Magnesium in PDB 5opk: Crystal Structure of D52N/R367Q Cn-II Mutant Bound to Datp and Free Phosphate

All present enzymatic activity of Crystal Structure of D52N/R367Q Cn-II Mutant Bound to Datp and Free Phosphate:
3.1.3.5;

The structure of Crystal Structure of D52N/R367Q Cn-II Mutant Bound to Datp and Free Phosphate, PDB code: 5opk was solved by A.Hnizda, P.Pachl, P.Rezacova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.99 / 1.74
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.579, 127.104, 130.317, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.3

The binding sites of Magnesium atom in the Crystal Structure of D52N/R367Q Cn-II Mutant Bound to Datp and Free Phosphate (pdb code 5opk). 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 D52N/R367Q Cn-II Mutant Bound to Datp and Free Phosphate, PDB code: 5opk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of D52N/R367Q Cn-II Mutant Bound to Datp and Free Phosphate


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 D52N/R367Q Cn-II Mutant Bound to Datp and Free Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg512 b:18.8 occ:1.00 O2 A:PO4510 1.9 15.0 1.0 O A:HOH631 2.1 19.3 1.0 O A:HOH641 2.2 17.8 1.0 ND2 A:ASN52 2.2 17.5 1.0 OD1 A:ASP351 2.2 17.5 1.0 O A:ASP54 2.2 16.9 1.0 CG A:ASP351 3.2 17.6 1.0 CG A:ASN52 3.3 18.8 1.0 P A:PO4510 3.3 16.4 1.0 C A:ASP54 3.3 16.3 1.0 OD2 A:ASP351 3.5 18.3 1.0 O1 A:PO4510 3.9 16.5 1.0 O A:HOH788 3.9 23.7 1.0 CA A:ASP54 3.9 16.9 1.0 N A:ASP54 4.0 16.8 1.0 O3 A:PO4510 4.0 16.6 1.0 CB A:ASN52 4.1 18.6 1.0 CB A:ASP54 4.1 17.3 1.0 OD1 A:ASN52 4.1 21.6 1.0 O A:HOH776 4.2 22.1 1.0 OG1 A:THR56 4.2 17.1 1.0 OD2 A:ASP356 4.3 16.0 1.0 O4 A:PO4510 4.4 16.1 1.0 N A:TYR55 4.5 15.8 1.0 CB A:ASP351 4.6 17.2 1.0 C A:MET53 4.6 16.6 1.0 CB A:TYR55 4.7 15.3 1.0 N A:ASP351 4.8 16.2 1.0 C A:TYR55 4.8 15.8 1.0 CA A:TYR55 4.8 15.8 1.0 N A:MET53 4.9 16.9 1.0 N A:THR56 4.9 15.4 1.0 CB A:THR56 5.0 16.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of D52N/R367Q Cn-II Mutant Bound to Datp and Free Phosphate


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 D52N/R367Q Cn-II Mutant Bound to Datp and Free Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg513 b:18.8 occ:0.50 O3G A:DTP514 1.7 30.4 0.8 O2B A:DTP514 2.1 23.6 0.8 O A:HOH605 2.2 21.7 0.5 O2A A:DTP514 2.9 33.3 0.8 PG A:DTP514 2.9 30.6 0.8 PB A:DTP514 3.1 24.5 0.8 O3B A:DTP514 3.1 29.9 0.8 O A:HOH604 3.4 32.8 0.5 NZ A:LYS362 3.6 24.1 0.5 O1G A:DTP514 3.8 29.5 0.8 PA A:DTP514 3.9 35.4 0.8 O3A A:DTP514 3.9 28.3 0.8 OH A:TYR457 3.9 22.8 1.0 NH1 A:ARG456 4.0 18.0 0.2 O2G A:DTP514 4.1 35.7 0.8 CE A:LYS362 4.2 22.1 0.5 NZ A:LYS362 4.3 22.8 0.5 O1B A:DTP514 4.3 24.3 0.8 CE A:LYS362 4.5 23.2 0.5 NH2 A:ARG456 4.6 18.9 0.2 CZ A:ARG456 4.7 17.8 0.2 O5' A:DTP514 4.7 33.0 0.8 C5' A:DTP514 5.0 30.1 0.8

A.Hnizda, M.Fabry, T.Moriyama, P.Pachl, M.Kugler, V.Brinsa, D.B.Ascher, W.L.Carroll, P.Novak, M.Zaliova, J.Trka, P.Rezacova, J.J.Yang, V.Veverka. Relapsed Acute Lymphoblastic Leukemia-Specific Mutations in NT5C2 Cluster Into Hotspots Driving Intersubunit Stimulation. Leukemia V. 32 1393 2018.
ISSN: ESSN 1476-5551
PubMed: 29535428
DOI: 10.1038/S41375-018-0073-5