Magnesium in PDB 4rnm: Crystal Structure of Human Polymerase Eta Inserting Dampnpp Opposite Dna Template Containing An Abasic Site

All present enzymatic activity of Crystal Structure of Human Polymerase Eta Inserting Dampnpp Opposite Dna Template Containing An Abasic Site:
2.7.7.7;

The structure of Crystal Structure of Human Polymerase Eta Inserting Dampnpp Opposite Dna Template Containing An Abasic Site, PDB code: 4rnm 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)	42.73 / 2.14
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.679, 98.679, 81.447, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 21.9

The binding sites of Magnesium atom in the Crystal Structure of Human Polymerase Eta Inserting Dampnpp Opposite Dna Template Containing An Abasic Site (pdb code 4rnm). 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 Polymerase Eta Inserting Dampnpp Opposite Dna Template Containing An Abasic Site, PDB code: 4rnm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Polymerase Eta Inserting Dampnpp Opposite Dna Template Containing An Abasic Site


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 Polymerase Eta Inserting Dampnpp Opposite Dna Template Containing An Abasic Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.4 occ:1.00 O3G A:DZ4501 2.0 20.3 1.0 OD2 A:ASP13 2.1 28.6 1.0 O1B A:DZ4501 2.1 20.5 1.0 OD2 A:ASP115 2.1 20.6 1.0 O1A A:DZ4501 2.2 23.3 1.0 O A:MET14 2.2 22.5 1.0 CG A:ASP13 3.1 26.4 1.0 PB A:DZ4501 3.1 23.6 1.0 CG A:ASP115 3.2 23.5 1.0 PG A:DZ4501 3.3 23.7 1.0 PA A:DZ4501 3.3 23.3 1.0 C A:MET14 3.4 21.2 1.0 N3A A:DZ4501 3.5 27.6 1.0 OD1 A:ASP13 3.5 24.8 1.0 MG A:MG503 3.5 17.6 1.0 O3B A:DZ4501 3.6 22.9 1.0 OD1 A:ASP115 3.7 22.4 1.0 O A:HOH689 3.7 26.9 1.0 NZ A:LYS231 3.8 19.9 1.0 N A:MET14 3.9 18.7 1.0 O1G A:DZ4501 4.0 16.9 1.0 C5' A:DZ4501 4.0 19.0 1.0 O A:HOH667 4.1 19.3 1.0 CA A:MET14 4.2 20.5 1.0 O5' A:DZ4501 4.2 23.2 1.0 C A:ASP13 4.3 20.7 1.0 CB A:ASP13 4.3 20.6 1.0 N A:ASP15 4.4 22.2 1.0 O2G A:DZ4501 4.5 21.1 1.0 O2B A:DZ4501 4.5 20.4 1.0 CB A:ASP115 4.5 17.8 1.0 O2A A:DZ4501 4.5 21.7 1.0 N A:CYS16 4.6 17.9 1.0 CA A:ASP15 4.6 20.1 1.0 CB A:MET14 4.6 22.6 1.0 O A:ASP13 4.7 19.0 1.0 C A:ASP15 4.7 23.0 1.0 N A:PHE17 4.8 19.0 1.0 CA A:ASP13 4.8 20.4 1.0 CB A:PHE17 4.8 17.3 1.0 CE A:LYS231 4.8 39.4 1.0 O A:ASP115 4.9 22.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Polymerase Eta Inserting Dampnpp Opposite Dna Template Containing An Abasic Site


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 Polymerase Eta Inserting Dampnpp Opposite Dna Template Containing An Abasic Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:17.6 occ:1.00 OD1 A:ASP13 2.0 24.8 1.0 OE2 A:GLU116 2.1 28.1 1.0 O A:HOH667 2.1 19.3 1.0 OD1 A:ASP115 2.1 22.4 1.0 O3' P:DT8 2.3 26.8 1.0 O1A A:DZ4501 2.3 23.3 1.0 CG A:ASP13 3.0 26.4 1.0 CG A:ASP115 3.1 23.5 1.0 CD A:GLU116 3.1 29.4 1.0 C3' P:DT8 3.2 22.1 1.0 OD2 A:ASP115 3.3 20.6 1.0 OD2 A:ASP13 3.3 28.6 1.0 PA A:DZ4501 3.5 23.3 1.0 MG A:MG502 3.5 20.4 1.0 OG A:SER113 3.7 21.9 1.0 O2A A:DZ4501 3.8 21.7 1.0 OE1 A:GLU116 3.8 29.6 1.0 O5' A:DZ4501 3.9 23.2 1.0 CG A:GLU116 4.0 24.3 1.0 CB A:GLU116 4.1 18.1 1.0 C4' P:DT8 4.1 25.7 1.0 C5' A:DZ4501 4.1 19.0 1.0 O A:HOH689 4.2 26.9 1.0 CB A:ASP13 4.4 20.6 1.0 NZ A:LYS224 4.4 31.8 1.0 O P:HOH105 4.5 26.8 1.0 CB A:ASP115 4.5 17.8 1.0 C2' P:DT8 4.5 27.9 1.0 C A:ASP115 4.5 24.3 1.0 O A:ASP115 4.6 22.8 1.0 O3G A:DZ4501 4.7 20.3 1.0 N A:GLU116 4.7 17.0 1.0 C5' P:DT8 4.8 28.0 1.0 CB A:SER113 4.8 25.4 1.0 O1B A:DZ4501 4.9 20.5 1.0 N3A A:DZ4501 4.9 27.6 1.0 CA A:ASP115 4.9 19.8 1.0

A.Patra, Q.Zhang, L.Lei, Y.Su, M.Egli, F.P.Guengerich. Structural and Kinetic Analysis of Nucleoside Triphosphate Incorporation Opposite An Abasic Site By Human Translesion Dna Polymerase Eta J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M115.637561