Magnesium 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:

Chlorine (Cl) 24 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine, PDB code: 7op9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 7op9

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Magnesium binding site 1 out of 12 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg303

b:17.4
occ:1.00
 O A:HOH415 3.0 21.2 1.0
O A:HOH414 3.0 21.4 1.0
NH2 A:ARG24 3.2 24.4 1.0
NH2 D:ARG43 3.3 22.3 1.0
N A:THR90 3.3 13.8 1.0
O A:HOH496 3.4 19.6 1.0
OG1 A:THR90 3.6 18.1 1.0
O A:HOH481 3.7 28.1 1.0
CA A:GLY89 3.7 15.5 1.0
N1 D:IMD302 3.8 25.7 1.0
C A:GLY89 4.0 15.3 1.0
CZ D:ARG43 4.3 17.9 1.0
OD1 A:OCS19 4.3 28.4 1.0
NH1 D:ARG43 4.3 16.6 1.0
CA A:THR90 4.3 11.9 1.0
CB A:THR90 4.4 15.0 1.0
O A:THR90 4.5 16.2 1.0
CZ A:ARG24 4.5 26.5 1.0
C5 D:IMD302 4.5 18.1 1.0
OD2 A:OCS19 4.6 25.9 1.0
C2 D:IMD302 4.6 22.6 1.0
O A:HOH531 4.7 15.9 1.0
CG2 A:THR90 4.8 20.2 1.0
N A:GLY20 4.8 13.4 1.0
C A:THR90 4.8 13.5 1.0
NH1 A:ARG87 4.9 20.9 1.0
OE1 A:GLU181 4.9 20.5 1.0
CA A:GLY20 5.0 13.1 1.0

Magnesium binding site 2 out of 12 in 7op9

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Magnesium binding site 2 out of 12 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg303

b:17.2
occ:1.00
 O B:HOH478 3.0 19.4 1.0
O B:HOH402 3.2 18.1 1.0
NH2 E:ARG43 3.3 22.6 1.0
NH2 B:ARG24 3.3 24.5 1.0
N B:THR90 3.3 13.2 1.0
O B:HOH565 3.4 17.2 1.0
OG1 B:THR90 3.6 16.5 1.0
O B:HOH536 3.7 27.5 1.0
CA B:GLY89 3.7 13.2 1.0
N1 E:IMD302 3.8 21.4 1.0
C B:GLY89 4.0 13.2 1.0
CZ E:ARG43 4.3 19.3 1.0
CA B:THR90 4.4 11.3 1.0
NH1 E:ARG43 4.4 16.6 1.0
CB B:THR90 4.4 14.9 1.0
OD1 B:OCS19 4.5 27.2 1.0
O B:THR90 4.5 15.5 1.0
C5 E:IMD302 4.5 16.4 1.0
OD2 B:OCS19 4.6 21.3 1.0
CZ B:ARG24 4.6 25.7 1.0
O B:HOH482 4.6 15.9 1.0
C2 E:IMD302 4.6 20.6 1.0
CG2 B:THR90 4.7 18.3 1.0
C B:THR90 4.8 13.6 1.0
N B:GLY20 4.8 12.5 1.0
NH1 B:ARG87 4.9 22.0 1.0

Magnesium binding site 3 out of 12 in 7op9

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Magnesium binding site 3 out of 12 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
C:Mg303

b:17.4
occ:1.00
 O C:HOH445 2.9 19.4 1.0
O C:HOH416 3.0 20.9 1.0
NH2 C:ARG24 3.3 25.3 1.0
O C:HOH550 3.4 21.0 1.0
N C:THR90 3.4 14.1 1.0
NH2 F:ARG43 3.4 19.0 1.0
OG1 C:THR90 3.6 17.2 1.0
O C:HOH502 3.7 29.2 1.0
CA C:GLY89 3.7 15.1 1.0
N1 F:IMD302 3.7 23.9 1.0
C C:GLY89 4.1 15.6 1.0
OD1 C:OCS19 4.3 24.0 1.0
NH1 F:ARG43 4.3 15.0 1.0
CZ F:ARG43 4.3 18.7 1.0
CA C:THR90 4.4 12.3 1.0
O C:THR90 4.4 15.0 1.0
C5 F:IMD302 4.4 17.4 1.0
CB C:THR90 4.5 16.1 1.0
OD2 C:OCS19 4.5 20.9 1.0
O C:HOH464 4.5 16.5 1.0
CZ C:ARG24 4.5 24.6 1.0
C2 F:IMD302 4.6 19.1 1.0
C C:THR90 4.8 13.6 1.0
N C:GLY20 4.8 11.6 1.0
CG2 C:THR90 4.9 18.0 1.0
NH1 C:ARG87 4.9 21.6 1.0

Magnesium binding site 4 out of 12 in 7op9

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Magnesium binding site 4 out of 12 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
D:Mg303

b:21.3
occ:1.00
 O D:HOH478 2.9 25.0 1.0
O D:HOH411 3.0 20.4 1.0
NH2 D:ARG24 3.1 27.2 1.0
O D:HOH544 3.3 18.0 1.0
N D:THR90 3.4 13.7 1.0
NH2 A:ARG43 3.4 22.0 1.0
O D:HOH469 3.6 30.4 1.0
OG1 D:THR90 3.7 17.9 1.0
N1 A:IMD302 3.7 23.2 1.0
CA D:GLY89 3.8 16.0 1.0
C D:GLY89 4.1 16.2 1.0
NH1 A:ARG43 4.3 16.7 1.0
CZ A:ARG43 4.4 18.3 1.0
CA D:THR90 4.4 14.8 1.0
C5 A:IMD302 4.4 17.7 1.0
O D:THR90 4.4 17.5 1.0
CZ D:ARG24 4.4 28.2 1.0
CB D:THR90 4.5 16.6 1.0
OD1 D:OCS19 4.5 24.9 1.0
O D:HOH546 4.5 19.2 1.0
OD2 D:OCS19 4.5 25.9 1.0
C2 A:IMD302 4.6 19.6 1.0
CG2 D:THR90 4.8 22.2 1.0
N D:GLY20 4.8 12.8 1.0
C D:THR90 4.8 16.9 1.0
NH1 D:ARG87 4.9 26.4 1.0
CA D:GLY20 5.0 12.6 1.0

Magnesium binding site 5 out of 12 in 7op9

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Magnesium binding site 5 out of 12 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
E:Mg304

b:23.8
occ:1.00
 O E:HOH479 2.9 27.8 1.0
NH2 E:ARG24 3.0 33.7 1.0
O E:HOH401 3.2 25.3 1.0
O E:HOH574 3.4 26.1 1.0
N E:THR90 3.4 14.6 1.0
O E:HOH500 3.5 31.6 1.0
NH2 B:ARG43 3.6 26.0 1.0
OG1 E:THR90 3.7 19.0 1.0
CA E:GLY89 3.8 20.1 1.0
N1 B:IMD302 3.9 23.0 1.0
C E:GLY89 4.1 17.1 1.0
OD2 E:OCS19 4.1 27.6 1.0
CZ E:ARG24 4.3 30.1 1.0
O E:THR90 4.4 16.3 1.0
OD1 E:OCS19 4.4 23.1 1.0
CA E:THR90 4.4 15.7 1.0
C5 B:IMD302 4.4 22.8 1.0
O E:HOH534 4.5 18.4 1.0
O E:HOH417 4.5 28.6 1.0
CB E:THR90 4.5 17.5 1.0
NH1 B:ARG43 4.5 17.9 1.0
CZ B:ARG43 4.6 18.7 1.0
NH1 E:ARG87 4.7 26.3 1.0
N E:GLY20 4.7 11.5 1.0
CG2 E:THR90 4.8 20.9 1.0
C2 B:IMD302 4.8 20.5 1.0
C E:THR90 4.8 14.3 1.0
NH1 E:ARG24 4.9 34.5 1.0
SG E:OCS19 4.9 23.6 1.0

Magnesium binding site 6 out of 12 in 7op9

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Magnesium binding site 6 out of 12 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
F:Mg303

b:22.2
occ:1.00
 O F:HOH453 3.0 26.4 1.0
NH2 F:ARG24 3.2 28.3 1.0
O F:HOH408 3.2 23.0 1.0
O C:HOH563 3.3 21.9 1.0
N F:THR90 3.4 16.9 1.0
NH2 C:ARG43 3.5 24.3 1.0
OG1 F:THR90 3.6 22.7 1.0
N1 C:IMD302 3.7 22.9 1.0
O F:HOH488 3.7 30.7 1.0
CA F:GLY89 3.8 18.5 1.0
C F:GLY89 4.2 20.1 1.0
NH1 C:ARG43 4.3 17.8 1.0
C5 C:IMD302 4.4 17.5 1.0
CZ C:ARG43 4.4 19.3 1.0
CA F:THR90 4.4 19.1 1.0
O F:THR90 4.4 19.1 1.0
OD2 F:OCS19 4.4 26.5 1.0
CZ F:ARG24 4.4 28.6 1.0
CB F:THR90 4.5 22.5 1.0
O F:HOH462 4.6 20.1 1.0
OD1 F:OCS19 4.6 23.7 1.0
C2 C:IMD302 4.6 24.2 1.0
C F:THR90 4.8 20.6 1.0
N F:GLY20 4.8 13.8 1.0
CG2 F:THR90 4.9 25.6 1.0
NH1 F:ARG24 4.9 32.8 1.0
NH1 F:ARG87 4.9 25.0 1.0

Magnesium binding site 7 out of 12 in 7op9

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Magnesium binding site 7 out of 12 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
G:Mg303

b:15.9
occ:1.00
 O G:HOH440 3.0 17.0 1.0
O G:HOH417 3.2 17.7 1.0
NH2 G:ARG24 3.2 23.8 1.0
N G:THR90 3.3 13.2 1.0
NH2 J:ARG43 3.3 19.5 1.0
O G:HOH537 3.5 18.6 1.0
OG1 G:THR90 3.6 15.2 1.0
O G:HOH517 3.6 25.4 1.0
N1 J:IMD302 3.6 21.5 1.0
CA G:GLY89 3.7 13.7 1.0
C G:GLY89 4.0 14.4 1.0
CA G:THR90 4.3 11.1 1.0
CZ J:ARG43 4.3 17.2 1.0
C5 J:IMD302 4.4 16.3 1.0
NH1 J:ARG43 4.4 15.4 1.0
CB G:THR90 4.4 14.4 1.0
OD2 G:OCS19 4.4 26.6 1.0
CZ G:ARG24 4.5 23.6 1.0
O G:THR90 4.5 15.8 1.0
C2 J:IMD302 4.5 23.3 1.0
O G:HOH515 4.7 18.9 1.0
OD1 G:OCS19 4.7 22.8 1.0
CG2 G:THR90 4.8 18.0 1.0
C G:THR90 4.8 12.4 1.0
N G:GLY20 4.9 13.0 1.0

Magnesium binding site 8 out of 12 in 7op9

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Magnesium binding site 8 out of 12 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
H:Mg303

b:17.2
occ:1.00
 O H:HOH457 2.9 21.5 1.0
O H:HOH408 3.1 22.1 1.0
NH2 H:ARG24 3.1 26.0 1.0
NH2 K:ARG43 3.3 19.9 1.0
O H:HOH517 3.3 17.9 1.0
N H:THR90 3.3 15.0 1.0
OG1 H:THR90 3.7 18.3 1.0
O H:HOH512 3.7 27.5 1.0
CA H:GLY89 3.7 15.2 1.0
N1 K:IMD302 3.7 24.1 1.0
C H:GLY89 4.0 15.7 1.0
CZ K:ARG43 4.2 17.2 1.0
NH1 K:ARG43 4.3 12.7 1.0
C2 K:IMD302 4.4 20.6 1.0
CA H:THR90 4.4 11.8 1.0
OD2 H:OCS19 4.4 26.1 1.0
CZ H:ARG24 4.4 27.0 1.0
CB H:THR90 4.5 15.4 1.0
OD1 H:OCS19 4.5 27.3 1.0
O H:THR90 4.5 15.3 1.0
O H:HOH553 4.6 14.6 1.0
C5 K:IMD302 4.6 18.9 1.0
CG2 H:THR90 4.7 16.9 1.0
N H:GLY20 4.8 13.3 1.0
C H:THR90 4.9 13.6 1.0
NH1 H:ARG87 4.9 22.2 1.0
NH1 H:ARG24 5.0 29.9 1.0
OE2 H:GLU181 5.0 24.1 1.0

Magnesium binding site 9 out of 12 in 7op9

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Magnesium binding site 9 out of 12 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
I:Mg303

b:17.1
occ:1.00
 O I:HOH463 2.9 22.1 1.0
NH2 I:ARG24 3.1 29.4 1.0
O I:HOH417 3.2 18.1 1.0
O I:HOH490 3.3 16.8 1.0
N I:THR90 3.3 14.2 1.0
NH2 L:ARG43 3.3 20.0 1.0
OG1 I:THR90 3.6 17.1 1.0
N1 L:IMD302 3.6 23.4 1.0
CA I:GLY89 3.7 15.0 1.0
O I:HOH524 3.8 27.4 1.0
C I:GLY89 4.0 13.9 1.0
CZ L:ARG43 4.3 18.5 1.0
CA I:THR90 4.3 14.8 1.0
NH1 L:ARG43 4.3 14.6 1.0
OD2 I:OCS19 4.4 26.1 1.0
C5 L:IMD302 4.4 17.6 1.0
CZ I:ARG24 4.4 26.3 1.0
O I:THR90 4.4 15.7 1.0
CB I:THR90 4.5 15.3 1.0
C2 L:IMD302 4.5 21.6 1.0
O I:HOH567 4.5 16.3 1.0
OD1 I:OCS19 4.6 24.9 1.0
C I:THR90 4.8 13.4 1.0
CG2 I:THR90 4.8 19.2 1.0
N I:GLY20 4.9 13.5 1.0
NH1 I:ARG24 4.9 30.5 1.0
NH1 I:ARG87 5.0 21.9 1.0
OE2 I:GLU181 5.0 22.1 1.0

Magnesium binding site 10 out of 12 in 7op9

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Magnesium binding site 10 out of 12 in the Purine Nucleoside Phosphorylase(Deod-Type) From H. Pylori with 2,6- Dichloropurine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
J:Mg303

b:26.4
occ:1.00
 O J:HOH504 2.8 29.0 1.0
O J:HOH403 3.1 21.1 1.0
NH2 J:ARG24 3.3 32.3 1.0
N J:THR90 3.4 16.5 1.0
O J:HOH566 3.5 24.4 1.0
O J:HOH454 3.6 31.6 1.0
OG1 J:THR90 3.6 21.1 1.0
NH2 G:ARG43 3.8 26.2 1.0
CA J:GLY89 3.8 18.2 1.0
N1 G:IMD302 3.9 23.8 1.0
C J:GLY89 4.1 17.5 1.0
OD1 J:OCS19 4.2 28.1 1.0
O J:THR90 4.3 17.5 1.0
CA J:THR90 4.4 16.2 1.0
O J:HOH452 4.4 19.6 1.0
CB J:THR90 4.4 19.4 1.0
CZ J:ARG24 4.5 28.5 1.0
C5 G:IMD302 4.5 20.6 1.0
NH1 G:ARG43 4.5 16.8 1.0
CZ G:ARG43 4.7 20.4 1.0
OD2 J:OCS19 4.7 25.3 1.0
C J:THR90 4.7 16.7 1.0
C2 G:IMD302 4.7 24.4 1.0
CG2 J:THR90 4.8 24.0 1.0
NH1 J:ARG87 4.8 24.6 1.0
N J:GLY20 4.8 12.6 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: Thu Apr 6 18:15:11 2023

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