Atomistry » Magnesium » PDB 4x7x-4xgq » 4xa5
Atomistry »
  Magnesium »
    PDB 4x7x-4xgq »
      4xa5 »

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 12 03:01:04 2025

Last articles

Mg in 5K0N
Mg in 5K0L
Mg in 5JZQ
Mg in 5K0K
Mg in 5JYG
Mg in 5JZJ
Mg in 5JZD
Mg in 5JYS
Mg in 5JYD
Mg in 5JYE
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy