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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

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