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

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

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Eta Extending An 1,N6- Ethenodeoxyadenosine : Da 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 : Da Pair By Inserting Dtmpnpp Opposite Template Da, PDB code: 5dgb 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) 32.29 / 1.79
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.660, 98.660, 82.004, 90.00, 90.00, 120.00
R / Rfree (%) 16.4 / 21.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Dna Polymerase Eta Extending An 1,N6- Ethenodeoxyadenosine : Da Pair By Inserting Dtmpnpp Opposite Template Da (pdb code 5dgb). 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 : Da Pair By Inserting Dtmpnpp Opposite Template Da, PDB code: 5dgb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5dgb

Go back to Magnesium Binding Sites List in 5dgb
Magnesium binding site 1 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Extending An 1,N6- Ethenodeoxyadenosine : Da 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 : Da Pair By Inserting Dtmpnpp Opposite Template Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:8.4
occ:1.00
 OD1 A:ASP13 2.0 11.2 1.0
O3G A:1FZ505 2.1 9.2 1.0
O2B A:1FZ505 2.1 10.1 1.0
OD2 A:ASP115 2.1 9.4 1.0
O1A A:1FZ505 2.1 11.6 1.0
O A:MET14 2.2 10.7 1.0
CG A:ASP13 3.0 10.9 1.0
CG A:ASP115 3.2 10.3 1.0
PB A:1FZ505 3.2 9.9 1.0
PG A:1FZ505 3.3 11.6 1.0
PA A:1FZ505 3.3 11.8 1.0
C A:MET14 3.3 11.5 1.0
OD2 A:ASP13 3.4 14.9 1.0
MG A:MG502 3.5 12.0 1.0
OD1 A:ASP115 3.6 7.3 1.0
O3B A:1FZ505 3.6 10.6 1.0
N3A A:1FZ505 3.6 12.8 1.0
NZ A:LYS231 3.8 9.8 1.0
O A:HOH789 3.9 17.4 1.0
N A:MET14 3.9 6.7 1.0
O2G A:1FZ505 4.0 9.0 1.0
C5' A:1FZ505 4.1 10.3 1.0
CA A:MET14 4.1 7.8 1.0
O5' A:1FZ505 4.2 10.7 1.0
C A:ASP13 4.2 8.2 1.0
CB A:ASP13 4.3 13.3 1.0
N A:ASP15 4.4 7.9 1.0
CB A:ASP115 4.4 10.6 1.0
O A:HOH830 4.4 13.0 1.0
CE A:LYS231 4.5 17.5 1.0
O1G A:1FZ505 4.5 10.4 1.0
O1B A:1FZ505 4.5 11.1 1.0
O2A A:1FZ505 4.5 14.0 1.0
CB A:MET14 4.6 10.0 1.0
CA A:ASP15 4.6 9.9 1.0
O A:ASP13 4.6 9.2 1.0
N A:CYS16 4.6 7.8 1.0
C A:ASP15 4.7 11.4 1.0
CA A:ASP13 4.8 9.1 1.0
N A:PHE17 4.8 8.4 1.0
CB A:PHE17 4.8 9.6 1.0
O A:ASP115 4.9 11.7 1.0

Magnesium binding site 2 out of 2 in 5dgb

Go back to Magnesium Binding Sites List in 5dgb
Magnesium binding site 2 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Extending An 1,N6- Ethenodeoxyadenosine : Da 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 : Da Pair By Inserting Dtmpnpp Opposite Template Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:12.0
occ:1.00
 OD1 A:ASP115 2.1 7.3 1.0
OD2 A:ASP13 2.1 14.9 1.0
OE2 A:GLU116 2.2 13.2 1.0
O1A A:1FZ505 2.2 11.6 1.0
O A:HOH830 2.2 13.0 1.0
O A:HOH797 2.2 15.0 1.0
CG A:ASP115 3.0 10.3 1.0
CG A:ASP13 3.1 10.9 1.0
PA A:1FZ505 3.2 11.8 1.0
CD A:GLU116 3.2 17.1 1.0
OD2 A:ASP115 3.3 9.4 1.0
OD1 A:ASP13 3.5 11.2 1.0
MG A:MG501 3.5 8.4 1.0
O2A A:1FZ505 3.6 14.0 1.0
OG A:SER113 3.7 12.2 1.0
O5' A:1FZ505 3.8 10.7 1.0
OE1 A:GLU116 4.0 16.1 1.0
O A:HOH789 4.1 17.4 1.0
O P:HOH102 4.1 34.6 1.0
C5' A:1FZ505 4.1 10.3 1.0
CG A:GLU116 4.2 10.1 1.0
CB A:GLU116 4.2 11.1 1.0
O P:HOH106 4.3 33.2 1.0
NZ A:LYS224 4.3 13.0 1.0
CB A:ASP13 4.4 13.3 1.0
CB A:ASP115 4.4 10.6 1.0
C A:ASP115 4.6 10.3 1.0
O A:HOH859 4.6 20.2 1.0
O3G A:1FZ505 4.6 9.2 1.0
O A:ASP115 4.6 11.7 1.0
CB A:SER113 4.6 14.5 1.0
N A:GLU116 4.8 8.7 1.0
N3A A:1FZ505 4.8 12.8 1.0
O2B A:1FZ505 4.8 10.1 1.0
CA A:ASP115 4.9 12.6 1.0
O A:HOH800 4.9 19.4 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 02:46:01 2024

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