Atomistry » Magnesium » PDB 4dh5-4dmz » 4dl4
Atomistry »
  Magnesium »
    PDB 4dh5-4dmz »
      4dl4 »

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

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy