Magnesium in PDB 6q02: Polymerase Eta-Catalyzed Insertion of the Mismatched A Opposite Template Cytarabine (Arac) Residue

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

The structure of Polymerase Eta-Catalyzed Insertion of the Mismatched A Opposite Template Cytarabine (Arac) Residue, PDB code: 6q02 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)	85.72 / 2.09
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.974, 98.974, 81.791, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 24

The binding sites of Magnesium atom in the Polymerase Eta-Catalyzed Insertion of the Mismatched A Opposite Template Cytarabine (Arac) Residue (pdb code 6q02). 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 the Mismatched A Opposite Template Cytarabine (Arac) Residue, PDB code: 6q02:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Polymerase Eta-Catalyzed Insertion of the Mismatched A 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 the Mismatched A Opposite Template Cytarabine (Arac) Residue within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:30.7 occ:1.00 OD1 A:ASP13 2.0 42.5 1.0 O1B A:DZ4503 2.0 36.4 1.0 O1G A:DZ4503 2.1 34.0 1.0 OD2 A:ASP115 2.1 35.5 1.0 O1A A:DZ4503 2.2 39.6 1.0 O A:MET14 2.3 35.4 1.0 CG A:ASP13 3.0 35.2 1.0 H5' A:DZ4503 3.0 42.4 1.0 CG A:ASP115 3.2 38.9 1.0 PB A:DZ4503 3.2 37.4 1.0 OD2 A:ASP13 3.2 46.5 1.0 MG A:MG502 3.2 36.9 0.5 PA A:DZ4503 3.4 39.4 1.0 PG A:DZ4503 3.4 37.6 1.0 C A:MET14 3.5 34.4 1.0 HZ1 A:LYS231 3.6 47.7 1.0 OD1 A:ASP115 3.6 35.9 1.0 O A:HOH601 3.6 45.3 1.0 N3A A:DZ4503 3.7 41.0 1.0 O3B A:DZ4503 3.8 39.1 1.0 C5' A:DZ4503 3.8 35.3 1.0 H A:MET14 4.0 44.3 1.0 N A:MET14 4.0 36.9 1.0 H5'A A:DZ4503 4.0 42.4 1.0 HB2 A:PHE17 4.1 38.5 1.0 O A:HOH737 4.1 45.1 1.0 H A:PHE17 4.1 42.3 1.0 O5' A:DZ4503 4.1 39.8 1.0 HB2 A:MET14 4.1 45.1 1.0 HO3' P:DT8 4.2 51.3 1.0 HA A:ASP15 4.2 41.5 1.0 HE2 A:LYS231 4.2 51.3 1.0 O2G A:DZ4503 4.2 38.1 1.0 CA A:MET14 4.3 36.9 1.0 CB A:ASP13 4.3 38.6 1.0 C A:ASP13 4.3 34.9 1.0 NZ A:LYS231 4.4 39.8 1.0 HB2 A:ASP115 4.4 37.1 1.0 CB A:ASP115 4.5 30.9 1.0 H A:CYS16 4.5 41.9 1.0 O3G A:DZ4503 4.5 38.9 1.0 O2B A:DZ4503 4.5 36.4 1.0 N A:ASP15 4.5 35.0 1.0 HZ3 A:LYS231 4.6 47.7 1.0 O2A A:DZ4503 4.6 37.4 1.0 HN3A A:DZ4503 4.6 49.3 1.0 HB3 A:ASP13 4.7 46.4 1.0 N A:CYS16 4.7 34.9 1.0 CE A:LYS231 4.7 42.7 1.0 HA A:ASP13 4.7 41.3 1.0 HE3 A:LYS231 4.7 51.3 1.0 CA A:ASP15 4.7 34.6 1.0 CB A:MET14 4.7 37.6 1.0 CA A:ASP13 4.8 34.4 1.0 O A:ASP115 4.8 38.2 1.0 N A:PHE17 4.8 35.2 1.0 O A:ASP13 4.8 37.7 1.0 HB3 A:ASP115 4.9 37.1 1.0 C A:ASP15 4.9 36.6 1.0 CB A:PHE17 4.9 32.1 1.0 HA A:CYS16 4.9 42.5 1.0 HB3 A:PHE17 4.9 38.5 1.0 O3' P:DT8 5.0 42.7 1.0 HB2 A:ASP13 5.0 46.4 1.0

Magnesium binding site 2 out of 2 in the Polymerase Eta-Catalyzed Insertion of the Mismatched A 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 the Mismatched A Opposite Template Cytarabine (Arac) Residue within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:36.9 occ:0.54 HO3' P:DT8 1.6 51.3 1.0 OE2 A:GLU116 2.1 56.2 1.0 OD1 A:ASP115 2.1 35.9 1.0 O A:HOH601 2.1 45.3 1.0 OD2 A:ASP13 2.2 46.5 1.0 O1A A:DZ4503 2.4 39.6 1.0 O3' P:DT8 2.4 42.7 1.0 CG A:ASP115 3.0 38.9 1.0 CG A:ASP13 3.0 35.2 1.0 H3' P:DT8 3.0 49.8 1.0 CD A:GLU116 3.1 45.8 1.0 HB3 A:GLU116 3.1 49.5 1.0 OD2 A:ASP115 3.1 35.5 1.0 HG A:SER113 3.2 47.8 1.0 MG A:MG501 3.2 30.7 1.0 C3' P:DT8 3.3 41.5 1.0 OD1 A:ASP13 3.4 42.5 1.0 H5'A A:DZ4503 3.6 42.4 1.0 PA A:DZ4503 3.6 39.4 1.0 OE1 A:GLU116 3.8 43.6 1.0 OG A:SER113 3.9 39.8 1.0 CG A:GLU116 3.9 39.8 1.0 CB A:GLU116 3.9 41.2 1.0 O5' A:DZ4503 4.0 39.8 1.0 H4' P:DT8 4.0 48.9 1.0 H5' A:DZ4503 4.0 42.4 1.0 HG2 A:GLU116 4.1 47.7 1.0 C5' A:DZ4503 4.1 35.3 1.0 O2A A:DZ4503 4.1 37.4 1.0 C4' P:DT8 4.2 40.7 1.0 HB2 A:ASP13 4.2 46.4 1.0 CB A:ASP13 4.2 38.6 1.0 H5'' P:DT8 4.2 52.1 1.0 O A:ASP115 4.3 38.2 1.0 C A:ASP115 4.3 37.2 1.0 CB A:ASP115 4.4 30.9 1.0 HA A:ASP13 4.4 41.3 1.0 O A:HOH737 4.5 45.1 1.0 H2'' P:DT8 4.5 51.3 1.0 C2' P:DT8 4.5 42.7 1.0 HB2 A:GLU116 4.5 49.5 1.0 H A:ASP115 4.5 44.1 1.0 N A:GLU116 4.6 42.6 1.0 O1G A:DZ4503 4.6 34.0 1.0 O1B A:DZ4503 4.7 36.4 1.0 C5' P:DT8 4.8 43.4 1.0 HG3 A:GLU116 4.8 47.7 1.0 HB3 A:ASP115 4.8 37.1 1.0 CA A:ASP115 4.8 36.5 1.0 H A:MET14 4.9 44.3 1.0 CA A:GLU116 4.9 38.3 1.0 CA A:ASP13 4.9 34.4 1.0 H A:GLU116 4.9 51.2 1.0 HZ1 A:LYS224 5.0 62.5 1.0 HB2 A:ASP115 5.0 37.1 1.0 HB3 A:ASP13 5.0 46.4 1.0 HO2A A:DZ4503 5.0 44.9 1.0 H2' P:DT8 5.0 51.3 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