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Magnesium in PDB 5cqz: Human Cytosolic 5'-Nucleotidase II in Complex with 3-(3-Imidazol-1- Ylphenyl)-N-(9H-Purin-6-Yl)Benzamide

Enzymatic activity of Human Cytosolic 5'-Nucleotidase II in Complex with 3-(3-Imidazol-1- Ylphenyl)-N-(9H-Purin-6-Yl)Benzamide

All present enzymatic activity of Human Cytosolic 5'-Nucleotidase II in Complex with 3-(3-Imidazol-1- Ylphenyl)-N-(9H-Purin-6-Yl)Benzamide:
3.1.3.5;

Protein crystallography data

The structure of Human Cytosolic 5'-Nucleotidase II in Complex with 3-(3-Imidazol-1- Ylphenyl)-N-(9H-Purin-6-Yl)Benzamide, PDB code: 5cqz was solved by P.Preeti, N.Aghajari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.88 / 2.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.890, 121.980, 90.150, 90.00, 114.29, 90.00
R / Rfree (%) 19 / 25.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Cytosolic 5'-Nucleotidase II in Complex with 3-(3-Imidazol-1- Ylphenyl)-N-(9H-Purin-6-Yl)Benzamide (pdb code 5cqz). 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 II in Complex with 3-(3-Imidazol-1- Ylphenyl)-N-(9H-Purin-6-Yl)Benzamide, PDB code: 5cqz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5cqz

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Magnesium binding site 1 out of 4 in the Human Cytosolic 5'-Nucleotidase II in Complex with 3-(3-Imidazol-1- Ylphenyl)-N-(9H-Purin-6-Yl)Benzamide


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 in Complex with 3-(3-Imidazol-1- Ylphenyl)-N-(9H-Purin-6-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg610

b:28.1
occ:1.00
 OD1 A:ASP351 2.0 32.8 1.0
O3 A:SO4603 2.2 36.8 1.0
OD1 A:ASP52 2.3 29.9 1.0
O A:ASP54 2.4 33.1 1.0
OD2 A:ASP52 2.8 38.1 1.0
CG A:ASP52 2.8 33.9 1.0
CG A:ASP351 2.9 32.0 1.0
O A:HOH729 3.0 39.3 1.0
OD2 A:ASP351 3.1 38.1 1.0
C A:ASP54 3.6 32.4 1.0
S A:SO4603 3.6 38.1 1.0
OG1 A:THR56 4.0 35.7 1.0
CB A:ASP54 4.1 32.6 1.0
O2 A:SO4603 4.1 31.3 1.0
O1 A:SO4603 4.2 30.1 1.0
CA A:ASP54 4.2 35.0 1.0
CB A:ASP351 4.3 24.3 1.0
CB A:ASP52 4.3 30.4 1.0
N A:ASP54 4.3 36.7 1.0
O A:HOH732 4.3 41.9 1.0
O A:HOH712 4.5 35.3 1.0
O4 A:SO4603 4.6 32.3 1.0
N A:ASP351 4.6 35.2 1.0
N A:TYR55 4.7 30.9 1.0
CB A:TYR55 4.7 25.1 1.0
N A:HIS352 4.8 38.2 1.0
CB A:HIS352 4.9 39.4 1.0
CA A:ASP351 4.9 34.6 1.0
C A:MET53 5.0 34.8 1.0

Magnesium binding site 2 out of 4 in 5cqz

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Magnesium binding site 2 out of 4 in the Human Cytosolic 5'-Nucleotidase II in Complex with 3-(3-Imidazol-1- Ylphenyl)-N-(9H-Purin-6-Yl)Benzamide


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 II in Complex with 3-(3-Imidazol-1- Ylphenyl)-N-(9H-Purin-6-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg611

b:44.1
occ:1.00
 OE2 A:GLU66 4.0 38.2 1.0
CG A:GLU374 4.1 34.9 1.0
OG A:SER62 4.2 37.7 1.0
CD2 A:LEU156 4.3 36.0 1.0
CB A:SER62 4.3 38.5 1.0
CD1 A:LEU159 4.5 36.6 1.0
CD A:GLU374 4.5 37.6 1.0
OE2 A:GLU374 4.8 39.1 1.0
CB A:PRO373 4.8 23.9 1.0
CG A:PRO373 4.8 29.5 1.0
N A:GLU374 5.0 34.1 1.0

Magnesium binding site 3 out of 4 in 5cqz

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Magnesium binding site 3 out of 4 in the Human Cytosolic 5'-Nucleotidase II in Complex with 3-(3-Imidazol-1- Ylphenyl)-N-(9H-Purin-6-Yl)Benzamide


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 II in Complex with 3-(3-Imidazol-1- Ylphenyl)-N-(9H-Purin-6-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:28.8
occ:1.00
 O B:HOH703 1.8 36.1 1.0
O1 B:SO4603 2.1 36.5 1.0
OD1 B:ASP351 2.2 36.5 1.0
OD1 B:ASP52 2.2 34.2 1.0
O B:ASP54 2.4 36.8 1.0
OD2 B:ASP52 2.6 38.7 1.0
CG B:ASP52 2.7 37.8 1.0
CG B:ASP351 3.2 34.2 1.0
S B:SO4603 3.5 43.6 1.0
OD2 B:ASP351 3.5 34.4 1.0
C B:ASP54 3.5 34.3 1.0
OG1 B:THR56 4.0 34.7 1.0
CB B:ASP54 4.0 30.4 1.0
O4 B:SO4603 4.0 37.3 1.0
O3 B:SO4603 4.1 36.1 1.0
CA B:ASP54 4.1 32.8 1.0
N B:ASP54 4.2 38.7 1.0
CB B:ASP52 4.2 31.7 1.0
O2 B:SO4603 4.4 38.1 1.0
CB B:ASP351 4.5 27.5 1.0
N B:TYR55 4.7 28.4 1.0
N B:ASP351 4.8 29.4 1.0
CB B:TYR55 4.8 31.9 1.0
C B:MET53 4.9 34.0 1.0
N B:MET53 5.0 35.3 1.0
N B:THR56 5.0 32.7 1.0

Magnesium binding site 4 out of 4 in 5cqz

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Magnesium binding site 4 out of 4 in the Human Cytosolic 5'-Nucleotidase II in Complex with 3-(3-Imidazol-1- Ylphenyl)-N-(9H-Purin-6-Yl)Benzamide


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 II in Complex with 3-(3-Imidazol-1- Ylphenyl)-N-(9H-Purin-6-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg608

b:41.9
occ:1.00
 O B:TYR457 3.7 42.4 1.0
NH2 B:ARG39 3.7 41.4 1.0
OD2 B:ASP459 3.8 49.1 1.0
OG1 B:THR368 3.9 32.7 1.0
CG2 B:THR368 4.1 27.5 1.0
O B:TRP366 4.2 40.5 1.0
C B:TYR457 4.6 38.2 1.0
CB B:THR368 4.7 32.7 1.0
CG B:ASP459 4.7 49.1 1.0
CZ B:ARG39 4.8 45.7 1.0

Reference:

Z.Marton, R.Guillon, I.Krimm, R.Rahimova, D.Egron, L.P.Jordheim, N.Aghajari, C.Dumontet, C.Perigaud, C.Lionne, S.Peyrottes, L.Chaloin. Identification of Noncompetitive Inhibitors of Cytosolic 5'-Nucleotidase II Using A Fragment-Based Approach. J.Med.Chem. V. 58 9680 2015.
ISSN: ISSN 0022-2623
PubMed: 26599519
DOI: 10.1021/ACS.JMEDCHEM.5B01616
Page generated: Sun Sep 29 02:16:19 2024

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