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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: Tue Aug 12 11:24:56 2025

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