.5 62.4 1.0
CA C:SER314 4.5 56.7 1.0
CB C:ALA316 4.5 59.0 1.0
CD C:ARG319 4.5 63.7 1.0
CZ C:ARG319 4.6 63.1 1.0
N C:SER320 4.8 68.4 1.0
CA B:ASP202 4.9 70.5 1.0
CG B:LEU198 5.0 62.5 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: Fri Jul 26 18:48:46 2024

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