Magnesium in PDB 4dl5: Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2).

All present enzymatic activity of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2).:
2.7.7.7;

The structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2)., PDB code: 4dl5 was solved by Y.Zhao, C.Biertumpfel, M.Gregory, F.Hanaoka, Y.Hua, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.92
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.414, 99.414, 82.085, 90.00, 90.00, 120.00
R / Rfree (%)	24.5 / 25.5

The structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2). also contains other interesting chemical elements:

Platinum

(Pt)

2 atoms

The binding sites of Magnesium atom in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2). (pdb code 4dl5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2)., PDB code: 4dl5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:67.5 occ:0.50 O2B A:0KX503 2.1 69.8 0.5 OD1 A:ASP115 2.2 75.2 1.0 O2G A:0KX503 2.2 68.6 0.5 OP1 P:DC9 2.3 80.0 0.5 O1A A:0KX503 2.3 78.3 0.5 O A:MET14 2.3 75.5 1.0 OD1 A:ASP13 2.4 72.1 1.0 PB A:0KX503 3.1 67.5 0.5 CG A:ASP115 3.1 72.5 1.0 CG A:ASP13 3.2 76.2 1.0 PG A:0KX503 3.3 63.4 0.5 PA A:0KX503 3.3 82.4 0.5 N3A A:0KX503 3.4 74.8 0.5 OD2 A:ASP13 3.4 80.0 1.0 C A:MET14 3.5 68.7 1.0 OD2 A:ASP115 3.5 73.3 1.0 MG A:MG502 3.6 71.0 0.5 O3B A:0KX503 3.6 73.0 0.5 P P:DC9 3.7 83.9 0.5 O1G A:0KX503 4.0 67.6 0.5 N A:MET14 4.0 71.4 1.0 C5' A:0KX503 4.0 76.9 0.5 NZ A:LYS231 4.0 70.7 1.0 O5' A:0KX503 4.1 79.3 0.5 CA A:MET14 4.2 64.8 1.0 O1B A:0KX503 4.2 71.6 0.5 C5' P:DC9 4.2 77.1 0.5 O5' P:DC9 4.3 80.2 0.5 CB A:ASP115 4.3 65.4 1.0 N A:CYS16 4.4 68.3 1.0 C A:ASP13 4.4 72.3 1.0 O3G A:0KX503 4.4 64.4 0.5 N A:ASP15 4.5 68.3 1.0 O2A A:0KX503 4.5 77.5 0.5 CB A:ASP13 4.5 70.6 1.0 CB A:MET14 4.6 62.1 1.0 O3' P:DA8 4.6 81.7 0.5 CE A:LYS231 4.6 75.7 1.0 CA A:ASP15 4.6 69.1 1.0 N A:PHE17 4.6 68.7 1.0 OP2 P:DC9 4.7 78.1 0.5 C A:ASP15 4.7 70.4 1.0 CB A:PHE17 4.8 66.5 1.0 O A:ASP13 4.9 73.5 1.0 CA A:ASP13 4.9 70.6 1.0 O A:ASP115 4.9 70.7 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 5'G of Cisplatin Crosslinked Gs (Pt-GG2). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:71.0 occ:0.50 O3' P:DA8 2.0 81.7 0.5 OE2 A:GLU116 2.2 80.3 1.0 OD2 A:ASP115 2.2 73.3 1.0 O1A A:0KX503 2.3 78.3 0.5 OD2 A:ASP13 2.3 80.0 1.0 OP1 P:DC9 2.3 80.0 0.5 O3' P:DC9 2.5 79.8 0.5 P P:DC9 2.7 83.9 0.5 C3' P:DC9 3.0 82.0 0.5 CG A:ASP115 3.2 72.5 1.0 PA A:0KX503 3.2 82.4 0.5 CD A:GLU116 3.3 78.1 1.0 C3' P:DA8 3.3 81.9 0.5 CG A:ASP13 3.4 76.2 1.0 OD1 A:ASP115 3.6 75.2 1.0 MG A:MG501 3.6 67.5 0.5 C4' P:DA8 3.6 80.8 0.5 O5' A:0KX503 3.6 79.3 0.5 O2A A:0KX503 3.6 77.5 0.5 OG A:SER113 3.7 76.3 1.0 O5' P:DC9 3.7 80.2 0.5 C5' P:DC9 3.8 77.1 0.5 OD1 A:ASP13 3.8 72.1 1.0 OP2 P:DC9 3.9 78.1 0.5 OE1 A:GLU116 4.1 80.5 1.0 C5' A:0KX503 4.1 76.9 0.5 C5' P:DA8 4.1 83.4 0.5 C2' P:DC9 4.1 82.2 0.5 C4' P:DC9 4.2 80.3 0.5 CG A:GLU116 4.2 69.1 1.0 CB A:GLU116 4.2 66.0 1.0 C2' P:DA8 4.3 82.6 0.5 NZ A:LYS224 4.5 75.4 1.0 CB A:ASP115 4.5 65.4 1.0 N3A A:0KX503 4.6 74.8 0.5 CB A:ASP13 4.7 70.6 1.0 CB A:SER113 4.7 69.8 1.0 C A:ASP115 4.7 74.9 1.0 O2G A:0KX503 4.7 68.6 0.5 C5' P:DC9 4.8 83.2 0.5 N A:GLU116 4.8 70.6 1.0 O2B A:0KX503 4.9 69.8 0.5 O A:ASP115 4.9 70.7 1.0 O4' P:DA8 4.9 80.5 0.5

Y.Zhao, C.Biertumpfel, M.T.Gregory, Y.J.Hua, F.Hanaoka, W.Yang. Structural Basis For Chemoresistance to Cisplatin Mediated By Dna Polymerase Eta Proc.Natl.Acad.Sci.Usa V. 109 7269 2012.
ISSN: ISSN 0027-8424
PubMed: 22529383
DOI: 10.1073/PNAS.1202681109