Magnesium in PDB 6ddz: Crystal Structure of the Double Mutant (D52N/R238W) of NT5C2-537X in the Active State, Northeast Structural Genomics Target

All present enzymatic activity of Crystal Structure of the Double Mutant (D52N/R238W) of NT5C2-537X in the Active State, Northeast Structural Genomics Target:
3.1.3.5;

The structure of Crystal Structure of the Double Mutant (D52N/R238W) of NT5C2-537X in the Active State, Northeast Structural Genomics Target, PDB code: 6ddz was solved by F.Forouhar, C.L.Dieck, G.Tzoneva, Z.Carpenter, A.Ambesi-Impiombato, M.Sanchez-Martin, R.Kirschner-Schwabe, S.Lew, J.Seetharaman, A.A.Ferrando, L.Tong, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.58 / 1.97
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.677, 127.293, 131.131, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.3

The binding sites of Magnesium atom in the Crystal Structure of the Double Mutant (D52N/R238W) of NT5C2-537X in the Active State, Northeast Structural Genomics Target (pdb code 6ddz). 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 Double Mutant (D52N/R238W) of NT5C2-537X in the Active State, Northeast Structural Genomics Target, PDB code: 6ddz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Double Mutant (D52N/R238W) of NT5C2-537X in the Active State, Northeast Structural Genomics Target


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 Double Mutant (D52N/R238W) of NT5C2-537X in the Active State, Northeast Structural Genomics Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:36.5 occ:0.50 O1B A:ATP601 2.0 57.8 1.0 O1G A:ATP601 2.0 65.1 1.0 O A:HOH739 2.1 37.8 1.0 PB A:ATP601 3.0 61.3 1.0 PG A:ATP601 3.3 76.4 1.0 O3B A:ATP601 3.3 68.8 1.0 O2B A:ATP601 3.7 75.6 1.0 O A:HOH853 4.2 60.3 1.0 O3G A:ATP601 4.2 81.5 1.0 NZ A:LYS362 4.2 63.6 1.0 O2G A:ATP601 4.4 93.5 1.0 OH A:TYR457 4.4 32.4 1.0 O3A A:ATP601 4.4 83.3 1.0 O A:HOH752 4.4 42.2 1.0 NH2 A:ARG456 4.5 76.5 1.0 O1A A:ATP601 4.8 0.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Double Mutant (D52N/R238W) of NT5C2-537X in the Active State, Northeast Structural Genomics Target


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 Double Mutant (D52N/R238W) of NT5C2-537X in the Active State, Northeast Structural Genomics Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:36.4 occ:1.00 O4 A:PO4603 1.9 28.0 1.0 OD1 A:ASN52 2.0 32.3 1.0 O A:HOH843 2.2 33.3 1.0 O A:ASP54 2.3 24.1 1.0 OD1 A:ASP351 2.3 31.3 1.0 O A:HOH734 2.8 33.8 1.0 CG A:ASN52 3.0 23.1 1.0 C A:ASP54 3.3 25.2 1.0 CG A:ASP351 3.3 27.6 1.0 P A:PO4603 3.3 26.0 1.0 N A:ASP54 3.7 22.1 1.0 O3 A:PO4603 3.7 24.4 1.0 CB A:ASP54 3.8 23.3 1.0 CA A:ASP54 3.8 27.0 1.0 OD2 A:ASP351 3.8 29.7 1.0 CB A:ASN52 3.9 21.1 1.0 ND2 A:ASN52 4.0 26.6 1.0 O1 A:PO4603 4.2 22.1 1.0 O2 A:PO4603 4.3 25.5 1.0 OD2 A:ASP356 4.3 22.3 1.0 OG1 A:THR56 4.4 26.6 1.0 C A:MET53 4.5 18.1 1.0 N A:TYR55 4.5 21.1 1.0 CB A:ASP351 4.5 24.6 1.0 O A:HOH1026 4.6 56.9 1.0 N A:MET53 4.6 20.9 1.0 O A:HOH736 4.7 50.4 1.0 N A:ASP351 4.8 20.7 1.0 CB A:TYR55 4.9 25.1 1.0 CG A:ASP54 4.9 28.5 1.0 N A:THR56 5.0 24.1 1.0

C.L.Dieck, G.Tzoneva, F.Forouhar, Z.Carpenter, A.Ambesi-Impiombato, M.Sanchez-Martin, R.Kirschner-Schwabe, S.Lew, J.Seetharaman, L.Tong, A.A.Ferrando. Structure and Mechanisms of NT5C2 Mutations Driving Thiopurine Resistance in Relapsed Lymphoblastic Leukemia. Cancer Cell V. 34 136 2018.
ISSN: ISSN 1878-3686
PubMed: 29990496
DOI: 10.1016/J.CCELL.2018.06.003