Magnesium in PDB 4o3n: Crystal Structure of Human Dna Polymerase Eta in Ternary Complex with Native Dna and Incoming Nucleotide (Dcp)

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Eta in Ternary Complex with Native Dna and Incoming Nucleotide (Dcp):
2.7.7.7;

The structure of Crystal Structure of Human Dna Polymerase Eta in Ternary Complex with Native Dna and Incoming Nucleotide (Dcp), PDB code: 4o3n 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)	42.24 / 1.58
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.662, 98.662, 81.787, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 21.5

The binding sites of Magnesium atom in the Crystal Structure of Human Dna Polymerase Eta in Ternary Complex with Native Dna and Incoming Nucleotide (Dcp) (pdb code 4o3n). 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 in Ternary Complex with Native Dna and Incoming Nucleotide (Dcp), PDB code: 4o3n:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Dna Polymerase Eta in Ternary Complex with Native Dna and Incoming Nucleotide (Dcp)


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 in Ternary Complex with Native Dna and Incoming Nucleotide (Dcp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:11.0 occ:1.00 OD2 A:ASP13 2.1 14.8 1.0 OD2 A:ASP115 2.1 14.1 1.0 O1B A:0KX501 2.2 13.2 1.0 O1G A:0KX501 2.2 14.8 1.0 O A:MET14 2.2 13.4 1.0 O2A A:0KX501 2.2 15.4 1.0 CG A:ASP13 3.0 16.4 1.0 PB A:0KX501 3.2 13.2 1.0 CG A:ASP115 3.2 14.9 1.0 PA A:0KX501 3.3 15.2 1.0 C A:MET14 3.4 13.5 1.0 OD1 A:ASP13 3.4 19.8 1.0 PG A:0KX501 3.4 14.6 1.0 MG A:MG503 3.5 16.2 1.0 N3A A:0KX501 3.5 13.8 1.0 OD1 A:ASP115 3.6 16.6 1.0 O3B A:0KX501 3.6 13.7 1.0 NZ A:LYS231 3.8 14.2 1.0 O A:HOH604 3.8 21.0 1.0 N A:MET14 3.8 12.3 1.0 C5' A:0KX501 4.0 13.4 1.0 CA A:MET14 4.1 13.2 1.0 O3G A:0KX501 4.1 14.7 1.0 O5' A:0KX501 4.1 14.5 1.0 C A:ASP13 4.2 13.6 1.0 O A:HOH603 4.2 20.2 1.0 CB A:ASP13 4.3 14.7 1.0 N A:ASP15 4.4 11.4 1.0 CB A:ASP115 4.5 13.6 1.0 CE A:LYS231 4.5 19.2 1.0 CB A:MET14 4.6 15.3 1.0 O2B A:0KX501 4.6 12.6 1.0 O1A A:0KX501 4.6 19.8 1.0 N A:CYS16 4.6 11.6 1.0 O A:ASP13 4.6 13.7 1.0 O2G A:0KX501 4.6 15.2 1.0 CA A:ASP15 4.6 12.5 1.0 CA A:ASP13 4.7 12.4 1.0 N A:PHE17 4.7 11.8 1.0 C A:ASP15 4.8 11.2 1.0 CB A:PHE17 4.8 14.0 1.0 O3' P:DT8 4.9 17.1 0.3 O A:ASP115 4.9 14.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Dna Polymerase Eta in Ternary Complex with Native Dna and Incoming Nucleotide (Dcp)


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 in Ternary Complex with Native Dna and Incoming Nucleotide (Dcp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:16.2 occ:1.00 OD1 A:ASP13 2.0 19.8 1.0 O3' P:DT8 2.0 17.1 0.3 OE1 A:GLU116 2.1 21.2 1.0 O A:HOH603 2.2 20.2 1.0 OD1 A:ASP115 2.2 16.6 1.0 O2A A:0KX501 2.2 15.4 1.0 O3' P:DT8 2.4 17.8 0.7 CG A:ASP13 3.1 16.4 1.0 CG A:ASP115 3.1 14.9 1.0 CD A:GLU116 3.1 23.8 1.0 C3' P:DT8 3.2 19.8 0.3 C3' P:DT8 3.2 19.8 0.7 PA A:0KX501 3.4 15.2 1.0 OD2 A:ASP115 3.4 14.1 1.0 OD2 A:ASP13 3.4 14.8 1.0 MG A:MG502 3.5 11.0 1.0 OE2 A:GLU116 3.8 23.0 1.0 OG A:SER113 3.8 16.4 1.0 O1A A:0KX501 3.8 19.8 1.0 O5' A:0KX501 3.9 14.5 1.0 C4' P:DT8 4.1 18.8 0.3 C4' P:DT8 4.1 19.1 0.7 CG A:GLU116 4.1 14.2 1.0 O A:HOH604 4.1 21.0 1.0 NZ A:LYS224 4.2 22.4 1.0 C5' A:0KX501 4.2 13.4 1.0 CB A:GLU116 4.2 16.6 1.0 CB A:ASP13 4.4 14.7 1.0 O P:HOH102 4.4 20.5 1.0 C2' P:DT8 4.4 19.4 0.3 C2' P:DT8 4.5 19.6 0.7 CB A:ASP115 4.6 13.6 1.0 C A:ASP115 4.6 14.5 1.0 O A:ASP115 4.6 14.3 1.0 C5' P:DT8 4.7 21.6 0.7 C5' P:DT8 4.7 19.9 0.3 O1G A:0KX501 4.8 14.8 1.0 N A:GLU116 4.8 14.0 1.0 N3A A:0KX501 4.8 13.8 1.0 CB A:SER113 4.9 17.5 1.0 O A:HOH605 4.9 29.1 1.0 O1B A:0KX501 5.0 13.2 1.0

A.Patra, L.D.Nagy, Q.Zhang, Y.Su, L.Muller, F.P.Guengerich, M.Egli. Kinetics, Structure, and Mechanism of 8-Oxo-7,8-Dihydro-2'-Deoxyguanosine Bypass By Human Dna Polymerase Eta J.Biol.Chem. V. 289 16867 2014.
ISSN: ISSN 0021-9258
PubMed: 24759104
DOI: 10.1074/JBC.M114.551820