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Manganese in PDB 6ddb: Crystal Structure of the Double Mutant (D52N/R367Q) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium Target

Enzymatic activity of Crystal Structure of the Double Mutant (D52N/R367Q) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium Target

All present enzymatic activity of Crystal Structure of the Double Mutant (D52N/R367Q) 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 Double Mutant (D52N/R367Q) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium Target, PDB code: 6ddb 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) 49.13 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.126, 123.123, 90.314, 90.00, 115.50, 90.00
R / Rfree (%) 21.7 / 29.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Double Mutant (D52N/R367Q) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium Target (pdb code 6ddb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of the Double Mutant (D52N/R367Q) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium Target, PDB code: 6ddb:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6ddb

Go back to Manganese Binding Sites List in 6ddb
Manganese binding site 1 out of 2 in the Crystal Structure of the Double Mutant (D52N/R367Q) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium Target


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Double Mutant (D52N/R367Q) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium Target within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:31.3
occ:1.00
 OD1 A:ASN52 2.1 26.3 1.0
O1 A:PO4602 2.2 25.0 1.0
OD1 A:ASP351 2.3 23.7 1.0
O A:ASP54 2.3 16.9 1.0
O A:HOH777 2.6 29.6 1.0
CG A:ASN52 2.8 25.4 1.0
ND2 A:ASN52 2.9 29.1 1.0
CG A:ASP351 3.3 26.4 1.0
C A:ASP54 3.4 17.1 1.0
OD2 A:ASP351 3.7 25.4 1.0
P A:PO4602 3.7 33.6 1.0
O A:HOH765 4.0 17.9 1.0
CB A:ASP54 4.0 24.7 1.0
CA A:ASP54 4.1 14.8 1.0
O A:HOH788 4.1 74.1 1.0
N A:ASP54 4.2 13.9 1.0
OG1 A:THR56 4.2 39.5 1.0
CB A:ASN52 4.3 32.1 1.0
O2 A:PO4602 4.3 31.4 1.0
O4 A:PO4602 4.4 31.6 1.0
N A:TYR55 4.6 27.6 1.0
O3 A:PO4602 4.6 33.2 1.0
CB A:ASP351 4.6 28.7 1.0
CB A:TYR55 4.7 18.6 1.0
C A:MET53 4.8 21.7 1.0
O A:HOH782 4.8 84.8 1.0
N A:ASP351 4.9 22.4 1.0
N A:MET53 5.0 27.2 1.0

Manganese binding site 2 out of 2 in 6ddb

Go back to Manganese Binding Sites List in 6ddb
Manganese binding site 2 out of 2 in the Crystal Structure of the Double Mutant (D52N/R367Q) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium Target


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Double Mutant (D52N/R367Q) of NT5C2-537X in the Basal State, Northeast Structural Genomics Consortium Target within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn601

b:37.9
occ:1.00
 OD1 B:ASN52 2.1 20.0 1.0
O4 B:PO4602 2.2 22.6 1.0
OD1 B:ASP351 2.2 26.6 1.0
O B:ASP54 2.3 28.1 1.0
CG B:ASN52 2.9 21.1 1.0
ND2 B:ASN52 3.0 31.5 1.0
CG B:ASP351 3.3 27.1 1.0
C B:ASP54 3.4 18.6 1.0
OD2 B:ASP351 3.6 26.1 1.0
P B:PO4602 3.7 33.7 1.0
CB B:ASP54 4.1 16.2 1.0
CA B:ASP54 4.1 19.5 1.0
O2 B:PO4602 4.2 31.1 1.0
N B:ASP54 4.2 27.6 1.0
O B:HOH784 4.2 53.0 1.0
OG1 B:THR56 4.3 21.4 1.0
CB B:ASN52 4.3 26.3 1.0
O1 B:PO4602 4.4 30.4 1.0
N B:TYR55 4.5 23.6 1.0
CB B:TYR55 4.6 28.6 1.0
O3 B:PO4602 4.6 35.0 1.0
CB B:ASP351 4.6 27.6 1.0
O B:HOH753 4.8 32.9 1.0
C B:MET53 4.8 27.3 1.0
N B:ASP351 4.9 27.6 1.0
CA B:TYR55 4.9 29.8 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: Sun Oct 6 04:03:27 2024

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