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Magnesium in PDB 4dl4: Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1).

Enzymatic activity of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1).

All present enzymatic activity of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1).:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1)., PDB code: 4dl4 was solved by Y.Zhao, C.Biertumpfel, M.Gregory, Y.-J.Hua, F.Hanaoka, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 99.210, 99.210, 82.150, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 21.7

Other elements in 4dl4:

The structure of Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1). also contains other interesting chemical elements:

Platinum (Pt) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1). (pdb code 4dl4). 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 3'G of Cisplatin Crosslinked Gs (Pt-GG1)., PDB code: 4dl4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4dl4

Go back to Magnesium Binding Sites List in 4dl4
Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1).


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 3'G of Cisplatin Crosslinked Gs (Pt-GG1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:16.6
occ:1.00
O1A P:0KX10 2.1 12.7 1.0
OD1 A:ASP13 2.2 17.4 1.0
OE1 A:GLU116 2.2 21.4 1.0
OD1 A:ASP115 2.3 13.5 1.0
O3' P:DG9 2.3 17.6 0.5
O A:HOH601 2.3 16.2 1.0
O3' P:DG9 2.4 17.9 0.5
CG A:ASP115 3.1 17.3 1.0
C3' P:DG9 3.2 24.0 0.5
CG A:ASP13 3.2 17.1 1.0
PA P:0KX10 3.2 14.2 1.0
CD A:GLU116 3.3 34.1 1.0
C3' P:DG9 3.3 24.2 0.5
OD2 A:ASP115 3.3 12.0 1.0
O2A P:0KX10 3.4 19.4 1.0
MG A:MG502 3.5 10.4 1.0
OD2 A:ASP13 3.5 12.9 1.0
O5' P:0KX10 3.6 20.8 1.0
O A:HOH617 3.9 16.4 1.0
OG A:SER113 4.0 21.5 1.0
C5' P:0KX10 4.0 16.2 1.0
OE2 A:GLU116 4.0 28.1 1.0
C4' P:DG9 4.1 26.1 0.5
CG A:GLU116 4.2 22.1 1.0
C4' P:DG9 4.2 25.8 0.5
CB A:GLU116 4.3 17.5 1.0
C2' P:DG9 4.4 21.4 0.5
C2' P:DG9 4.4 21.5 0.5
CB A:ASP115 4.5 14.3 1.0
CB A:ASP13 4.5 11.8 1.0
O2G P:0KX10 4.6 10.1 1.0
N3A P:0KX10 4.7 15.2 1.0
C A:ASP115 4.7 18.4 1.0
O A:ASP115 4.7 14.1 1.0
O2B P:0KX10 4.7 11.8 1.0
C5' P:DG9 4.8 23.6 0.5
N A:GLU116 4.9 12.2 1.0

Magnesium binding site 2 out of 2 in 4dl4

Go back to Magnesium Binding Sites List in 4dl4
Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta Inserting Dcmpnpp Opposite the 3'G of Cisplatin Crosslinked Gs (Pt-GG1).


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 3'G of Cisplatin Crosslinked Gs (Pt-GG1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:10.4
occ:1.00
O1A P:0KX10 2.2 12.7 1.0
OD2 A:ASP13 2.2 12.9 1.0
O2B P:0KX10 2.2 11.8 1.0
O A:MET14 2.2 7.2 1.0
OD2 A:ASP115 2.2 12.0 1.0
O2G P:0KX10 2.2 10.1 1.0
CG A:ASP13 3.1 17.1 1.0
PB P:0KX10 3.1 14.4 1.0
CG A:ASP115 3.3 17.3 1.0
PG P:0KX10 3.3 12.9 1.0
C A:MET14 3.4 9.3 1.0
PA P:0KX10 3.4 14.2 1.0
MG A:MG501 3.5 16.6 1.0
OD1 A:ASP13 3.5 17.4 1.0
O3B P:0KX10 3.6 11.3 1.0
N3A P:0KX10 3.7 15.2 1.0
OD1 A:ASP115 3.7 13.5 1.0
O A:HOH617 3.8 16.4 1.0
NZ A:LYS231 3.9 16.0 1.0
N A:MET14 3.9 12.4 1.0
O3G P:0KX10 4.0 12.2 1.0
C5' P:0KX10 4.0 16.2 1.0
CA A:MET14 4.1 11.3 1.0
O5' P:0KX10 4.2 20.8 1.0
N A:CYS16 4.3 15.9 1.0
C A:ASP13 4.3 12.0 1.0
N A:ASP15 4.4 11.6 1.0
CB A:ASP13 4.4 11.8 1.0
CE A:LYS231 4.4 18.6 1.0
O1B P:0KX10 4.5 12.9 1.0
O1G P:0KX10 4.5 13.1 1.0
O A:HOH601 4.5 16.2 1.0
CB A:ASP115 4.5 14.3 1.0
CA A:ASP15 4.5 11.3 1.0
O2A P:0KX10 4.6 19.4 1.0
CB A:MET14 4.6 16.6 1.0
C A:ASP15 4.7 15.3 1.0
N A:PHE17 4.7 11.1 1.0
O A:ASP13 4.7 15.0 1.0
CB A:PHE17 4.8 11.3 1.0
CA A:ASP13 4.8 9.7 1.0
O A:ASP115 4.9 14.1 1.0

Reference:

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
Page generated: Mon Dec 14 12:32:36 2020

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