Atomistry » Magnesium » PDB 5i9e-5imn » 5iii
Atomistry »
  Magnesium »
    PDB 5i9e-5imn »
      5iii »

Magnesium in PDB 5iii: Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Datp

Enzymatic activity of Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Datp

All present enzymatic activity of Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Datp:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Datp, PDB code: 5iii was solved by M.J.Burak, K.E.Guja, M.Garcia-Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.70 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.848, 62.681, 140.024, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 22.5

Other elements in 5iii:

The structure of Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Datp also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Datp (pdb code 5iii). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Datp, PDB code: 5iii:

Magnesium binding site 1 out of 1 in 5iii

Go back to Magnesium Binding Sites List in 5iii
Magnesium binding site 1 out of 1 in the Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Datp


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 the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:21.7
occ:1.00
 O1B A:DTP601 2.0 19.8 1.0
OD2 A:ASP429 2.0 24.3 1.0
OD1 A:ASP427 2.1 21.4 1.0
O1A A:DTP601 2.1 21.1 1.0
O1G A:DTP601 2.2 24.1 1.0
O A:HOH741 2.3 21.8 1.0
CG A:ASP429 3.0 21.9 1.0
PB A:DTP601 3.1 21.9 1.0
CG A:ASP427 3.2 23.8 1.0
PA A:DTP601 3.3 22.6 1.0
PG A:DTP601 3.4 24.0 1.0
OD1 A:ASP429 3.4 22.5 1.0
O3A A:DTP601 3.4 21.5 1.0
O A:HOH705 3.5 16.2 1.0
O3B A:DTP601 3.6 23.6 1.0
OD2 A:ASP427 3.6 26.6 1.0
O3G A:DTP601 4.0 24.4 1.0
O A:ASP427 4.1 24.0 1.0
O A:HOH758 4.1 27.4 1.0
C5' A:DTP601 4.1 19.0 1.0
O A:HOH743 4.2 22.3 1.0
OG A:SER417 4.2 20.8 1.0
O5' A:DTP601 4.2 19.4 1.0
C A:ASP427 4.3 24.5 1.0
N A:ASP427 4.3 23.3 1.0
CB A:ASP429 4.4 22.0 1.0
O2A A:DTP601 4.4 21.9 1.0
O2B A:DTP601 4.4 22.9 1.0
N A:SER417 4.4 20.5 1.0
CB A:ASP427 4.5 22.8 1.0
CA A:GLY416 4.6 21.7 1.0
O2G A:DTP601 4.6 25.7 1.0
CA A:ASP427 4.6 22.1 1.0
O A:HOH795 4.7 26.1 1.0
N A:ASP429 4.8 19.5 1.0
N A:VAL428 4.9 20.8 1.0
CB A:SER417 5.0 24.4 1.0

Reference:

M.J.Burak, K.E.Guja, E.Hambardjieva, B.Derkunt, M.Garcia-Diaz. A Fidelity Mechanism in Dna Polymerase Lambda Promotes Error-Free Bypass of 8-Oxo-Dg. Embo J. V. 35 2045 2016.
ISSN: ESSN 1460-2075
PubMed: 27481934
DOI: 10.15252/EMBJ.201694332
Page generated: Sun Sep 29 16:42:04 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy