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Magnesium in PDB 4xa5: Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating A and An Incoming 8-Oxo-Dgtp

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

All present enzymatic activity of Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating A and An Incoming 8-Oxo-Dgtp:
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 A and An Incoming 8-Oxo-Dgtp, PDB code: 4xa5 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) 46.79 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.967, 62.340, 141.613, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 22.7

Other elements in 4xa5:

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

Arsenic (As) 1 atom

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 A and An Incoming 8-Oxo-Dgtp (pdb code 4xa5). 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 the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating A and An Incoming 8-Oxo-Dgtp, PDB code: 4xa5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4xa5

Go back to Magnesium Binding Sites List in 4xa5
Magnesium binding site 1 out of 2 in the Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating A and An Incoming 8-Oxo-Dgtp


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 A and An Incoming 8-Oxo-Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:32.6
occ:1.00
 O2B A:8DG601 2.0 25.9 0.9
O2A A:8DG601 2.0 29.0 0.9
OD1 A:ASP427 2.1 29.1 1.0
O A:HOH768 2.1 34.0 1.0
O2G A:8DG601 2.1 28.3 0.9
OD2 A:ASP429 2.3 30.0 1.0
CG A:ASP427 3.1 29.3 1.0
PB A:8DG601 3.1 30.3 0.9
PA A:8DG601 3.2 28.9 0.9
CG A:ASP429 3.2 33.7 1.0
O3A A:8DG601 3.4 29.7 0.9
PG A:8DG601 3.4 32.0 0.9
OD1 A:ASP429 3.4 31.2 1.0
O A:HOH746 3.4 22.7 1.0
OD2 A:ASP427 3.5 35.8 1.0
O3B A:8DG601 3.7 30.1 0.9
O A:ASP427 3.8 27.8 1.0
O1G A:8DG601 4.0 29.1 0.9
O A:HOH785 4.1 38.2 1.0
C A:ASP427 4.1 29.4 1.0
N A:ASP427 4.2 27.4 1.0
O1A A:8DG601 4.3 32.1 0.9
O A:HOH763 4.3 32.4 1.0
C5' A:8DG601 4.3 27.0 0.9
O5' A:8DG601 4.3 28.3 0.9
CB A:ASP427 4.3 29.1 1.0
CA A:ASP427 4.5 29.0 1.0
OG A:SER417 4.5 26.8 1.0
O1B A:8DG601 4.5 32.9 0.9
O A:HOH818 4.6 44.2 1.0
CB A:ASP429 4.6 30.9 1.0
O3G A:8DG601 4.6 33.5 0.9
N A:VAL428 4.7 30.0 1.0
CA A:GLY416 4.7 26.3 1.0
N A:SER417 4.7 25.7 1.0
N A:ASP429 4.9 25.3 1.0

Magnesium binding site 2 out of 2 in 4xa5

Go back to Magnesium Binding Sites List in 4xa5
Magnesium binding site 2 out of 2 in the Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating A and An Incoming 8-Oxo-Dgtp


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 the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating A and An Incoming 8-Oxo-Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:25.1
occ:1.00
 O A:ALA344 2.2 21.9 1.0
O A:SER339 2.4 22.3 1.0
O A:ILE341 2.4 23.8 1.0
OP1 P:DA5 2.4 22.6 1.0
O A:HOH760 2.4 31.3 1.0
O P:HOH110 2.7 29.4 1.0
C A:ILE341 3.3 23.6 1.0
C A:ALA344 3.4 20.7 1.0
C A:SER339 3.4 22.4 1.0
P P:DA5 3.4 24.2 1.0
O A:HOH854 3.6 51.1 1.0
OP2 P:DA5 3.6 22.6 1.0
N A:ALA344 3.7 23.0 1.0
CA A:TRP342 3.9 22.3 1.0
N A:GLY343 3.9 21.5 1.0
N A:TRP342 3.9 22.4 1.0
N A:ILE341 4.1 21.5 1.0
CA A:ALA344 4.2 23.0 1.0
CA A:SER339 4.2 21.3 1.0
O P:HOH124 4.2 44.0 1.0
C A:TRP342 4.3 22.6 1.0
O3' P:DT4 4.3 23.1 1.0
C A:ASN340 4.3 22.4 1.0
N A:ASN340 4.3 21.1 1.0
CA A:ILE341 4.4 22.5 1.0
N A:GLY345 4.4 21.1 1.0
CA A:ASN340 4.5 21.0 1.0
CB A:ALA344 4.6 21.8 1.0
C A:GLY343 4.7 24.8 1.0
CA A:GLY345 4.7 24.2 1.0
CB A:SER339 4.7 26.3 1.0
O5' P:DA5 4.8 23.7 1.0
CA A:GLY343 4.8 23.5 1.0
O A:HOH814 4.8 43.3 1.0
O A:ASN340 4.9 23.6 1.0
O A:HOH861 5.0 53.8 1.0

Reference:

M.J.Burak, K.E.Guja, M.Garcia-Diaz. Nucleotide Binding Interactions Modulate Dntp Selectivity and Facilitate 8-Oxo-Dgtp Incorporation By Dna Polymerase Lambda. Nucleic Acids Res. V. 43 8089 2015.
ISSN: ESSN 1362-4962
PubMed: 26220180
DOI: 10.1093/NAR/GKV760
Page generated: Tue Aug 20 15:24:14 2024

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