Magnesium in PDB 2xcw: Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Inosine Monophosphate and Atp

All present enzymatic activity of Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Inosine Monophosphate and Atp:
3.1.3.5;

The structure of Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Inosine Monophosphate and Atp, PDB code: 2xcw was solved by K.Wallden, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.560, 127.440, 130.440, 90.00, 90.00, 90.00
R / Rfree (%)	16.676 / 19.357

The binding sites of Magnesium atom in the Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Inosine Monophosphate and Atp (pdb code 2xcw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Inosine Monophosphate and Atp, PDB code: 2xcw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Inosine Monophosphate and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Inosine Monophosphate and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1497 b:28.6 occ:0.50 O3G A:ATP1489 1.9 34.5 1.0 O1B A:ATP1489 2.0 38.5 1.0 O A:HOH2396 2.2 33.8 1.0 PB A:ATP1489 3.2 38.1 1.0 PG A:ATP1489 3.2 36.9 1.0 O3B A:ATP1489 3.4 35.9 1.0 O A:HOH2395 3.8 40.6 1.0 O A:HOH2390 4.0 35.8 0.5 NZ A:LYS362 4.0 41.8 1.0 NH1 A:ARG456 4.0 44.2 1.0 O2B A:ATP1489 4.1 39.0 1.0 O1G A:ATP1489 4.1 35.0 1.0 OH A:TYR457 4.2 30.8 1.0 O2G A:ATP1489 4.2 37.6 1.0 O3A A:ATP1489 4.3 37.7 1.0 O A:HOH2386 4.5 39.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Inosine Monophosphate and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Inosine Monophosphate and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1498 b:22.6 occ:1.00 O3P A:IMP1490 2.0 21.6 1.0 O A:HOH2331 2.1 20.2 1.0 O A:HOH2332 2.1 20.2 1.0 OD1 A:ASP351 2.1 22.4 1.0 O A:ASP54 2.1 22.3 0.5 O A:ASP54 2.2 21.8 0.5 OD1 A:ASN52 2.2 24.4 1.0 CG A:ASP351 3.1 22.4 1.0 CG A:ASN52 3.2 25.3 1.0 C A:ASP54 3.3 21.1 0.5 C A:ASP54 3.3 21.7 0.5 OD2 A:ASP351 3.4 22.1 1.0 P A:IMP1490 3.4 27.1 1.0 ND2 A:ASN52 3.6 29.2 1.0 CA A:ASP54 3.9 21.4 0.5 N A:ASP54 4.0 21.5 0.5 N A:ASP54 4.0 22.1 0.5 CA A:ASP54 4.0 22.4 0.5 O2P A:IMP1490 4.0 20.7 1.0 O A:HOH2283 4.1 37.8 1.0 O1P A:IMP1490 4.1 26.2 1.0 CB A:ASP54 4.1 21.4 0.5 CB A:ASP54 4.2 23.4 0.5 OD2 A:ASP356 4.2 21.5 1.0 OG1 A:THR56 4.3 19.9 1.0 O A:HOH2056 4.3 20.5 1.0 N A:TYR55 4.4 21.3 1.0 CB A:ASN52 4.4 23.1 1.0 O5' A:IMP1490 4.5 28.8 1.0 CB A:ASP351 4.5 20.6 1.0 CB A:TYR55 4.7 21.2 1.0 C A:MET53 4.7 21.9 1.0 C5' A:IMP1490 4.8 27.9 1.0 CA A:TYR55 4.8 21.8 1.0 N A:ASP351 4.8 20.0 1.0 N A:THR56 4.9 21.6 1.0 C A:TYR55 4.9 22.2 1.0

K.Wallden, P.Nordlund. Structural Basis For the Allosteric Regulation and Substrate Recognition of Human Cytosolic 5'-Nucleotidase II J.Mol.Biol. V. 408 684 2011.
ISSN: ISSN 0022-2836
PubMed: 21396942
DOI: 10.1016/J.JMB.2011.02.059