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Magnesium in PDB 6fiw: Human Cytosolic 5'-Nucleotidase II Co-Crystallized with 10MM Sodium ((4-(3'-((7H-Purin-6-Yl)Carbamoyl)-[1,1'-Biphenyl]-3-Yl)-1H-Imidazol- 1-Yl) Methyl) Phosphonate

Enzymatic activity of Human Cytosolic 5'-Nucleotidase II Co-Crystallized with 10MM Sodium ((4-(3'-((7H-Purin-6-Yl)Carbamoyl)-[1,1'-Biphenyl]-3-Yl)-1H-Imidazol- 1-Yl) Methyl) Phosphonate

All present enzymatic activity of Human Cytosolic 5'-Nucleotidase II Co-Crystallized with 10MM Sodium ((4-(3'-((7H-Purin-6-Yl)Carbamoyl)-[1,1'-Biphenyl]-3-Yl)-1H-Imidazol- 1-Yl) Methyl) Phosphonate:
3.1.3.5;

Protein crystallography data

The structure of Human Cytosolic 5'-Nucleotidase II Co-Crystallized with 10MM Sodium ((4-(3'-((7H-Purin-6-Yl)Carbamoyl)-[1,1'-Biphenyl]-3-Yl)-1H-Imidazol- 1-Yl) Methyl) Phosphonate, PDB code: 6fiw was solved by N.Aghajari, P.Preeti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.85 / 2.20
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 91.070, 128.350, 129.720, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Cytosolic 5'-Nucleotidase II Co-Crystallized with 10MM Sodium ((4-(3'-((7H-Purin-6-Yl)Carbamoyl)-[1,1'-Biphenyl]-3-Yl)-1H-Imidazol- 1-Yl) Methyl) Phosphonate (pdb code 6fiw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Human Cytosolic 5'-Nucleotidase II Co-Crystallized with 10MM Sodium ((4-(3'-((7H-Purin-6-Yl)Carbamoyl)-[1,1'-Biphenyl]-3-Yl)-1H-Imidazol- 1-Yl) Methyl) Phosphonate, PDB code: 6fiw:

Magnesium binding site 1 out of 1 in 6fiw

Go back to Magnesium Binding Sites List in 6fiw
Magnesium binding site 1 out of 1 in the Human Cytosolic 5'-Nucleotidase II Co-Crystallized with 10MM Sodium ((4-(3'-((7H-Purin-6-Yl)Carbamoyl)-[1,1'-Biphenyl]-3-Yl)-1H-Imidazol- 1-Yl) Methyl) Phosphonate


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 II Co-Crystallized with 10MM Sodium ((4-(3'-((7H-Purin-6-Yl)Carbamoyl)-[1,1'-Biphenyl]-3-Yl)-1H-Imidazol- 1-Yl) Methyl) Phosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:37.5
occ:1.00
 O A:HOH738 2.0 36.2 1.0
O A:HOH761 2.1 35.6 1.0
OD1 A:ASP351 2.1 36.0 1.0
OD2 A:ASP52 2.1 42.1 1.0
O A:ASP54 2.2 35.6 1.0
O A:HOH719 2.2 34.3 1.0
CG A:ASP52 3.0 40.5 1.0
CG A:ASP351 3.1 34.8 1.0
C A:ASP54 3.3 40.8 1.0
OD1 A:ASP52 3.4 43.1 1.0
OD2 A:ASP351 3.4 36.7 1.0
O2 A:SO4601 4.0 52.4 1.0
CA A:ASP54 4.0 36.6 1.0
N A:ASP54 4.0 38.4 1.0
OG1 A:THR56 4.1 35.5 1.0
CB A:ASP54 4.2 39.3 1.0
OD2 A:ASP356 4.2 38.6 1.0
O4 A:SO4601 4.2 54.6 1.0
CB A:ASP52 4.3 35.2 1.0
O3 A:SO4601 4.3 48.4 1.0
CB A:ASP351 4.4 32.4 1.0
N A:TYR55 4.4 37.8 1.0
S A:SO4601 4.4 58.1 1.0
CB A:TYR55 4.4 35.7 1.0
N A:ASP351 4.6 35.6 1.0
O A:HOH707 4.6 46.2 1.0
O A:HOH734 4.6 44.1 1.0
CA A:TYR55 4.7 39.5 1.0
N A:THR56 4.7 37.9 1.0
C A:MET53 4.8 40.4 1.0
C A:TYR55 4.8 36.6 1.0
N A:HIS352 4.9 33.4 1.0
CA A:ASP351 5.0 35.4 1.0

Reference:

R.Guillon, R.Rahimova, D.Egron, S.Rouanet, C.Dumontet, N.Aghajari, L.P.Jordheim, L.Chaloin, S.Peyrottes. Lead Optimization and Biological Evaluation of Fragment-Based Cn-II Inhibitors. Eur J Med Chem V. 168 28 2019.
ISSN: ISSN 1768-3254
PubMed: 30798051
DOI: 10.1016/J.EJMECH.2019.02.040
Page generated: Tue Oct 1 00:29:50 2024

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