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Magnesium in PDB 6ddc: Crystal Structure of the Single Mutant (D52N) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium Target

Enzymatic activity of Crystal Structure of the Single Mutant (D52N) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium Target

All present enzymatic activity of Crystal Structure of the Single Mutant (D52N) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium Target:
3.1.3.5;

Protein crystallography data

The structure of Crystal Structure of the Single Mutant (D52N) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium Target, PDB code: 6ddc 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) 39.42 / 2.91
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 144.555, 124.151, 90.736, 90.00, 116.25, 90.00
R / Rfree (%) 18.1 / 26.4

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 6ddc

Go back to Magnesium Binding Sites List in 6ddc
Magnesium binding site 1 out of 2 in the Crystal Structure of the Single Mutant (D52N) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium 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 Single Mutant (D52N) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium Target within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:34.5
occ:1.00
OD1 A:ASP351 2.4 43.7 1.0
O1 A:PO4602 2.4 36.8 1.0
O A:ASP54 2.5 34.5 1.0
CE1 A:HIS352 2.7 50.8 1.0
ND2 A:ASN52 2.7 28.2 1.0
ND1 A:HIS352 3.2 55.0 1.0
CG A:ASP351 3.3 42.9 1.0
OD2 A:ASP351 3.5 44.6 1.0
C A:ASP54 3.5 29.6 1.0
NE2 A:HIS352 3.8 49.2 1.0
P A:PO4602 3.8 42.4 1.0
O A:HOH786 3.8 68.1 1.0
CG A:ASN52 3.8 43.6 1.0
CB A:ASP54 3.9 30.0 1.0
O A:HOH778 4.0 25.3 1.0
OD1 A:ASN52 4.1 68.9 1.0
O4 A:PO4602 4.1 49.9 1.0
CA A:ASP54 4.2 29.0 1.0
CG A:HIS352 4.4 49.3 1.0
CB A:TYR55 4.5 23.8 1.0
O3 A:PO4602 4.5 32.1 1.0
N A:ASP54 4.5 31.5 1.0
N A:TYR55 4.6 22.6 1.0
CD2 A:HIS352 4.7 52.6 1.0
CB A:ASP351 4.7 37.9 1.0
O2 A:PO4602 4.8 37.6 1.0
OG1 A:THR56 4.9 23.7 1.0

Magnesium binding site 2 out of 2 in 6ddc

Go back to Magnesium Binding Sites List in 6ddc
Magnesium binding site 2 out of 2 in the Crystal Structure of the Single Mutant (D52N) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium 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 Single Mutant (D52N) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium Target within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:28.6
occ:1.00
OD1 B:ASP351 2.1 37.8 1.0
ND2 B:ASN52 2.1 31.0 1.0
O B:ASP54 2.4 11.4 1.0
O1 B:PO4602 2.7 51.0 1.0
O4 B:PO4602 3.2 60.6 1.0
CG B:ASN52 3.2 39.8 1.0
CG B:ASP351 3.3 36.1 1.0
ND1 B:HIS352 3.3 55.8 1.0
CE1 B:HIS352 3.4 53.7 1.0
OD1 B:ASN52 3.5 53.4 1.0
P B:PO4602 3.5 52.3 1.0
C B:ASP54 3.6 16.9 1.0
OD2 B:ASP351 3.8 34.5 1.0
CB B:ASP54 4.2 33.3 1.0
CA B:ASP54 4.2 22.6 1.0
N B:ASP54 4.3 23.9 1.0
O2 B:PO4602 4.4 39.6 1.0
CB B:ASP351 4.5 32.5 1.0
CB B:ASN52 4.5 19.6 1.0
OG1 B:THR56 4.6 39.8 1.0
CG B:HIS352 4.6 54.2 1.0
N B:TYR55 4.6 19.9 1.0
CB B:TYR55 4.7 19.0 1.0
O3 B:PO4602 4.7 39.5 1.0
NE2 B:HIS352 4.7 56.8 1.0
N B:ASP351 4.9 11.1 1.0

Reference:

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
Page generated: Mon Sep 30 23:07:09 2024

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