Atomistry » Magnesium » PDB 7oiw-7opq » 7op9
Atomistry »
  Magnesium »
    PDB 7oiw-7opq »
      7op9 »

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

Go back to Magnesium Binding Sites List in 7op9
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

Go back to Magnesium Binding Sites List in 7op9
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

Go back to Magnesium Binding Sites List in 7op9
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

Go back to Magnesium Binding Sites List in 7op9
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

Go back to Magnesium Binding Sites List in 7op9
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

Go back to Magnesium Binding Sites List in 7op9
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

Go back to Magnesium Binding Sites List in 7op9
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

Go back to Magnesium Binding Sites List in 7op9
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

Go back to Magnesium Binding Sites List in 7op9
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

Go back to Magnesium Binding Sites List in 7op9
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 Oct 3 03:28:24 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy