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Chlorine in PDB 5yfj: Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate

Enzymatic activity of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate

All present enzymatic activity of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate:
5.3.1.29;

Protein crystallography data

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate, PDB code: 5yfj was solved by P.Gogoi, S.P.Kanaujia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.69 / 2.20
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 98.630, 98.630, 257.061, 90.00, 90.00, 120.00
R / Rfree (%) 15 / 19

Other elements in 5yfj:

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate also contains other interesting chemical elements:

Potassium (K) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate (pdb code 5yfj). 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 Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate, PDB code: 5yfj:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5yfj

Go back to Chlorine Binding Sites List in 5yfj
Chlorine binding site 1 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate


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 Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:62.3
occ:1.00
 N A:VAL251 3.2 29.9 1.0
CB A:VAL251 3.9 31.6 1.0
CG2 A:VAL251 4.0 33.8 1.0
CA A:LEU250 4.0 33.5 1.0
CD2 A:LEU250 4.0 46.9 1.0
CA A:VAL251 4.1 32.2 1.0
C A:LEU250 4.1 31.1 1.0
O A:VAL251 4.3 30.3 1.0
CB A:LEU250 4.5 40.0 1.0
CG2 A:THR207 4.6 29.9 1.0
C A:VAL251 4.7 30.4 1.0
CD1 A:ILE213 4.8 35.5 1.0
CG A:LEU250 4.9 43.6 1.0

Chlorine binding site 2 out of 3 in 5yfj

Go back to Chlorine Binding Sites List in 5yfj
Chlorine binding site 2 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate


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 Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:62.4
occ:1.00
 N B:VAL251 3.4 33.8 1.0
CD2 B:LEU250 3.7 50.6 1.0
CG2 B:VAL251 3.9 31.7 1.0
CB B:VAL251 4.0 31.2 1.0
CA B:LEU250 4.1 37.0 1.0
CA B:VAL251 4.3 31.8 1.0
C B:LEU250 4.3 36.3 1.0
CG2 B:THR207 4.4 25.8 1.0
O B:VAL251 4.5 29.2 1.0
CD1 B:ILE213 4.6 28.9 1.0
CB B:LEU250 4.7 38.7 1.0
CG B:LEU250 4.8 44.5 1.0
C B:VAL251 4.9 28.9 1.0
O B:GLN249 5.0 30.8 1.0

Chlorine binding site 3 out of 3 in 5yfj

Go back to Chlorine Binding Sites List in 5yfj
Chlorine binding site 3 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate


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 Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:57.3
occ:1.00
 N C:VAL251 3.4 33.0 1.0
CD2 C:LEU250 3.8 52.4 1.0
CG2 C:VAL251 4.0 35.8 1.0
CB C:VAL251 4.0 34.1 1.0
CA C:LEU250 4.2 38.2 1.0
CA C:VAL251 4.3 32.9 1.0
C C:LEU250 4.3 37.6 1.0
O C:VAL251 4.4 32.1 1.0
CG2 C:THR207 4.5 29.6 1.0
CB C:LEU250 4.6 43.5 1.0
CD1 C:ILE213 4.7 36.8 1.0
CG C:LEU250 4.8 46.5 1.0
C C:VAL251 4.9 32.5 1.0

Reference:

P.Gogoi, S.P.Kanaujia. A Presumed Homologue of the Regulatory Subunits of EIF2B Functions As Ribose-1,5-Bisphosphate Isomerase in Pyrococcus Horikoshii OT3. Sci Rep V. 8 1891 2018.
ISSN: ESSN 2045-2322
PubMed: 29382938
DOI: 10.1038/S41598-018-20418-W
Page generated: Fri Jul 26 21:22:53 2024

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