Magnesium in PDB 7zeh: Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE

Enzymatic activity of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE

All present enzymatic activity of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE:
3.1.3.5; 3.1.3.91;

Protein crystallography data

The structure of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE, PDB code: 7zeh was solved by D.Kubacka, M.Kozarski, M.R.Baranowski, R.Wojcik, J.Jemielity, J.Kowalska, J.Basquin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.08 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.59, 80.89, 83.17, 82.22, 72.46, 68.2
R / Rfree (%) 18.8 / 22

Other elements in 7zeh:

The structure of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE also contains other interesting chemical elements:

Fluorine (F) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE (pdb code 7zeh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE, PDB code: 7zeh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7zeh

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Magnesium binding site 1 out of 4 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:17.0
occ:1.00
 OD2 A:ASP41 2.0 19.7 1.0
O A:HOH541 2.0 17.2 1.0
OD1 A:ASP230 2.0 18.9 1.0
O A:ASP43 2.1 20.1 1.0
O A:HOH522 2.1 19.6 1.0
O A:HOH582 2.1 21.2 1.0
CG A:ASP41 3.0 18.3 1.0
CG A:ASP230 3.0 19.4 1.0
C A:ASP43 3.3 19.9 1.0
OD2 A:ASP230 3.3 21.2 1.0
OD1 A:ASP41 3.4 20.3 1.0
CA A:ASP43 4.0 19.5 1.0
OD2 A:ASP234 4.0 21.0 1.0
N A:ASP43 4.1 18.4 1.0
OG1 A:THR45 4.1 16.9 1.0
CB A:ASP43 4.1 21.5 1.0
OG A:SER231 4.2 21.9 0.6
O A:HOH645 4.3 23.4 1.0
CB A:ASP41 4.3 17.8 1.0
N A:MET44 4.3 18.7 1.0
O1 A:PO4410 4.4 22.7 1.0
CB A:ASP230 4.4 16.9 1.0
CB A:MET44 4.4 18.4 1.0
O A:HOH742 4.4 32.7 1.0
N A:THR45 4.5 16.7 1.0
C A:MET44 4.6 18.1 1.0
CA A:MET44 4.6 18.4 1.0
C A:PHE42 4.7 18.1 1.0
N A:ASP230 4.7 16.6 1.0
CB A:THR45 4.9 15.9 1.0
CG A:MET44 4.9 20.1 1.0
CG A:ASP234 4.9 20.3 1.0
O A:PHE42 5.0 18.0 1.0
OD1 A:ASP234 5.0 20.3 1.0

Magnesium binding site 2 out of 4 in 7zeh

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Magnesium binding site 2 out of 4 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg408

b:17.3
occ:1.00
 OD2 B:ASP41 2.0 18.8 1.0
O B:HOH544 2.0 15.8 1.0
O B:ASP43 2.1 19.5 1.0
OD1 B:ASP230 2.1 18.3 1.0
O B:HOH582 2.1 19.7 1.0
O B:HOH526 2.1 18.4 1.0
CG B:ASP41 3.0 18.2 1.0
CG B:ASP230 3.0 18.7 1.0
C B:ASP43 3.2 18.5 1.0
OD1 B:ASP41 3.4 18.5 1.0
OD2 B:ASP230 3.4 20.6 1.0
CA B:ASP43 3.9 19.4 1.0
N B:ASP43 4.0 19.1 1.0
CB B:ASP43 4.1 20.1 1.0
OD2 B:ASP234 4.1 18.8 1.0
OG1 B:THR45 4.1 16.5 1.0
O B:HOH643 4.3 25.2 1.0
CB B:ASP41 4.3 17.7 1.0
N B:MET44 4.3 17.4 1.0
O4 B:PO4409 4.3 22.4 1.0
CB B:MET44 4.4 17.6 1.0
CB B:ASP230 4.4 17.5 1.0
O B:HOH734 4.4 32.4 1.0
OG B:SER231 4.4 19.2 0.5
N B:THR45 4.5 18.2 1.0
CA B:MET44 4.6 16.8 1.0
C B:MET44 4.6 16.7 1.0
C B:PHE42 4.6 18.2 1.0
N B:ASP230 4.8 16.3 1.0
CG B:MET44 4.9 20.5 1.0
CB B:THR45 4.9 16.8 1.0
CG B:ASP234 5.0 17.9 1.0
NZ B:LYS205 5.0 20.5 1.0
O B:PHE42 5.0 18.9 1.0
OD1 B:ASP234 5.0 18.8 1.0
CA B:ASP230 5.0 16.9 1.0

Magnesium binding site 3 out of 4 in 7zeh

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Magnesium binding site 3 out of 4 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg413

b:14.0
occ:1.00
 O C:HOH576 2.0 17.2 1.0
O C:HOH542 2.0 15.9 1.0
OD2 C:ASP41 2.0 17.1 1.0
O C:ASP43 2.1 16.7 1.0
OD1 C:ASP230 2.1 17.4 1.0
O C:HOH527 2.1 18.5 1.0
CG C:ASP41 3.0 16.7 1.0
CG C:ASP230 3.1 15.9 1.0
C C:ASP43 3.2 15.9 1.0
OD2 C:ASP230 3.4 17.1 1.0
OD1 C:ASP41 3.4 17.8 1.0
CA C:ASP43 4.0 17.0 1.0
OD2 C:ASP234 4.0 17.4 1.0
N C:ASP43 4.1 16.5 1.0
CB C:ASP43 4.1 18.0 1.0
OG1 C:THR45 4.1 17.3 1.0
O C:HOH671 4.1 39.8 1.0
O C:HOH732 4.3 24.8 1.0
O C:HOH612 4.3 25.2 1.0
CB C:ASP41 4.3 17.2 1.0
O2 C:PO4414 4.3 28.1 1.0
N C:MET44 4.3 16.5 1.0
OG C:SER231 4.3 16.2 0.5
CB C:MET44 4.4 19.1 1.0
CB C:ASP230 4.4 16.0 1.0
N C:THR45 4.6 16.9 1.0
CA C:MET44 4.6 16.9 1.0
C C:MET44 4.6 17.2 1.0
C C:PHE42 4.7 18.1 1.0
N C:ASP230 4.7 14.8 1.0
CG C:MET44 4.9 21.8 1.0
CB C:THR45 4.9 16.8 1.0
CG C:ASP234 4.9 17.5 1.0
O C:HOH645 4.9 20.3 1.0
OD1 C:ASP234 4.9 19.4 1.0

Magnesium binding site 4 out of 4 in 7zeh

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Magnesium binding site 4 out of 4 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg411

b:14.1
occ:1.00
 O D:HOH2642 1.9 17.8 1.0
OD2 D:ASP41 2.0 17.9 1.0
O D:HOH2628 2.0 15.2 1.0
OD1 D:ASP230 2.0 18.6 1.0
O D:HOH2634 2.1 18.3 1.0
O D:ASP43 2.1 18.3 1.0
CG D:ASP41 3.0 16.4 1.0
CG D:ASP230 3.0 18.3 1.0
C D:ASP43 3.3 18.7 1.0
OD2 D:ASP230 3.3 18.3 1.0
OD1 D:ASP41 3.4 18.1 1.0
OD2 D:ASP234 4.0 18.2 1.0
CA D:ASP43 4.0 19.1 1.0
CB D:ASP43 4.1 20.6 1.0
OG1 D:THR45 4.1 16.8 1.0
N D:ASP43 4.1 18.4 1.0
OG D:SER231 4.2 17.8 0.5
O D:HOH2832 4.3 27.4 1.0
O D:HOH2750 4.3 24.4 1.0
CB D:ASP41 4.3 17.7 1.0
O4 D:PO4412 4.3 26.3 1.0
N D:MET44 4.3 17.6 1.0
CB D:MET44 4.3 19.5 1.0
CB D:ASP230 4.4 17.1 1.0
N D:THR45 4.5 17.5 1.0
CA D:MET44 4.6 17.9 1.0
C D:MET44 4.6 17.7 1.0
C D:PHE42 4.7 18.1 1.0
N D:ASP230 4.7 16.9 1.0
CG D:MET44 4.9 21.1 1.0
CG D:ASP234 4.9 17.9 1.0
OD1 D:ASP234 4.9 19.2 1.0
CB D:THR45 4.9 16.7 1.0
O D:PHE42 5.0 18.1 1.0
NZ D:LYS205 5.0 20.7 1.0
O D:HOH2720 5.0 21.7 1.0

Reference:

D.Kubacka, M.Kozarski, M.R.Baranowski, R.Wojcik, J.Panecka-Hofman, D.Strzelecka, J.Basquin, J.Jemielity, J.Kowalska. Substrate-Based Design of Cytosolic Nucleotidase Iiib Inhibitors and Structural Insights Into Inhibition Mechanism. Pharmaceuticals V. 15 2022.
ISSN: ESSN 1424-8247
PubMed: 35631380
DOI: 10.3390/PH15050554
Page generated: Fri Apr 7 04:31:45 2023

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