Chlorine in PDB 8c25: Purine Nucleoside Phosphorylase in Complex with Js-375

Enzymatic activity of Purine Nucleoside Phosphorylase in Complex with Js-375

All present enzymatic activity of Purine Nucleoside Phosphorylase in Complex with Js-375:
2.4.2.1;

Protein crystallography data

The structure of Purine Nucleoside Phosphorylase in Complex with Js-375, PDB code: 8c25 was solved by S.Djukic, P.Pachl, P.Rezacova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.28 / 1.56
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 125.12, 125.12, 125.12, 90, 90, 90
R / Rfree (%) 15.3 / 18.5

Other elements in 8c25:

The structure of Purine Nucleoside Phosphorylase in Complex with Js-375 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Purine Nucleoside Phosphorylase in Complex with Js-375 (pdb code 8c25). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Purine Nucleoside Phosphorylase in Complex with Js-375, PDB code: 8c25:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 8c25

Go back to Chlorine Binding Sites List in 8c25
Chlorine binding site 1 out of 7 in the Purine Nucleoside Phosphorylase in Complex with Js-375


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Purine Nucleoside Phosphorylase in Complex with Js-375 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:21.1
occ:1.00
 N A:GLY37 3.1 14.4 1.0
CD A:PRO40 3.5 16.3 1.0
CA A:SER36 3.7 16.1 1.0
CB A:LEU39 3.7 15.5 1.0
N A:LEU39 3.7 13.8 1.0
C A:SER36 3.9 14.3 1.0
CA A:GLY37 4.0 14.3 1.0
N A:TRP38 4.1 13.0 1.0
CD2 A:LEU247 4.1 16.6 1.0
C A:GLY37 4.2 13.9 1.0
O A:HOH454 4.3 49.7 1.0
CA A:LEU39 4.3 13.5 1.0
CD2 A:LEU39 4.3 24.1 1.0
O A:GLY35 4.3 17.1 1.0
CG A:PRO40 4.4 17.3 1.0
CG A:LEU39 4.5 19.3 1.0
CB A:SER36 4.6 17.0 1.0
N A:PRO40 4.6 14.8 1.0
N A:SER36 4.7 16.6 1.0
C A:TRP38 4.8 13.6 1.0
C A:GLY35 4.9 17.8 1.0
C A:LEU39 4.9 15.4 1.0

Chlorine binding site 2 out of 7 in 8c25

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Chlorine binding site 2 out of 7 in the Purine Nucleoside Phosphorylase in Complex with Js-375


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Purine Nucleoside Phosphorylase in Complex with Js-375 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:18.8
occ:1.00
 O A:HOH672 3.0 36.9 1.0
N A:ARG88 3.3 15.9 1.0
CE1 A:HIS90 3.5 16.4 1.0
N A:SER36 3.5 16.6 1.0
CA A:GLY35 3.6 16.3 1.0
CA A:GLY87 3.8 15.3 1.0
OG A:SER36 3.8 24.1 1.0
O A:ARG88 3.8 23.1 1.0
O A:HOH422 3.9 41.7 1.0
C A:GLY35 4.0 17.8 1.0
C A:GLY87 4.1 16.6 1.0
CB A:ARG88 4.2 20.9 1.0
CA A:ARG88 4.3 17.5 1.0
O A:HOH454 4.3 49.7 1.0
NE2 A:HIS90 4.3 14.9 1.0
CD2 A:LEU39 4.4 24.1 1.0
ND1 A:HIS90 4.5 15.7 1.0
CA A:SER36 4.5 16.1 1.0
C A:ARG88 4.5 20.2 1.0
O A:HOH491 4.6 34.2 1.0
O A:LEU34 4.6 16.1 1.0
O4 A:JU9301 4.7 16.9 1.0
CB A:SER36 4.8 17.0 1.0
CG A:ARG88 4.8 15.5 1.0
N A:GLY87 4.8 14.1 1.0
N A:GLY35 4.9 16.1 1.0

Chlorine binding site 3 out of 7 in 8c25

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Chlorine binding site 3 out of 7 in the Purine Nucleoside Phosphorylase in Complex with Js-375


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Purine Nucleoside Phosphorylase in Complex with Js-375 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:22.1
occ:1.00
 O A:HOH405 2.9 38.6 1.0
OG1 A:THR237 2.9 20.0 0.5
O A:HOH486 2.9 16.4 0.5
O A:HOH728 3.0 31.7 1.0
N A:LEU232 3.2 10.6 1.0
CA A:ASN231 3.7 10.7 1.0
CB A:THR237 3.8 22.0 0.5
C A:ASN231 3.9 10.2 1.0
CB A:ASN231 3.9 10.1 1.0
CG2 A:VAL130 4.0 16.9 1.0
O A:HOH407 4.0 25.5 1.0
CB A:LEU232 4.1 12.0 1.0
CA A:LEU232 4.2 10.2 1.0
CG2 A:THR237 4.2 18.1 0.5
CG A:LEU232 4.2 16.9 1.0
O A:LEU232 4.4 10.6 1.0
OE1 A:GLU239 4.4 31.7 0.5
O A:HOH727 4.5 50.7 1.0
CG A:GLU239 4.5 30.5 0.5
CA A:THR237 4.6 22.1 0.5
OE1 A:GLU245 4.6 20.4 1.0
O A:HOH457 4.7 20.4 1.0
C A:LEU232 4.8 10.7 1.0
CB A:GLU239 4.8 25.1 0.5
CD A:GLU239 4.9 35.8 0.5
CG2 A:THR237 4.9 21.8 0.5
O A:HOH465 5.0 12.4 0.5
CD1 A:LEU232 5.0 19.3 1.0
N A:ASN231 5.0 10.8 1.0
OG1 A:THR237 5.0 16.7 0.5

Chlorine binding site 4 out of 7 in 8c25

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Chlorine binding site 4 out of 7 in the Purine Nucleoside Phosphorylase in Complex with Js-375


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Purine Nucleoside Phosphorylase in Complex with Js-375 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:19.5
occ:1.00
 OG1 B:THR237 3.0 17.6 1.0
N B:LEU232 3.1 10.5 1.0
O B:HOH538 3.4 30.6 1.0
CB B:THR237 3.7 18.4 1.0
CA B:ASN231 3.9 10.8 1.0
CB B:LEU232 3.9 11.8 1.0
C B:ASN231 4.0 9.8 1.0
CG B:LEU232 4.0 13.9 1.0
CA B:LEU232 4.1 10.6 1.0
O B:HOH427 4.1 17.6 1.0
CG2 B:VAL130 4.1 13.6 1.0
CB B:ASN231 4.3 10.9 1.0
CA B:THR237 4.3 19.1 1.0
O B:LEU232 4.5 11.6 1.0
CD1 B:LEU232 4.7 16.4 1.0
C B:LEU232 4.8 10.3 1.0
OE1 B:GLU245 4.8 16.2 1.0
CG B:GLU239 4.9 26.1 1.0
CG2 B:THR237 5.0 19.1 1.0
N B:GLY238 5.0 22.0 1.0
CB B:GLU239 5.0 21.6 1.0
O B:HOH532 5.0 21.2 1.0

Chlorine binding site 5 out of 7 in 8c25

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Chlorine binding site 5 out of 7 in the Purine Nucleoside Phosphorylase in Complex with Js-375


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Purine Nucleoside Phosphorylase in Complex with Js-375 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl305

b:25.4
occ:1.00
 N B:GLY37 3.0 15.8 1.0
O B:HOH459 3.3 26.3 1.0
O B:HOH641 3.5 26.9 1.0
CD B:PRO40 3.5 18.9 1.0
CB B:LEU39 3.8 17.1 1.0
CD2 B:LEU247 3.8 19.6 1.0
CA B:SER36 3.9 19.3 1.0
CA B:GLY37 3.9 15.9 1.0
N B:LEU39 3.9 17.4 1.0
C B:SER36 3.9 16.6 1.0
CG B:LEU39 4.0 20.4 1.0
CD1 B:LEU39 4.1 23.6 1.0
C B:GLY37 4.2 14.2 1.0
N B:TRP38 4.2 15.4 1.0
CG B:PRO40 4.4 22.0 1.0
CA B:LEU39 4.4 17.0 1.0
O B:GLY35 4.6 19.2 1.0
CB B:SER36 4.7 22.3 1.0
N B:PRO40 4.7 18.4 1.0
N B:SER36 4.9 18.0 1.0
CA B:LEU247 4.9 14.4 1.0
O B:HOH637 4.9 38.0 1.0
C B:TRP38 4.9 15.8 1.0
O B:GLY37 5.0 16.4 1.0

Chlorine binding site 6 out of 7 in 8c25

Go back to Chlorine Binding Sites List in 8c25
Chlorine binding site 6 out of 7 in the Purine Nucleoside Phosphorylase in Complex with Js-375


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Purine Nucleoside Phosphorylase in Complex with Js-375 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl306

b:24.8
occ:1.00
 O B:HOH444 2.8 40.0 1.0
O B:HOH659 3.4 35.1 1.0
N B:ARG88 3.4 19.9 1.0
O B:HOH664 3.4 47.3 1.0
CE1 B:HIS90 3.6 19.2 1.0
CA B:GLY35 3.6 18.5 1.0
N B:SER36 3.6 18.0 1.0
O B:ARG88 3.7 24.9 1.0
O B:HOH457 3.7 43.4 1.0
CA B:GLY87 3.8 19.2 1.0
OG B:SER36 3.9 28.2 1.0
C B:GLY35 4.0 16.7 1.0
C B:GLY87 4.1 21.1 1.0
CG B:ARG88 4.2 21.1 1.0
CD1 B:LEU39 4.3 23.6 1.0
NE2 B:HIS90 4.4 17.5 1.0
CA B:ARG88 4.4 20.6 1.0
C B:ARG88 4.5 20.4 1.0
ND1 B:HIS90 4.6 18.5 1.0
O B:LEU34 4.6 16.9 1.0
CA B:SER36 4.6 19.3 1.0
CD2 B:LEU39 4.7 21.6 1.0
N B:GLY87 4.8 17.9 1.0
CG B:LEU39 4.8 20.4 1.0
O3 B:JU9301 4.9 20.8 1.0
CB B:SER36 4.9 22.3 1.0
CB B:ARG88 4.9 21.5 1.0
N B:GLY35 4.9 17.0 1.0
O B:GLY35 5.0 19.2 1.0

Chlorine binding site 7 out of 7 in 8c25

Go back to Chlorine Binding Sites List in 8c25
Chlorine binding site 7 out of 7 in the Purine Nucleoside Phosphorylase in Complex with Js-375


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Purine Nucleoside Phosphorylase in Complex with Js-375 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl307

b:36.6
occ:1.00
 O B:HOH410 3.1 30.7 0.5
N B:ARG163 3.3 14.2 1.0
CB B:ARG163 3.4 19.7 1.0
O B:HOH555 3.5 44.1 1.0
CD B:PRO162 3.5 14.8 1.0
OG B:SER161 3.5 15.0 1.0
N B:PRO162 3.7 13.3 1.0
CB B:PRO162 4.0 16.0 1.0
CA B:ARG163 4.0 16.2 1.0
CG B:PRO162 4.0 16.6 1.0
CA B:PRO162 4.2 13.8 1.0
C B:PRO162 4.2 13.9 1.0
C B:SER161 4.4 12.6 1.0
CA B:SER161 4.5 12.8 1.0
CB B:SER161 4.5 13.9 1.0
O B:HOH521 4.6 36.5 1.0
CG B:ARG163 4.7 26.1 1.0
O B:HOH533 4.8 29.3 1.0
OE1 B:GLU222 4.8 36.7 1.0
CD B:ARG163 4.9 27.7 1.0

Reference:

J.Skacel, S.Djukic, O.Baszczynski, F.Kalcic, T.Bilek, K.Chalupsky, J.Kozak, A.Dvorakova, E.Tloust'ova, Z.Kral'ova, M.Smidkova, J.Voldrich, M.Rumlova, P.Pachl, J.Brynda, T.Vuckova, M.Fabry, J.Snasel, I.Pichova, P.Rezacova, H.Mertlikova-Kaiserova, Z.Janeba. Design, Synthesis, Biological Evaluation, and Crystallographic Study of Novel Purine Nucleoside Phosphorylase Inhibitors. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37134237
DOI: 10.1021/ACS.JMEDCHEM.2C02097
Page generated: Wed Jul 26 15:46:35 2023

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