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Chlorine in PDB 5yfs: Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate

Enzymatic activity of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate

All present enzymatic activity of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate:
5.3.1.29;

Protein crystallography data

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate, PDB code: 5yfs 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) 85.58 / 2.30
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 98.650, 98.650, 256.731, 90.00, 90.00, 120.00
R / Rfree (%) 14.4 / 19.8

Other elements in 5yfs:

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-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 Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate (pdb code 5yfs). 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 Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate, PDB code: 5yfs:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5yfs

Go back to Chlorine Binding Sites List in 5yfs
Chlorine binding site 1 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-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 Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:56.4
occ:1.00
 O C:HOH643 3.2 57.0 1.0
N A:VAL251 3.3 22.9 1.0
CA A:LEU250 3.9 28.8 1.0
CG2 A:VAL251 3.9 21.6 1.0
CB A:VAL251 4.0 20.8 1.0
CD2 A:LEU250 4.0 41.2 1.0
C A:LEU250 4.1 26.1 1.0
CA A:VAL251 4.2 21.4 1.0
CB A:LEU250 4.4 30.8 1.0
CG2 A:THR207 4.5 20.4 1.0
CD1 A:ILE213 4.6 24.1 1.0
O A:VAL251 4.6 22.8 1.0
O A:GLN249 4.7 25.4 1.0
CG A:LEU250 4.9 35.9 1.0
C A:VAL251 4.9 20.5 1.0

Chlorine binding site 2 out of 3 in 5yfs

Go back to Chlorine Binding Sites List in 5yfs
Chlorine binding site 2 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-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 Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:51.8
occ:1.00
 O B:HOH678 2.5 46.1 1.0
N B:VAL251 3.5 26.4 1.0
CD2 B:LEU250 3.9 35.6 1.0
CA B:LEU250 4.1 27.9 1.0
CB B:VAL251 4.1 25.9 1.0
CG2 B:VAL251 4.2 28.2 1.0
C B:LEU250 4.3 27.1 1.0
CA B:VAL251 4.3 24.4 1.0
O B:VAL251 4.4 23.0 1.0
CB B:LEU250 4.4 30.6 1.0
CD1 B:ILE213 4.6 29.6 1.0
CG2 B:THR207 4.7 19.9 1.0
CG B:LEU250 4.8 35.0 1.0
C B:VAL251 4.9 23.2 1.0

Chlorine binding site 3 out of 3 in 5yfs

Go back to Chlorine Binding Sites List in 5yfs
Chlorine binding site 3 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-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 Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:58.0
occ:1.00
 O C:HOH661 2.5 40.0 1.0
O B:HOH616 3.2 56.5 1.0
N C:VAL251 3.5 24.6 1.0
CD2 C:LEU250 4.0 30.6 1.0
CB C:VAL251 4.1 25.9 1.0
CA C:LEU250 4.1 25.5 1.0
CG2 C:VAL251 4.2 26.8 1.0
C C:LEU250 4.3 25.0 1.0
CA C:VAL251 4.3 25.0 1.0
O C:VAL251 4.4 29.3 1.0
CB C:LEU250 4.5 26.7 1.0
CD1 C:ILE213 4.5 27.2 1.0
CG2 C:THR207 4.7 18.6 1.0
CG C:LEU250 4.9 29.1 1.0
C C:VAL251 4.9 25.5 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 21:23:12 2024

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