Magnesium in PDB 6pz3: Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue

All present enzymatic activity of Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue:
2.7.7.7;

The structure of Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue, PDB code: 6pz3 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)	42.53 / 2.40
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.221, 98.221, 81.348, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 21.6

The binding sites of Magnesium atom in the Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue (pdb code 6pz3). 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-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue, PDB code: 6pz3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:32.0 occ:1.00 OD1 A:ASP13 2.0 30.1 1.0 O1B A:XG4501 2.0 34.8 1.0 O1G A:XG4501 2.1 30.7 1.0 O1A A:XG4501 2.1 35.3 1.0 OD1 A:ASP115 2.2 36.5 1.0 O A:MET14 2.3 27.9 1.0 CG A:ASP13 2.9 29.3 1.0 H5' A:XG4501 3.0 45.0 1.0 PB A:XG4501 3.1 34.0 1.0 MG A:MG503 3.1 42.4 1.0 CG A:ASP115 3.1 35.0 1.0 PA A:XG4501 3.3 37.5 1.0 OD2 A:ASP13 3.3 32.0 1.0 PG A:XG4501 3.4 34.8 1.0 C A:MET14 3.5 28.6 1.0 N3A A:XG4501 3.5 40.0 1.0 OD2 A:ASP115 3.5 36.3 1.0 O3B A:XG4501 3.6 38.5 1.0 HZ2 A:LYS231 3.8 42.0 1.0 C5' A:XG4501 3.8 37.6 1.0 H A:MET14 3.9 30.8 1.0 N A:MET14 3.9 25.8 1.0 HZ3 A:LYS231 4.0 42.0 1.0 O5' A:XG4501 4.0 43.9 1.0 O A:HOH615 4.0 37.7 1.0 H5'A A:XG4501 4.0 45.0 1.0 H A:PHE17 4.1 30.2 1.0 HB2 A:PHE17 4.1 31.1 1.0 HO3' P:DT8 4.1 48.3 1.0 HB2 A:MET14 4.1 35.9 1.0 HA A:ASP15 4.2 34.9 1.0 O2G A:XG4501 4.2 38.1 1.0 CB A:ASP13 4.2 22.5 1.0 CA A:MET14 4.2 30.2 1.0 C A:ASP13 4.3 22.9 1.0 H A:CYS16 4.3 34.2 1.0 NZ A:LYS231 4.3 35.1 1.0 CB A:ASP115 4.4 30.0 1.0 HB2 A:ASP115 4.4 35.9 1.0 O2B A:XG4501 4.4 38.4 1.0 HN3A A:XG4501 4.4 47.9 1.0 HB3 A:ASP13 4.5 26.9 1.0 O3G A:XG4501 4.5 36.4 1.0 N A:ASP15 4.5 28.6 1.0 O2A A:XG4501 4.6 39.8 1.0 N A:CYS16 4.6 28.6 1.0 HA A:ASP13 4.6 30.4 1.0 CA A:ASP13 4.7 25.4 1.0 HE3 A:LYS231 4.7 48.8 1.0 CA A:ASP15 4.7 29.2 1.0 O A:ASP115 4.7 30.6 1.0 CB A:MET14 4.8 30.0 1.0 O A:ASP13 4.8 25.9 1.0 OE2 A:GLU116 4.8 39.9 1.0 HB3 A:ASP115 4.8 35.9 1.0 N A:PHE17 4.8 25.3 1.0 C A:ASP15 4.8 28.5 1.0 O3' P:DT8 4.9 40.4 1.0 HB2 A:ASP13 4.9 26.9 1.0 HA A:CYS16 4.9 37.3 1.0 CB A:PHE17 4.9 26.0 1.0 HB3 A:PHE17 4.9 31.1 1.0 HZ1 A:LYS231 5.0 42.0 1.0 H3' A:XG4501 5.0 43.2 1.0

Magnesium binding site 2 out of 2 in the Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:42.4 occ:1.00 HO3' P:DT8 1.7 48.3 1.0 OE2 A:GLU116 1.9 39.9 1.0 OD2 A:ASP13 2.1 32.0 1.0 O1A A:XG4501 2.1 35.3 1.0 O A:HOH615 2.1 37.7 1.0 OD2 A:ASP115 2.1 36.3 1.0 O3' P:DT8 2.5 40.4 1.0 H3' P:DT8 2.7 46.1 1.0 CG A:ASP115 2.9 35.0 1.0 CG A:ASP13 3.0 29.3 1.0 C3' P:DT8 3.1 38.5 1.0 MG A:MG502 3.1 32.0 1.0 CD A:GLU116 3.1 37.1 1.0 OD1 A:ASP115 3.1 36.5 1.0 PA A:XG4501 3.2 37.5 1.0 OD1 A:ASP13 3.4 30.1 1.0 HG A:SER113 3.4 38.2 1.0 H5'A A:XG4501 3.4 45.0 1.0 HB3 A:GLU116 3.4 38.9 1.0 O5' A:XG4501 3.7 43.9 1.0 O2A A:XG4501 3.7 39.8 1.0 H5' A:XG4501 3.8 45.0 1.0 HG2 A:GLU116 3.8 40.5 1.0 C5' A:XG4501 3.8 37.6 1.0 CG A:GLU116 3.9 33.9 1.0 H4' P:DT8 3.9 44.4 1.0 OE1 A:GLU116 4.0 35.8 1.0 C4' P:DT8 4.0 37.1 1.0 OG A:SER113 4.0 31.9 1.0 H5'' P:DT8 4.1 49.8 1.0 CB A:GLU116 4.1 32.5 1.0 C2' P:DT8 4.3 38.2 1.0 CB A:ASP13 4.4 22.5 1.0 H2'' P:DT8 4.4 45.8 1.0 CB A:ASP115 4.4 30.0 1.0 O1G A:XG4501 4.4 30.7 1.0 HB2 A:ASP13 4.5 26.9 1.0 O1B A:XG4501 4.5 34.8 1.0 C A:ASP115 4.5 27.8 1.0 O A:ASP115 4.5 30.6 1.0 HA A:ASP13 4.6 30.4 1.0 C5' P:DT8 4.6 41.5 1.0 HO2A A:XG4501 4.6 47.6 1.0 HB3 A:ASP115 4.6 35.9 1.0 N3A A:XG4501 4.7 40.0 1.0 H A:ASP115 4.7 34.4 1.0 N A:GLU116 4.7 30.8 1.0 H2' P:DT8 4.8 45.8 1.0 HG3 A:GLU116 4.8 40.5 1.0 HB2 A:GLU116 4.8 38.9 1.0 H A:MET14 4.9 30.8 1.0 HZ3 A:LYS224 4.9 47.8 1.0 CA A:ASP115 4.9 30.3 1.0 H A:GLU116 5.0 36.9 1.0 HB2 A:ASP115 5.0 35.9 1.0 CA A:ASP13 5.0 25.4 1.0

O.Rechkoblit, R.E.Johnson, A.Buku, L.Prakash, S.Prakash, A.K.Aggarwal. Structural Insights Into Mutagenicity of Anticancer Nucleoside Analog Cytarabine During Replication By Dna Polymerase Eta. Sci Rep V. 9 16400 2019.
ISSN: ESSN 2045-2322
PubMed: 31704958
DOI: 10.1038/S41598-019-52703-7