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Magnesium in PDB 4q8f: Human Dna Polymerase Eta Extending Primer Immediately After A Phenanthriplatin Adducted G

Enzymatic activity of Human Dna Polymerase Eta Extending Primer Immediately After A Phenanthriplatin Adducted G

All present enzymatic activity of Human Dna Polymerase Eta Extending Primer Immediately After A Phenanthriplatin Adducted G:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta Extending Primer Immediately After A Phenanthriplatin Adducted G, PDB code: 4q8f was solved by M.T.Gregory, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.55 / 2.80
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.692, 98.692, 81.812, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 24.3

Other elements in 4q8f:

The structure of Human Dna Polymerase Eta Extending Primer Immediately After A Phenanthriplatin Adducted G 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 A Phenanthriplatin Adducted G (pdb code 4q8f). 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 A Phenanthriplatin Adducted G, PDB code: 4q8f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4q8f

Go back to Magnesium Binding Sites List in 4q8f
Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta Extending Primer Immediately After A Phenanthriplatin Adducted G


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 A Phenanthriplatin Adducted G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:16.4
occ:1.00
O1B A:XG4503 2.1 21.2 0.2
OD1 A:ASP13 2.1 23.9 1.0
OD2 A:ASP115 2.1 23.6 1.0
O1B A:XG4503 2.2 20.9 0.8
O1A A:XG4503 2.2 21.4 0.8
O A:MET14 2.2 23.0 1.0
O1G A:XG4503 2.2 20.5 0.8
O1G A:XG4503 2.3 20.7 0.2
O1A A:XG4503 2.3 22.0 0.2
CG A:ASP13 2.8 23.2 1.0
OD2 A:ASP13 2.9 25.3 1.0
CG A:ASP115 3.2 23.8 1.0
PB A:XG4503 3.3 22.0 0.2
PB A:XG4503 3.3 22.0 0.8
C A:MET14 3.4 19.6 1.0
PA A:XG4503 3.5 22.3 0.8
PA A:XG4503 3.6 22.4 0.2
OD1 A:ASP115 3.6 25.5 1.0
PG A:XG4503 3.6 20.7 0.8
PG A:XG4503 3.6 20.8 0.2
MG A:MG502 3.6 29.3 1.0
N3A A:XG4503 3.8 20.9 0.8
N3A A:XG4503 3.8 20.8 0.2
N A:MET14 3.9 17.2 1.0
O3B A:XG4503 3.9 24.2 0.2
O3B A:XG4503 3.9 24.6 0.8
C5' A:XG4503 4.0 24.0 0.2
O A:HOH616 4.1 22.7 1.0
CA A:MET14 4.1 19.2 1.0
CB A:ASP13 4.2 18.1 1.0
C A:ASP13 4.2 21.1 1.0
C5' A:XG4503 4.2 24.4 0.8
NZ A:LYS231 4.2 22.0 1.0
O A:HOH615 4.2 25.8 1.0
O5' A:XG4503 4.3 24.3 0.2
O2G A:XG4503 4.4 19.8 0.8
O5' A:XG4503 4.4 24.3 0.8
CB A:ASP115 4.5 20.0 1.0
N A:ASP15 4.5 17.9 1.0
O2G A:XG4503 4.5 20.1 0.2
O2B A:XG4503 4.5 21.7 0.2
O A:ASP13 4.6 19.7 1.0
O2A A:XG4503 4.6 27.3 0.8
O3G A:XG4503 4.6 21.4 0.2
O2B A:XG4503 4.6 21.7 0.8
CA A:ASP13 4.6 18.8 1.0
CB A:MET14 4.7 18.8 1.0
O3G A:XG4503 4.7 21.4 0.8
CA A:ASP15 4.7 18.0 1.0
N A:CYS16 4.7 19.3 1.0
O2A A:XG4503 4.8 26.6 0.2
O A:ASP115 4.9 21.0 1.0
C A:ASP15 4.9 20.9 1.0
N A:PHE17 5.0 21.7 1.0
CE A:LYS231 5.0 21.8 1.0
CB A:PHE17 5.0 17.4 1.0

Magnesium binding site 2 out of 2 in 4q8f

Go back to Magnesium Binding Sites List in 4q8f
Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta Extending Primer Immediately After A Phenanthriplatin Adducted G


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 A Phenanthriplatin Adducted G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:29.3
occ:1.00
OD1 A:ASP115 2.1 25.5 1.0
OE2 A:GLU116 2.1 30.9 1.0
O A:HOH615 2.3 25.8 1.0
O1A A:XG4503 2.4 21.4 0.8
O1A A:XG4503 2.4 22.0 0.2
OD2 A:ASP13 2.4 25.3 1.0
O3' P:DC8 2.7 28.5 0.5
O3' P:DC8 2.8 28.4 0.5
CG A:ASP115 3.1 23.8 1.0
C3' P:DC8 3.1 30.2 0.5
C3' P:DC8 3.2 30.2 0.5
PA A:XG4503 3.3 22.3 0.8
CD A:GLU116 3.3 25.5 1.0
PA A:XG4503 3.3 22.4 0.2
OG A:SER113 3.4 23.4 1.0
OD2 A:ASP115 3.5 23.6 1.0
O2A A:XG4503 3.5 27.3 0.8
CG A:ASP13 3.6 23.2 1.0
O5' A:XG4503 3.6 24.3 0.2
O5' A:XG4503 3.6 24.3 0.8
MG A:MG501 3.6 16.4 1.0
O2A A:XG4503 3.7 26.6 0.2
C5' A:XG4503 3.8 24.0 0.2
C5' A:XG4503 3.9 24.4 0.8
C4' P:DC8 4.0 31.1 0.5
C4' P:DC8 4.1 31.1 0.5
CG A:GLU116 4.1 19.0 1.0
OD1 A:ASP13 4.1 23.9 1.0
OE1 A:GLU116 4.2 27.9 1.0
CB A:GLU116 4.3 20.9 1.0
C5' P:DC8 4.3 32.9 0.5
O A:HOH616 4.3 22.7 1.0
C5' P:DC8 4.3 31.4 0.5
C2' P:DC8 4.4 30.4 0.5
O5' P:DC8 4.4 35.1 0.5
CB A:ASP115 4.4 20.0 1.0
C2' P:DC8 4.5 30.4 0.5
CB A:SER113 4.5 21.0 1.0
C A:ASP115 4.6 21.7 1.0
NZ A:LYS224 4.7 26.6 1.0
N A:GLU116 4.7 20.5 1.0
CB A:ASP13 4.8 18.1 1.0
O1B A:XG4503 4.8 21.2 0.2
O A:ASP115 4.9 21.0 1.0
O1B A:XG4503 4.9 20.9 0.8
CA A:ASP115 4.9 22.0 1.0
N3A A:XG4503 4.9 20.9 0.8
N A:ASP115 4.9 20.7 1.0
N3A A:XG4503 4.9 20.8 0.2
O5' P:DC8 4.9 36.6 0.5

Reference:

M.T.Gregory, G.Y.Park, T.C.Johnstone, Y.S.Lee, W.Yang, S.J.Lippard. Structural and Mechanistic Studies of Polymerase Eta Bypass of Phenanthriplatin Dna Damage. Proc.Natl.Acad.Sci.Usa V. 111 9133 2014.
ISSN: ISSN 0027-8424
PubMed: 24927576
DOI: 10.1073/PNAS.1405739111
Page generated: Mon Dec 14 19:22:06 2020

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