Magnesium in PDB 4o1l: Human Adenosine Kinase in Complex with Inhibitor

All present enzymatic activity of Human Adenosine Kinase in Complex with Inhibitor:
2.7.1.20;

The structure of Human Adenosine Kinase in Complex with Inhibitor, PDB code: 4o1l was solved by J.Brynda, J.Dostal, I.Pichova, M.Hodcek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	156.59 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.310, 156.590, 58.210, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 26.3

The binding sites of Magnesium atom in the Human Adenosine Kinase in Complex with Inhibitor (pdb code 4o1l). 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 Adenosine Kinase in Complex with Inhibitor, PDB code: 4o1l:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Adenosine Kinase in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Adenosine Kinase in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:23.1 occ:1.00 OG1 A:THR66 2.9 26.2 1.0 O A:HOH504 3.2 20.1 1.0 N A:ASN14 3.3 25.8 1.0 N A:THR66 3.3 26.1 1.0 C2 A:HO4403 3.4 23.6 1.0 CB A:THR66 3.6 24.5 1.0 CA A:GLY13 3.6 26.1 1.0 CB A:ALA168 3.9 24.3 1.0 N A:SER65 3.9 29.1 1.0 C A:GLY13 4.0 26.1 1.0 CA A:THR66 4.0 25.5 1.0 CB A:PHE170 4.2 27.2 1.0 N3 A:HO4403 4.2 22.4 1.0 CB A:SER65 4.2 27.0 1.0 CA A:ASN14 4.2 24.4 1.0 N1 A:HO4403 4.3 22.1 1.0 O A:ASN14 4.3 21.6 1.0 CB A:ASN14 4.3 23.2 1.0 C A:SER65 4.3 27.4 1.0 CA A:SER65 4.4 27.5 1.0 ND2 A:ASN14 4.5 24.4 1.0 CG A:ASN14 4.6 26.4 1.0 C A:ASN14 4.6 25.3 1.0 CD2 A:PHE170 4.6 26.6 1.0 C A:GLY64 4.7 29.7 1.0 N A:GLY13 4.8 26.6 1.0 N A:GLN67 4.9 27.6 1.0 CG A:PHE170 4.9 25.5 1.0 O A:MET12 4.9 32.8 1.0 CA A:ALA168 4.9 26.4 1.0 N A:PHE171 4.9 27.9 1.0 N A:ALA168 4.9 23.8 1.0

Magnesium binding site 2 out of 4 in the Human Adenosine Kinase in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Adenosine Kinase in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:37.3 occ:1.00 O A:HOH506 2.0 33.2 1.0 O A:HOH507 2.1 17.2 1.0 O A:HOH508 2.1 28.2 1.0 O A:HOH509 2.2 27.4 1.0 O A:HOH510 2.2 26.0 1.0 O A:HOH501 4.1 25.4 1.0 O A:ASN296 4.1 32.5 1.0 OD1 A:ASP300 4.2 26.8 1.0 O A:SER198 4.3 25.8 1.0 O A:HOH511 4.3 17.8 1.0 OE2 A:GLU226 4.5 33.1 1.0 OD1 A:ASN196 4.6 23.6 1.0 OE1 A:GLU226 4.6 34.1 1.0 CA A:GLY299 4.7 24.9 1.0 CA A:ASN296 4.7 36.9 1.0 N A:ASP300 4.8 26.8 1.0 C A:ASN296 4.8 34.7 1.0 C A:GLY299 4.8 26.4 1.0 ND2 A:ASN223 5.0 24.7 1.0 CD A:GLU226 5.0 33.8 1.0

Magnesium binding site 3 out of 4 in the Human Adenosine Kinase in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Adenosine Kinase in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:18.6 occ:1.00 OG1 B:THR66 3.0 22.6 1.0 O B:HOH501 3.1 21.5 1.0 N B:THR66 3.3 29.9 1.0 N B:ASN14 3.4 25.4 1.0 C2 B:HO4403 3.5 29.1 1.0 CB B:ALA168 3.6 27.5 1.0 CB B:THR66 3.7 27.9 1.0 CA B:GLY13 3.8 28.6 1.0 N B:SER65 3.9 27.1 1.0 CA B:THR66 4.1 27.2 1.0 CB B:PHE170 4.1 26.7 1.0 C B:GLY13 4.1 27.7 1.0 CB B:SER65 4.2 24.9 1.0 N3 B:HO4403 4.2 25.7 1.0 C B:SER65 4.3 31.2 1.0 N1 B:HO4403 4.3 29.5 1.0 CA B:SER65 4.3 26.4 1.0 CB B:ASN14 4.4 26.4 1.0 CA B:ASN14 4.4 26.1 1.0 O B:ASN14 4.4 30.4 1.0 OD1 B:ASN14 4.5 25.2 1.0 CD2 B:PHE170 4.6 27.2 1.0 CG B:ASN14 4.6 27.2 1.0 C B:GLY64 4.6 27.1 1.0 N B:PHE171 4.7 23.4 1.0 C B:ASN14 4.8 28.4 1.0 CA B:ALA168 4.8 29.0 1.0 CG B:PHE170 4.8 27.5 1.0 N B:ALA168 4.9 29.9 1.0 N B:GLN67 4.9 27.2 1.0 N B:GLY13 5.0 28.4 1.0 CB B:PHE171 5.0 22.6 1.0

Magnesium binding site 4 out of 4 in the Human Adenosine Kinase in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Adenosine Kinase in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:34.5 occ:1.00 O B:HOH504 2.1 19.0 1.0 O B:HOH507 2.3 27.7 1.0 O B:HOH506 2.4 25.1 1.0 O B:HOH505 2.5 23.6 1.0 O B:HOH508 3.6 48.5 1.0 O B:SER198 4.1 28.4 1.0 O B:ASN296 4.1 35.3 1.0 OE2 B:GLU226 4.2 35.9 1.0 OD1 B:ASP300 4.4 25.3 1.0 O B:HOH509 4.4 24.0 1.0 OE1 B:GLN38 4.5 31.7 1.0 CA B:ASN296 4.6 33.3 1.0 OE1 B:GLU226 4.6 35.0 1.0 ND2 B:ASN223 4.8 29.8 1.0 C B:ASN296 4.8 33.6 1.0 CD B:GLU226 4.9 35.3 1.0 CA B:GLY299 4.9 25.5 1.0 OD1 B:ASN296 4.9 28.4 1.0 C B:SER198 4.9 25.8 1.0 OD1 B:ASN196 5.0 23.3 1.0

J.Snasel, P.Naus, J.Dostal, A.Hnizda, J.Fanfrlik, J.Brynda, A.Bourderioux, M.Dusek, H.Dvorakova, J.Stolarikova, H.Zabranska, R.Pohl, P.Konecny, P.Dzubak, I.Votruba, M.Hajduch, P.Rezacova, V.Veverka, M.Hocek, I.Pichova. Structural Basis For Inhibition of Mycobacterial and Human Adenosine Kinase By 7-Substituted 7-(Het)Aryl-7-Deazaadenine Ribonucleosides J.Med.Chem. V. 57 8268 2014.
ISSN: ISSN 0022-2623
PubMed: 25259627
DOI: 10.1021/JM500497V