Magnesium in PDB 6d0z: Polymerase Eta Cytarabine (Arac) Extension Ternary Complex

All present enzymatic activity of Polymerase Eta Cytarabine (Arac) Extension Ternary Complex:
2.7.7.7;

The structure of Polymerase Eta Cytarabine (Arac) Extension Ternary Complex, PDB code: 6d0z was solved by O.Rechkoblit, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.11 / 1.75
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.789, 98.789, 81.772, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 19.5

The binding sites of Magnesium atom in the Polymerase Eta Cytarabine (Arac) Extension Ternary Complex (pdb code 6d0z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Polymerase Eta Cytarabine (Arac) Extension Ternary Complex, PDB code: 6d0z:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Polymerase Eta Cytarabine (Arac) Extension Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Polymerase Eta Cytarabine (Arac) Extension Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:17.4 occ:1.00 OD1 A:ASP13 2.1 30.0 1.0 O1G A:DZ4503 2.2 25.4 1.0 O1B A:DZ4503 2.2 25.5 1.0 OD2 A:ASP115 2.2 29.3 1.0 O1A A:DZ4503 2.2 27.2 1.0 O A:MET14 2.2 25.9 1.0 H5'A A:DZ4503 3.2 30.8 1.0 CG A:ASP115 3.2 32.9 1.0 CG A:ASP13 3.3 37.3 1.0 PB A:DZ4503 3.3 24.9 1.0 PA A:DZ4503 3.4 27.2 1.0 MG A:MG502 3.4 52.7 1.0 C A:MET14 3.4 22.2 1.0 HZ1 A:LYS231 3.5 32.8 1.0 PG A:DZ4503 3.5 26.9 1.0 OD1 A:ASP115 3.6 30.8 1.0 HZ2 A:LYS231 3.8 32.8 1.0 OD2 A:ASP13 3.8 46.7 1.0 N3A A:DZ4503 3.8 25.9 1.0 O3B A:DZ4503 3.8 25.1 1.0 HE3 A:LYS231 3.9 40.2 1.0 N A:MET14 3.9 25.8 1.0 H A:MET14 4.0 31.0 1.0 HB2 A:PHE17 4.0 28.0 1.0 NZ A:LYS231 4.0 27.3 1.0 C5' A:DZ4503 4.0 25.6 1.0 O A:HOH630 4.0 40.6 1.0 HB2 A:MET14 4.0 28.6 1.0 H A:PHE17 4.1 28.5 1.0 H5' A:DZ4503 4.1 30.8 1.0 HA A:ASP15 4.2 30.8 1.0 CA A:MET14 4.2 23.9 1.0 O5' A:DZ4503 4.2 25.5 1.0 C A:ASP13 4.2 24.8 1.0 O2G A:DZ4503 4.3 24.9 1.0 N A:ASP15 4.5 22.5 1.0 CB A:ASP13 4.5 25.3 1.0 CE A:LYS231 4.5 33.5 1.0 CB A:ASP115 4.6 25.9 1.0 H A:CYS16 4.6 28.4 1.0 HB2 A:ASP115 4.6 31.1 1.0 O3G A:DZ4503 4.6 26.6 1.0 HA A:ASP13 4.6 31.5 1.0 O2A A:DZ4503 4.6 31.9 1.0 CB A:MET14 4.7 23.9 1.0 O A:ASP13 4.7 26.2 1.0 CA A:ASP15 4.7 25.6 1.0 O2B A:DZ4503 4.7 27.1 1.0 N A:CYS16 4.7 23.7 1.0 H3' P:CAR8 4.7 42.5 0.2 CA A:ASP13 4.7 26.2 1.0 O A:HOH763 4.7 39.3 1.0 HO3' P:CAR8 4.8 40.6 0.8 HN3A A:DZ4503 4.8 31.1 1.0 HZ3 A:LYS231 4.8 32.8 1.0 N A:PHE17 4.8 23.8 1.0 HB3 A:ASP13 4.8 30.3 1.0 H3' P:CAR8 4.8 42.5 0.8 C A:ASP15 4.8 25.4 1.0 CB A:PHE17 4.8 23.3 1.0 O A:ASP115 4.8 26.7 1.0 HB3 A:PHE17 4.9 28.0 1.0 HB3 A:ASP115 5.0 31.1 1.0

Magnesium binding site 2 out of 2 in the Polymerase Eta Cytarabine (Arac) Extension Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Polymerase Eta Cytarabine (Arac) Extension Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:52.7 occ:1.00 OE2 A:GLU116 2.1 52.9 1.0 O A:HOH630 2.1 40.6 1.0 OD1 A:ASP115 2.5 30.8 1.0 H3' P:CAR8 2.5 42.5 0.8 H3' P:CAR8 2.5 42.5 0.2 O1A A:DZ4503 2.6 27.2 1.0 HO3' P:CAR8 2.8 40.6 0.8 HO3' P:CAR8 2.8 41.2 0.2 CD A:GLU116 2.9 46.1 1.0 OD1 A:ASP13 3.0 30.0 1.0 OD2 A:ASP13 3.0 46.7 1.0 H5' P:CAR8 3.1 42.8 0.8 H5'' P:CAR8 3.2 44.1 0.2 HG A:SER113 3.2 37.3 1.0 CG A:ASP13 3.2 37.3 1.0 C3' P:CAR8 3.2 35.4 0.2 C3' P:CAR8 3.2 35.5 0.8 O3' P:CAR8 3.3 33.9 0.8 O3' P:CAR8 3.3 34.3 0.2 HB3 A:GLU116 3.3 49.6 1.0 CG A:ASP115 3.4 32.9 1.0 MG A:MG501 3.4 17.4 1.0 H4' P:CAR8 3.5 43.2 0.2 OE1 A:GLU116 3.6 40.2 1.0 H4' P:CAR8 3.6 42.9 0.8 OD2 A:ASP115 3.6 29.3 1.0 C4' P:CAR8 3.7 36.0 0.2 C4' P:CAR8 3.7 35.8 0.8 PA A:DZ4503 3.8 27.2 1.0 HG2 A:GLU116 3.8 45.8 1.0 C5' P:CAR8 3.8 36.7 0.2 CG A:GLU116 3.8 38.1 1.0 C5' P:CAR8 3.9 35.7 0.8 H5' P:CAR8 3.9 44.1 0.2 OG A:SER113 3.9 31.1 1.0 H5' A:DZ4503 4.0 30.8 1.0 CB A:GLU116 4.0 41.3 1.0 O5' A:DZ4503 4.2 25.5 1.0 HZ2 A:LYS224 4.2 54.1 1.0 HZ3 A:LYS224 4.2 54.1 1.0 O2A A:DZ4503 4.2 31.9 1.0 H5'' P:CAR8 4.3 42.8 0.8 HA A:ASP13 4.4 31.5 1.0 CB A:ASP13 4.4 25.3 1.0 H5'A A:DZ4503 4.5 30.8 1.0 C5' A:DZ4503 4.5 25.6 1.0 HZ1 A:LYS224 4.5 54.1 1.0 NZ A:LYS224 4.5 45.1 1.0 HB2 A:ASP13 4.5 30.3 1.0 O A:ASP115 4.6 26.7 1.0 C A:ASP115 4.6 24.5 1.0 C2' P:CAR8 4.6 35.0 0.8 C2' P:CAR8 4.6 34.9 0.2 HE3 A:LYS224 4.7 45.6 0.0 H A:ASP115 4.7 29.5 1.0 HG3 A:GLU116 4.7 45.8 1.0 N A:GLU116 4.7 25.5 1.0 HB2 A:GLU116 4.7 49.6 1.0 HO2' P:CAR8 4.8 37.3 0.8 O1G A:DZ4503 4.8 25.4 1.0 HO2' P:CAR8 4.8 40.0 0.2 CB A:ASP115 4.8 25.9 1.0 O P:HOH103 4.8 41.1 1.0 H A:GLU116 4.9 30.6 1.0 CA A:ASP13 4.9 26.2 1.0 H2' P:CAR8 5.0 42.0 0.8 CA A:GLU116 5.0 28.4 1.0

O.Rechkoblit, J.R.Choudhury, A.Buku, L.Prakash, S.Prakash, A.K.Aggarwal. Structural Basis For Polymerase Eta-Promoted Resistance to the Anticancer Nucleoside Analog Cytarabine. Sci Rep V. 8 12702 2018.
ISSN: ESSN 2045-2322
PubMed: 30140014
DOI: 10.1038/S41598-018-30796-W