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Magnesium in PDB 5dga: Crystal Structure of Human Dna Polymerase Eta Extending An 1,N6- Ethenodeoxyadenosine : Dt Pair By Inserting Dtmpnpp Opposite Template Da

Enzymatic activity of Crystal Structure of Human Dna Polymerase Eta Extending An 1,N6- Ethenodeoxyadenosine : Dt Pair By Inserting Dtmpnpp Opposite Template Da

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Eta Extending An 1,N6- Ethenodeoxyadenosine : Dt Pair By Inserting Dtmpnpp Opposite Template Da:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Human Dna Polymerase Eta Extending An 1,N6- Ethenodeoxyadenosine : Dt Pair By Inserting Dtmpnpp Opposite Template Da, PDB code: 5dga was solved by A.Patra, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.21 / 2.30
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.419, 98.419, 81.974, 90.00, 90.00, 120.00
R / Rfree (%) 15.6 / 23.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Dna Polymerase Eta Extending An 1,N6- Ethenodeoxyadenosine : Dt Pair By Inserting Dtmpnpp Opposite Template Da (pdb code 5dga). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Dna Polymerase Eta Extending An 1,N6- Ethenodeoxyadenosine : Dt Pair By Inserting Dtmpnpp Opposite Template Da, PDB code: 5dga:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5dga

Go back to Magnesium Binding Sites List in 5dga
Magnesium binding site 1 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Extending An 1,N6- Ethenodeoxyadenosine : Dt Pair By Inserting Dtmpnpp Opposite Template Da


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Dna Polymerase Eta Extending An 1,N6- Ethenodeoxyadenosine : Dt Pair By Inserting Dtmpnpp Opposite Template Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:13.5
occ:1.00
 O2B A:1FZ501 2.1 11.4 1.0
OD1 A:ASP13 2.1 12.7 1.0
O3G A:1FZ501 2.1 11.1 1.0
O1A A:1FZ501 2.1 12.1 1.0
O A:MET14 2.1 12.1 1.0
OD2 A:ASP115 2.2 12.0 1.0
CG A:ASP13 3.0 13.2 1.0
PB A:1FZ501 3.1 15.9 1.0
CG A:ASP115 3.2 14.6 1.0
PG A:1FZ501 3.3 14.5 1.0
PA A:1FZ501 3.3 14.6 1.0
C A:MET14 3.3 12.3 1.0
OD2 A:ASP13 3.3 16.3 1.0
N3A A:1FZ501 3.5 16.2 1.0
O3B A:1FZ501 3.5 15.2 1.0
MG A:MG503 3.6 15.5 1.0
OD1 A:ASP115 3.6 15.1 1.0
O A:HOH637 3.7 17.4 1.0
O2G A:1FZ501 3.9 10.9 1.0
N A:MET14 3.9 11.2 1.0
NZ A:LYS231 3.9 11.6 1.0
C5' A:1FZ501 4.0 17.6 1.0
CA A:MET14 4.1 13.1 1.0
O5' A:1FZ501 4.1 15.6 1.0
C A:ASP13 4.2 12.7 1.0
N A:ASP15 4.3 12.6 1.0
CB A:ASP13 4.3 14.5 1.0
O1B A:1FZ501 4.4 12.4 1.0
O A:HOH689 4.4 15.1 1.0
O2A A:1FZ501 4.4 13.7 1.0
N A:CYS16 4.5 13.3 1.0
O1G A:1FZ501 4.5 13.9 1.0
CB A:ASP115 4.5 10.2 1.0
CA A:ASP15 4.6 14.2 1.0
CB A:MET14 4.6 12.0 1.0
O A:ASP13 4.6 18.0 1.0
N A:PHE17 4.7 13.6 1.0
C A:ASP15 4.7 14.8 1.0
CE A:LYS231 4.7 17.1 1.0
CB A:PHE17 4.8 10.3 1.0
CA A:ASP13 4.8 12.3 1.0

Magnesium binding site 2 out of 2 in 5dga

Go back to Magnesium Binding Sites List in 5dga
Magnesium binding site 2 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Extending An 1,N6- Ethenodeoxyadenosine : Dt Pair By Inserting Dtmpnpp Opposite Template Da


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Dna Polymerase Eta Extending An 1,N6- Ethenodeoxyadenosine : Dt Pair By Inserting Dtmpnpp Opposite Template Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:15.5
occ:1.00
 OD2 A:ASP13 2.0 16.3 1.0
OD1 A:ASP115 2.1 15.1 1.0
OE2 A:GLU116 2.1 12.8 1.0
O A:HOH668 2.1 15.3 1.0
O A:HOH689 2.1 15.1 1.0
O1A A:1FZ501 2.2 12.1 1.0
CG A:ASP115 3.1 14.6 1.0
CG A:ASP13 3.1 13.2 1.0
CD A:GLU116 3.2 15.5 1.0
PA A:1FZ501 3.2 14.6 1.0
OD2 A:ASP115 3.4 12.0 1.0
O2A A:1FZ501 3.5 13.7 1.0
MG A:MG502 3.6 13.5 1.0
OD1 A:ASP13 3.6 12.7 1.0
O5' A:1FZ501 3.6 15.6 1.0
OG A:SER113 3.7 11.2 1.0
OE1 A:GLU116 3.9 14.4 1.0
O A:HOH637 3.9 17.4 1.0
C5' A:1FZ501 4.0 17.6 1.0
CG A:GLU116 4.2 14.0 1.0
CB A:GLU116 4.3 11.9 1.0
O P:HOH101 4.4 35.2 1.0
CB A:ASP13 4.4 14.5 1.0
NZ A:LYS224 4.4 20.8 1.0
CB A:ASP115 4.5 10.2 1.0
O3G A:1FZ501 4.6 11.1 1.0
C A:ASP115 4.6 12.6 1.0
CB A:SER113 4.6 12.0 1.0
N3A A:1FZ501 4.7 16.2 1.0
O A:HOH760 4.7 24.6 1.0
O A:ASP115 4.8 15.5 1.0
O5' P:DT8 4.8 47.8 1.0
N A:GLU116 4.8 13.2 1.0
O2B A:1FZ501 4.8 11.4 1.0
CA A:ASP115 5.0 13.4 1.0

Reference:

A.Patra, Y.Su, Q.Zhang, K.M.Johnson, F.P.Guengerich, M.Egli. Structural and Kinetic Analysis of Miscoding Opposite the Dna Adduct 1,N6-Ethenodeoxyadenosine By Human Translesion Dna Polymerase Eta. J.Biol.Chem. V. 291 14134 2016.
ISSN: ESSN 1083-351X
PubMed: 27226627
DOI: 10.1074/JBC.M116.732487
Page generated: Sun Sep 29 02:45:10 2024

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