Magnesium in PDB 5opm: Crystal Structure of D52N/R238W Cn-II Mutant Bound to Datp and Free Phosphate

All present enzymatic activity of Crystal Structure of D52N/R238W Cn-II Mutant Bound to Datp and Free Phosphate:
3.1.3.5;

The structure of Crystal Structure of D52N/R238W Cn-II Mutant Bound to Datp and Free Phosphate, PDB code: 5opm 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)	45.67 / 1.68
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.087, 127.454, 130.948, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 19.7

The binding sites of Magnesium atom in the Crystal Structure of D52N/R238W Cn-II Mutant Bound to Datp and Free Phosphate (pdb code 5opm). 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/R238W Cn-II Mutant Bound to Datp and Free Phosphate, PDB code: 5opm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of D52N/R238W 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/R238W Cn-II Mutant Bound to Datp and Free Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:15.8 occ:1.00 O2 A:PO4501 1.9 13.9 1.0 O A:ASP54 2.1 14.7 1.0 ND2 A:ASN52 2.1 15.6 1.0 O A:HOH627 2.1 14.8 1.0 OD1 A:ASP351 2.1 16.3 1.0 O A:HOH654 2.1 15.4 1.0 CG A:ASP351 3.1 16.7 1.0 CG A:ASN52 3.2 16.2 1.0 C A:ASP54 3.2 15.4 1.0 P A:PO4501 3.4 15.2 1.0 OD2 A:ASP351 3.5 17.0 1.0 CA A:ASP54 3.8 15.4 1.0 N A:ASP54 3.8 15.4 1.0 O1 A:PO4501 3.9 15.0 1.0 CB A:ASN52 4.0 15.9 1.0 CB A:ASP54 4.0 15.5 1.0 OD1 A:ASN52 4.0 17.8 1.0 O A:HOH806 4.1 18.9 1.0 O3 A:PO4501 4.1 14.9 1.0 OG1 A:THR56 4.2 16.0 1.0 N A:TYR55 4.3 15.4 1.0 O A:HOH920 4.3 18.7 1.0 OD2 A:ASP356 4.4 15.4 1.0 O4 A:PO4501 4.4 15.3 1.0 CB A:ASP351 4.5 16.5 1.0 C A:MET53 4.5 15.8 1.0 CB A:TYR55 4.6 15.5 1.0 N A:THR56 4.7 16.2 1.0 CA A:TYR55 4.7 15.8 1.0 C A:TYR55 4.7 16.3 1.0 N A:MET53 4.8 15.8 1.0 N A:ASP351 4.8 15.9 1.0 CB A:THR56 4.8 16.4 1.0 O A:MET53 4.9 15.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of D52N/R238W 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/R238W Cn-II Mutant Bound to Datp and Free Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:21.2 occ:0.50 O3G A:DTP504 1.7 35.8 0.7 O2B A:DTP504 2.1 28.6 0.7 PG A:DTP504 2.9 35.3 0.7 O2A A:DTP504 3.0 36.8 0.7 O3B A:DTP504 3.1 33.7 0.7 PB A:DTP504 3.2 29.9 0.7 CE A:LYS362 3.6 31.7 1.0 O1G A:DTP504 3.8 36.4 0.7 OH A:TYR457 4.0 21.3 1.0 O2G A:DTP504 4.0 38.1 0.7 O3A A:DTP504 4.0 32.3 0.7 PA A:DTP504 4.0 38.0 0.7 NZ A:LYS362 4.1 33.7 1.0 NH1 A:ARG456 4.1 24.4 0.5 NH2 A:ARG456 4.3 25.6 0.5 O1B A:DTP504 4.4 30.3 0.7 CZ A:ARG456 4.6 24.2 0.5 CD A:LYS362 4.9 29.1 1.0 O5' A:DTP504 5.0 35.5 0.7

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