Magnesium in PDB 4ru9: Crystal Structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Mefapy-Dg Adducted Dna Template

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Mefapy-Dg Adducted Dna Template:
2.7.7.7;

The structure of Crystal Structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Mefapy-Dg Adducted Dna Template, PDB code: 4ru9 was solved by A.Patra, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.65
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.971, 98.971, 81.624, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 22.9

The binding sites of Magnesium atom in the Crystal Structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Mefapy-Dg Adducted Dna Template (pdb code 4ru9). 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 Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Mefapy-Dg Adducted Dna Template, PDB code: 4ru9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Mefapy-Dg Adducted Dna Template


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 Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Mefapy-Dg Adducted Dna Template within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:24.3 occ:1.00 OD2 A:ASP13 1.9 30.1 1.0 O1B A:0KX501 1.9 31.1 1.0 OD2 A:ASP115 2.1 34.4 1.0 O1A A:0KX501 2.1 32.5 1.0 O3G A:0KX501 2.2 27.6 1.0 O A:MET14 2.2 28.1 1.0 CG A:ASP13 2.8 32.1 1.0 PB A:0KX501 3.0 28.3 1.0 CG A:ASP115 3.1 35.5 1.0 OD1 A:ASP13 3.1 31.6 1.0 MG A:MG503 3.2 39.8 1.0 PA A:0KX501 3.3 30.2 1.0 PG A:0KX501 3.4 31.2 1.0 C A:MET14 3.4 31.1 1.0 N3A A:0KX501 3.5 32.6 1.0 OD1 A:ASP115 3.5 40.8 1.0 O3B A:0KX501 3.6 29.7 1.0 C5' A:0KX501 3.8 35.0 1.0 N A:MET14 3.9 30.1 1.0 O A:HOH695 3.9 41.0 1.0 O5' A:0KX501 4.0 34.2 1.0 O2G A:0KX501 4.0 30.3 1.0 NZ A:LYS231 4.1 41.4 1.0 CA A:MET14 4.2 32.5 1.0 CB A:ASP13 4.2 30.9 1.0 O2B A:0KX501 4.3 30.1 1.0 C A:ASP13 4.3 30.3 1.0 O A:HOH617 4.4 38.0 1.0 CB A:ASP115 4.4 34.4 1.0 N A:ASP15 4.4 30.1 1.0 O2A A:0KX501 4.6 31.9 1.0 N A:CYS16 4.6 29.0 1.0 O1G A:0KX501 4.6 31.5 1.0 CE A:LYS231 4.7 40.7 1.0 CB A:MET14 4.7 31.5 1.0 CA A:ASP15 4.7 29.8 1.0 N A:PHE17 4.7 25.8 1.0 CA A:ASP13 4.7 30.2 1.0 C A:ASP15 4.8 28.4 1.0 CB A:PHE17 4.8 23.9 1.0 O A:ASP13 4.9 32.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Mefapy-Dg Adducted Dna Template


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 Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Mefapy-Dg Adducted Dna Template within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:39.8 occ:1.00 O1A A:0KX501 2.0 32.5 1.0 OD1 A:ASP13 2.1 31.6 1.0 OD1 A:ASP115 2.2 40.8 1.0 OE2 A:GLU116 2.2 42.0 1.0 O A:HOH617 2.3 38.0 1.0 O3' P:DT8 2.3 38.0 1.0 PA A:0KX501 2.9 30.2 1.0 C3' P:DT8 3.1 38.4 1.0 CG A:ASP115 3.1 35.5 1.0 CG A:ASP13 3.1 32.1 1.0 MG A:MG502 3.2 24.3 1.0 O5' A:0KX501 3.3 34.2 1.0 OD2 A:ASP115 3.3 34.4 1.0 CD A:GLU116 3.4 40.0 1.0 OD2 A:ASP13 3.5 30.1 1.0 O2A A:0KX501 3.5 31.9 1.0 C5' A:0KX501 3.8 35.0 1.0 O A:HOH695 3.9 41.0 1.0 OG A:SER113 4.0 30.3 1.0 C4' P:DT8 4.1 39.2 1.0 OE1 A:GLU116 4.1 43.2 1.0 C2' P:DT8 4.2 39.5 1.0 N3A A:0KX501 4.4 32.6 1.0 CG A:GLU116 4.4 38.4 1.0 O A:HOH618 4.4 36.4 1.0 O1B A:0KX501 4.4 31.1 1.0 O3G A:0KX501 4.4 27.6 1.0 CB A:ASP13 4.5 30.9 1.0 CB A:ASP115 4.5 34.4 1.0 CB A:GLU116 4.6 35.4 1.0 C5' P:DT8 4.7 41.6 1.0 C A:ASP115 4.9 36.0 1.0 CB A:SER113 5.0 31.2 1.0

A.Patra, S.Banerjee, T.L.Johnson Salyard, C.K.Malik, P.P.Christov, C.J.Rizzo, M.P.Stone, M.Egli. Structural Basis For Error-Free Bypass of the 5-N-Methylformamidopyrimidine-Dg Lesion By Human Dna Polymerase Eta and Sulfolobus Solfataricus P2 Polymerase IV. J.Am.Chem.Soc. V. 137 7011 2015.
ISSN: ISSN 0002-7863
PubMed: 25988947
DOI: 10.1021/JACS.5B02701