Chlorine in PDB 7op9: Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine

Enzymatic activity of Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine

All present enzymatic activity of Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine:
2.4.2.1;

Protein crystallography data

The structure of Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine, PDB code: 7op9 was solved by M.Narczyk, Z.Stefanic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.59 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 93.419, 93.428, 95.459, 81.91, 79.35, 60.09
R / Rfree (%) 17.3 / 19.6

Other elements in 7op9:

The structure of Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine also contains other interesting chemical elements:

Magnesium (Mg) 12 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Chlorine atom in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine (pdb code 7op9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 24 binding sites of Chlorine where determined in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine, PDB code: 7op9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 24 in 7op9

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Chlorine binding site 1 out of 24 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


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(Deod-Type) From H. Pylori with 2,6- Dichloropurine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:22.6
occ:1.00
 CL1 A:06K301 0.0 22.6 1.0
C2 A:06K301 1.7 17.6 1.0
N1 A:06K301 2.6 16.1 1.0
N3 A:06K301 2.7 16.6 1.0
OD2 A:ASP204 3.3 20.8 1.0
CB A:ASP204 3.5 21.2 1.0
O A:HOH454 3.6 21.0 1.0
CG A:ASP204 3.7 21.6 1.0
O A:HOH547 3.8 24.4 1.0
CA A:GLY92 3.8 14.6 1.0
C6 A:06K301 3.8 15.6 1.0
CD2 A:LEU206 3.9 18.4 1.0
C4 A:06K301 3.9 13.7 1.0
N A:GLY92 4.1 10.9 1.0
OG A:SER203 4.2 20.4 1.0
O A:HOH611 4.3 37.1 1.0
O A:HOH598 4.3 26.4 1.0
C5 A:06K301 4.4 16.6 1.0
O A:CYS91 4.4 14.8 1.0
CZ A:PHE159 4.4 12.8 1.0
C A:CYS91 4.4 14.9 1.0
CE1 A:PHE159 4.5 14.7 1.0
O A:HOH564 4.7 33.8 1.0
CA A:ASP204 4.7 19.0 1.0
OD1 A:ASP204 4.7 26.1 1.0
N A:ASP204 4.8 19.4 1.0
O A:HOH613 4.9 37.3 1.0
O A:ASP204 4.9 18.6 1.0
CG A:LEU206 4.9 17.4 1.0

Chlorine binding site 2 out of 24 in 7op9

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Chlorine binding site 2 out of 24 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


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(Deod-Type) From H. Pylori with 2,6- Dichloropurine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:21.5
occ:1.00
 CL2 A:06K301 0.0 21.5 1.0
C6 A:06K301 1.7 15.6 1.0
N1 A:06K301 2.7 16.1 1.0
C5 A:06K301 2.7 16.6 1.0
N1 D:IMD302 3.2 25.7 1.0
O A:THR90 3.2 16.2 1.0
C5 D:IMD302 3.3 18.1 1.0
N7 A:06K301 3.3 15.0 1.0
O A:HOH531 3.6 15.9 1.0
CA A:CYS91 3.6 12.1 1.0
CA A:GLU179 3.7 11.9 1.0
O A:HOH415 3.7 21.2 1.0
CB A:GLU179 3.7 11.8 1.0
C A:THR90 3.8 13.5 1.0
O A:ILE178 3.8 12.3 1.0
C2 A:06K301 3.9 17.6 1.0
O A:HOH454 3.9 21.0 1.0
C4 A:06K301 4.0 13.7 1.0
N A:CYS91 4.0 12.3 1.0
C2 D:IMD302 4.1 22.6 1.0
C4 D:IMD302 4.2 17.5 1.0
OG1 A:THR90 4.3 18.1 1.0
C A:CYS91 4.4 14.9 1.0
N3 A:06K301 4.4 16.6 1.0
N A:GLY92 4.5 10.9 1.0
C8 A:06K301 4.6 12.9 1.0
N3 D:IMD302 4.6 19.1 1.0
C A:GLU179 4.6 12.1 1.0
CB A:CYS91 4.6 12.3 1.0
C A:ILE178 4.6 11.1 1.0
N A:GLU179 4.7 9.3 1.0
N A:MET180 4.8 12.1 1.0
CE1 A:PHE159 4.9 14.7 1.0
N9 A:06K301 4.9 14.0 1.0
CA A:THR90 4.9 11.9 1.0

Chlorine binding site 3 out of 24 in 7op9

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Chlorine binding site 3 out of 24 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


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(Deod-Type) From H. Pylori with 2,6- Dichloropurine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:21.5
occ:1.00
 CL1 B:06K301 0.0 21.5 1.0
C2 B:06K301 1.8 15.4 1.0
N1 B:06K301 2.6 14.7 1.0
N3 B:06K301 2.7 14.4 1.0
OD2 B:ASP204 3.5 21.8 1.0
O B:HOH450 3.6 19.2 1.0
CB B:ASP204 3.7 22.1 1.0
O B:HOH570 3.8 29.9 1.0
CA B:GLY92 3.8 9.8 1.0
C6 B:06K301 3.9 12.8 1.0
CG B:ASP204 3.9 25.1 1.0
C4 B:06K301 3.9 13.1 1.0
CD2 B:LEU206 4.0 18.2 1.0
O B:HOH572 4.0 34.1 1.0
N B:GLY92 4.1 10.1 1.0
O B:HOH633 4.3 38.2 1.0
O B:CYS91 4.3 14.7 1.0
C B:CYS91 4.4 14.6 1.0
OG B:SER203 4.4 23.9 1.0
O B:HOH627 4.4 28.9 1.0
C5 B:06K301 4.4 12.0 1.0
CZ B:PHE159 4.5 14.6 1.0
CE1 B:PHE159 4.6 13.2 1.0
O B:HOH649 4.7 38.3 1.0
CA B:ASP204 4.9 20.8 1.0
OD1 B:ASP204 4.9 31.3 1.0
CG B:LEU206 5.0 15.9 1.0
N B:ASP204 5.0 19.6 1.0

Chlorine binding site 4 out of 24 in 7op9

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Chlorine binding site 4 out of 24 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


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(Deod-Type) From H. Pylori with 2,6- Dichloropurine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:20.3
occ:1.00
 CL2 B:06K301 0.0 20.3 1.0
C6 B:06K301 1.8 12.8 1.0
N1 B:06K301 2.7 14.7 1.0
C5 B:06K301 2.7 12.0 1.0
N1 E:IMD302 3.0 21.4 1.0
N7 B:06K301 3.3 15.9 1.0
C5 E:IMD302 3.3 16.4 1.0
O B:THR90 3.4 15.5 1.0
O B:HOH482 3.5 15.9 1.0
O B:HOH478 3.7 19.4 1.0
CA B:GLU179 3.7 11.6 1.0
CA B:CYS91 3.8 14.3 1.0
CB B:GLU179 3.8 11.4 1.0
C2 B:06K301 3.9 15.4 1.0
O B:ILE178 3.9 11.6 1.0
C2 E:IMD302 3.9 20.6 1.0
O B:HOH450 4.0 19.2 1.0
C B:THR90 4.0 13.6 1.0
C4 B:06K301 4.0 13.1 1.0
N B:CYS91 4.1 13.6 1.0
OG1 B:THR90 4.3 16.5 1.0
C4 E:IMD302 4.3 17.3 1.0
N3 B:06K301 4.4 14.4 1.0
C B:CYS91 4.5 14.6 1.0
C8 B:06K301 4.5 11.2 1.0
N B:GLY92 4.6 10.1 1.0
N3 E:IMD302 4.6 17.5 1.0
C B:GLU179 4.6 12.6 1.0
C B:ILE178 4.7 10.1 1.0
N B:GLU179 4.7 10.3 1.0
N B:MET180 4.7 10.7 1.0
CB B:CYS91 4.8 13.3 1.0
CE1 B:PHE159 4.9 13.2 1.0
N9 B:06K301 4.9 13.5 1.0

Chlorine binding site 5 out of 24 in 7op9

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Chlorine binding site 5 out of 24 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


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(Deod-Type) From H. Pylori with 2,6- Dichloropurine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:23.1
occ:1.00
 CL1 C:06K301 0.0 23.1 1.0
C2 C:06K301 1.8 16.8 1.0
N1 C:06K301 2.6 15.0 1.0
N3 C:06K301 2.7 15.4 1.0
CB C:ASP204 3.4 22.4 1.0
OD1 C:ASP204 3.6 27.3 1.0
CG C:ASP204 3.6 25.1 1.0
O C:HOH561 3.7 32.5 1.0
O C:HOH487 3.7 18.8 1.0
CD2 C:LEU206 3.8 19.5 1.0
O C:HOH569 3.8 26.6 1.0
C6 C:06K301 3.9 12.8 1.0
C4 C:06K301 3.9 12.4 1.0
CA C:GLY92 4.0 12.2 1.0
O C:HOH618 4.1 29.3 1.0
CZ C:PHE159 4.3 14.1 1.0
N C:GLY92 4.4 12.8 1.0
O C:HOH604 4.4 27.5 1.0
C5 C:06K301 4.4 13.3 1.0
CE2 C:PHE159 4.4 12.6 1.0
OD2 C:ASP204 4.5 31.6 1.0
O C:CYS91 4.6 14.6 1.0
O C:HOH450 4.7 31.9 1.0
C C:CYS91 4.7 13.0 1.0
CA C:ASP204 4.8 20.4 1.0
CG C:LEU206 4.9 19.1 1.0
OG C:SER203 4.9 27.0 1.0

Chlorine binding site 6 out of 24 in 7op9

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Chlorine binding site 6 out of 24 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


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(Deod-Type) From H. Pylori with 2,6- Dichloropurine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:18.9
occ:1.00
 CL2 C:06K301 0.0 18.9 1.0
C6 C:06K301 1.7 12.8 1.0
N1 C:06K301 2.7 15.0 1.0
C5 C:06K301 2.7 13.3 1.0
N1 F:IMD302 3.1 23.9 1.0
N7 C:06K301 3.2 13.8 1.0
C5 F:IMD302 3.3 17.4 1.0
O C:THR90 3.3 15.0 1.0
CA C:CYS91 3.6 11.1 1.0
O C:HOH464 3.7 16.5 1.0
CA C:GLU179 3.8 10.9 1.0
O C:HOH487 3.8 18.8 1.0
CB C:GLU179 3.8 12.8 1.0
O C:ILE178 3.8 11.8 1.0
C C:THR90 3.9 13.6 1.0
C2 C:06K301 3.9 16.8 1.0
O C:HOH445 3.9 19.4 1.0
C4 C:06K301 4.0 12.4 1.0
N C:CYS91 4.0 12.4 1.0
C2 F:IMD302 4.1 19.1 1.0
C4 F:IMD302 4.3 18.0 1.0
OG1 C:THR90 4.3 17.2 1.0
C C:CYS91 4.3 13.0 1.0
N3 C:06K301 4.4 15.4 1.0
N C:GLY92 4.4 12.8 1.0
C8 C:06K301 4.5 12.1 1.0
N3 F:IMD302 4.6 17.6 1.0
CB C:CYS91 4.7 12.7 1.0
C C:ILE178 4.7 10.4 1.0
C C:GLU179 4.7 10.5 1.0
N C:GLU179 4.7 10.6 1.0
N C:MET180 4.8 11.7 1.0
CE2 C:PHE159 4.9 12.6 1.0
CG C:MET180 4.9 12.0 1.0
N9 C:06K301 4.9 12.1 1.0
CA C:THR90 5.0 12.3 1.0

Chlorine binding site 7 out of 24 in 7op9

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Chlorine binding site 7 out of 24 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


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(Deod-Type) From H. Pylori with 2,6- Dichloropurine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:23.4
occ:1.00
 CL1 D:06K301 0.0 23.4 1.0
C2 D:06K301 1.8 18.8 1.0
N1 D:06K301 2.6 16.2 1.0
N3 D:06K301 2.7 18.2 1.0
OD2 D:ASP204 3.3 24.0 1.0
O D:HOH481 3.5 19.0 1.0
CB D:ASP204 3.6 21.7 1.0
CG D:ASP204 3.7 25.4 1.0
CA D:GLY92 3.8 13.3 1.0
C6 D:06K301 3.8 16.0 1.0
O D:HOH507 3.9 28.9 1.0
CD2 D:LEU206 3.9 22.6 1.0
C4 D:06K301 3.9 17.3 1.0
O D:HOH552 4.1 31.3 1.0
N D:GLY92 4.1 14.3 1.0
O D:HOH611 4.2 36.6 1.0
OG D:SER203 4.3 25.1 1.0
O D:CYS91 4.4 18.2 1.0
C5 D:06K301 4.4 11.8 1.0
O D:HOH606 4.4 26.6 1.0
C D:CYS91 4.4 17.2 1.0
CZ D:PHE159 4.5 15.2 1.0
CE1 D:PHE159 4.6 15.5 1.0
OD1 D:ASP204 4.8 32.1 1.0
CA D:ASP204 4.8 21.4 1.0
CG D:LEU206 4.8 20.6 1.0
N D:ASP204 4.9 20.4 1.0
O D:ASP204 5.0 20.3 1.0

Chlorine binding site 8 out of 24 in 7op9

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Chlorine binding site 8 out of 24 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:21.6
occ:1.00
 CL2 D:06K301 0.0 21.6 1.0
C6 D:06K301 1.8 16.0 1.0
N1 D:06K301 2.7 16.2 1.0
C5 D:06K301 2.7 11.8 1.0
N1 A:IMD302 3.2 23.2 1.0
N7 D:06K301 3.3 17.7 1.0
C5 A:IMD302 3.3 17.7 1.0
O D:THR90 3.4 17.5 1.0
O D:HOH546 3.4 19.2 1.0
CA D:GLU179 3.7 14.1 1.0
CA D:CYS91 3.8 15.1 1.0
CB D:GLU179 3.8 10.8 1.0
C2 D:06K301 3.9 18.8 1.0
O D:HOH481 3.9 19.0 1.0
O D:HOH478 3.9 25.0 1.0
O D:ILE178 3.9 13.9 1.0
C D:THR90 3.9 16.9 1.0
C4 D:06K301 4.0 17.3 1.0
C2 A:IMD302 4.1 19.6 1.0
N D:CYS91 4.1 14.9 1.0
OG1 D:THR90 4.3 17.9 1.0
C4 A:IMD302 4.3 17.2 1.0
N3 D:06K301 4.4 18.2 1.0
C D:CYS91 4.5 17.2 1.0
N D:GLY92 4.5 14.3 1.0
C8 D:06K301 4.6 13.3 1.0
C D:GLU179 4.6 10.8 1.0
N3 A:IMD302 4.6 19.2 1.0
C D:ILE178 4.7 11.8 1.0
N D:GLU179 4.7 10.9 1.0
CB D:CYS91 4.8 14.4 1.0
N D:MET180 4.8 12.6 1.0
CE1 D:PHE159 4.9 15.5 1.0
N9 D:06K301 4.9 14.8 1.0

Chlorine binding site 9 out of 24 in 7op9

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Chlorine binding site 9 out of 24 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl301

b:23.3
occ:1.00
 CL1 E:06K301 0.0 23.3 1.0
C2 E:06K301 1.8 16.8 1.0
N1 E:06K301 2.6 15.1 1.0
N3 E:06K301 2.7 18.8 1.0
O E:HOH423 3.7 20.7 1.0
OD2 E:ASP204 3.7 25.1 1.0
CA E:GLY92 3.7 15.0 1.0
CD2 E:LEU206 3.8 21.0 1.0
C6 E:06K301 3.9 17.5 1.0
CB E:ASP204 3.9 19.4 1.0
C4 E:06K301 3.9 17.3 1.0
N E:GLY92 4.0 13.3 1.0
CG E:ASP204 4.1 25.1 1.0
O E:CYS91 4.3 16.6 1.0
C E:CYS91 4.4 16.9 1.0
OG E:SER203 4.4 28.0 1.0
C5 E:06K301 4.4 16.6 1.0
O E:HOH622 4.6 38.6 1.0
CE1 E:PHE159 4.7 16.2 1.0
CG E:LEU206 4.8 19.2 1.0
CZ E:PHE159 4.8 17.1 1.0
O E:HOH580 4.9 35.0 1.0
CA E:ASP204 5.0 20.7 1.0

Chlorine binding site 10 out of 24 in 7op9

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Chlorine binding site 10 out of 24 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl301

b:23.6
occ:1.00
 CL2 E:06K301 0.0 23.6 1.0
C6 E:06K301 1.8 17.5 1.0
N1 E:06K301 2.7 15.1 1.0
C5 E:06K301 2.8 16.6 1.0
N1 B:IMD302 3.1 23.0 1.0
O E:HOH534 3.2 18.4 1.0
C5 B:IMD302 3.3 22.8 1.0
N7 E:06K301 3.3 18.0 1.0
O E:THR90 3.4 16.3 1.0
O E:HOH479 3.7 27.8 1.0
CA E:GLU179 3.7 11.5 1.0
CB E:GLU179 3.8 11.5 1.0
O E:HOH423 3.8 20.7 1.0
CA E:CYS91 3.9 13.0 1.0
C2 E:06K301 3.9 16.8 1.0
O E:ILE178 4.0 12.9 1.0
C E:THR90 4.0 14.3 1.0
C4 E:06K301 4.0 17.3 1.0
C2 B:IMD302 4.1 20.5 1.0
OG1 E:THR90 4.3 19.0 1.0
N E:CYS91 4.3 14.1 1.0
C4 B:IMD302 4.3 21.1 1.0
N3 E:06K301 4.5 18.8 1.0
C E:CYS91 4.6 16.9 1.0
C E:GLU179 4.6 11.9 1.0
C8 E:06K301 4.6 14.1 1.0
N E:GLY92 4.7 13.3 1.0
CG E:MET180 4.7 15.2 1.0
N E:MET180 4.7 11.3 1.0
N E:GLU179 4.7 11.2 1.0
N3 B:IMD302 4.7 19.3 1.0
C E:ILE178 4.8 12.4 1.0
CB E:CYS91 4.9 14.2 1.0
N9 E:06K301 5.0 17.8 1.0

Reference:

M.Narczyk, M.I.Wojtys, I.Lescic Asler, B.Zinic, M.Luic, E.K.Jagusztyn-Krynicka, Z.Stefanic, A.Bzowska. Interactions of 2,6-Substituted Purines with Purine Nucleoside Phosphorylase From Helicobacter Pylori in Solution and in the Crystal, and the Effects of These Compounds on Cell Cultures of This Bacterium. J Enzyme Inhib Med Chem V. 37 1083 2022.
ISSN: ESSN 1475-6374
PubMed: 35437103
DOI: 10.1080/14756366.2022.2061965
Page generated: Tue Jul 30 02:00:16 2024

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