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

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

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 Dctp:
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 Dctp, PDB code: 5iij 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) 41.71 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.749, 62.850, 140.076, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.4

Other elements in 5iij:

The structure of Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating 8-Oxo-Dg and An Incoming Dctp 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 Dctp (pdb code 5iij). 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 Dctp, PDB code: 5iij:

Magnesium binding site 1 out of 1 in 5iij

Go back to Magnesium Binding Sites List in 5iij
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 Dctp


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 Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:22.2
occ:1.00
 O1A A:DCT601 2.1 21.8 1.0
OD1 A:ASP427 2.1 21.1 1.0
O1B A:DCT601 2.1 20.1 1.0
OD2 A:ASP429 2.1 23.6 1.0
O1G A:DCT601 2.1 23.0 1.0
O A:HOH804 2.1 20.9 1.0
PB A:DCT601 3.1 22.6 1.0
CG A:ASP429 3.1 23.7 1.0
CG A:ASP427 3.1 26.6 1.0
PA A:DCT601 3.2 23.0 1.0
PG A:DCT601 3.3 25.2 1.0
O3A A:DCT601 3.4 21.6 1.0
OD1 A:ASP429 3.4 23.1 1.0
OD2 A:ASP427 3.6 27.3 1.0
O A:HOH705 3.6 19.3 1.0
O3B A:DCT601 3.6 23.2 1.0
O3G A:DCT601 3.9 24.3 1.0
O A:HOH781 4.0 30.0 1.0
O A:ASP427 4.1 22.0 1.0
C5' A:DCT601 4.1 20.0 1.0
N A:ASP427 4.2 24.3 1.0
O5' A:DCT601 4.2 22.8 1.0
OG A:SER417 4.2 23.2 1.0
O A:HOH758 4.3 21.3 1.0
C A:ASP427 4.4 22.8 1.0
O2A A:DCT601 4.4 22.9 1.0
CB A:ASP427 4.4 24.7 1.0
N A:SER417 4.4 21.1 1.0
CB A:ASP429 4.4 21.4 1.0
O2B A:DCT601 4.4 22.5 1.0
O2G A:DCT601 4.5 25.8 1.0
CA A:ASP427 4.6 21.1 1.0
CA A:GLY416 4.6 21.5 1.0
O P:HOH114 4.8 25.8 1.0
N A:ASP429 4.9 21.2 1.0
N A:VAL428 5.0 21.1 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 16:42:10 2024

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