Atomistry » Magnesium » PDB 4dhf-4do9 » 4dl6
Atomistry »
  Magnesium »
    PDB 4dhf-4do9 »
      4dl6 »

Magnesium in PDB 4dl6: Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3).

Enzymatic activity of Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3).

All present enzymatic activity of Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3).:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3)., PDB code: 4dl6 was solved by Y.Zhao, C.Biertumpfel, M.Gregory, Y.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 / 2.50
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.780, 98.780, 81.510, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 22

Other elements in 4dl6:

The structure of Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3). 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 Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3). (pdb code 4dl6). 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 Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3)., PDB code: 4dl6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4dl6

Go back to Magnesium Binding Sites List in 4dl6
Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3).


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 Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:39.0
occ:1.00
O1B A:XG4503 2.0 35.7 1.0
OD1 A:ASP115 2.1 40.1 1.0
O A:MET14 2.1 33.6 1.0
OD1 A:ASP13 2.1 35.4 1.0
O1G A:XG4503 2.2 37.9 1.0
O1A A:XG4503 2.2 31.6 1.0
CG A:ASP13 3.1 35.3 1.0
PB A:XG4503 3.2 37.8 1.0
CG A:ASP115 3.3 36.5 1.0
C A:MET14 3.3 36.0 1.0
PA A:XG4503 3.5 35.2 1.0
PG A:XG4503 3.5 33.9 1.0
O3B A:XG4503 3.5 34.5 1.0
OD2 A:ASP13 3.6 40.3 1.0
N3A A:XG4503 3.6 37.3 1.0
MG A:MG502 3.8 38.4 1.0
C5' A:XG4503 3.8 33.3 1.0
OD2 A:ASP115 3.9 37.8 1.0
N A:MET14 3.9 30.3 1.0
O2G A:XG4503 4.0 34.5 1.0
O5' A:XG4503 4.1 35.6 1.0
CA A:MET14 4.1 29.9 1.0
C A:ASP13 4.3 35.5 1.0
N A:ASP15 4.3 36.0 1.0
NZ A:LYS231 4.3 31.5 1.0
CB A:ASP13 4.4 32.8 1.0
CA A:ASP15 4.4 36.4 1.0
CB A:ASP115 4.4 30.3 1.0
N A:CYS16 4.5 38.0 1.0
O A:HOH631 4.5 43.5 1.0
O2B A:XG4503 4.5 40.3 1.0
CB A:MET14 4.6 37.7 1.0
O2A A:XG4503 4.6 37.4 1.0
O3G A:XG4503 4.7 35.1 1.0
C A:ASP15 4.7 38.2 1.0
CB A:PHE17 4.7 27.4 1.0
N A:PHE17 4.7 32.2 1.0
CA A:ASP13 4.8 30.5 1.0
O A:ASP13 4.8 39.7 1.0
O A:ASP115 4.8 36.9 1.0
CE A:LYS231 5.0 33.2 1.0

Magnesium binding site 2 out of 2 in 4dl6

Go back to Magnesium Binding Sites List in 4dl6
Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3).


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 Extending Primer Immediately After Cisplatin Crosslink (Pt-GG3). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:38.4
occ:1.00
O3' P:DC9 2.3 38.0 1.0
OD2 A:ASP13 2.3 40.3 1.0
O1A A:XG4503 2.4 31.6 1.0
OD2 A:ASP115 2.4 37.8 1.0
O A:HOH631 2.5 43.5 1.0
C3' P:DC9 2.9 47.2 1.0
OE2 A:GLU116 3.0 51.1 1.0
CG A:ASP115 3.3 36.5 1.0
CG A:ASP13 3.3 35.3 1.0
OD1 A:ASP115 3.4 40.1 1.0
PA A:XG4503 3.4 35.2 1.0
CD A:GLU116 3.5 46.2 1.0
O2A A:XG4503 3.6 37.4 1.0
O5' A:XG4503 3.6 35.6 1.0
OD1 A:ASP13 3.6 35.4 1.0
OG A:SER113 3.7 40.9 1.0
MG A:MG501 3.8 39.0 1.0
CG A:GLU116 3.8 38.1 1.0
C4' P:DC9 3.9 51.3 1.0
C2' P:DC9 4.1 50.9 1.0
CB A:GLU116 4.1 29.4 1.0
C5' A:XG4503 4.2 33.3 1.0
OE1 A:GLU116 4.2 51.7 1.0
C5' P:DC9 4.4 52.2 1.0
CB A:ASP13 4.7 32.8 1.0
CB A:ASP115 4.7 30.3 1.0
N A:GLU116 4.7 31.9 1.0
C A:ASP115 4.7 34.5 1.0
O5' P:DC9 4.8 58.2 1.0
O1G A:XG4503 4.8 37.9 1.0
CB A:SER113 4.9 38.4 1.0
N3A A:XG4503 4.9 37.3 1.0
O A:ASP115 5.0 36.9 1.0
NZ A:LYS224 5.0 45.7 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 12:34:18 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy