Magnesium in PDB 4xus: Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating A and An Incoming Dttp

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

The structure of Crystal Structure of the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with A Templating A and An Incoming Dttp, PDB code: 4xus 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)	41.96 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.050, 63.280, 141.060, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.6

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 Dttp (pdb code 4xus). 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 Dttp, PDB code: 4xus:
Jump to Magnesium binding site number: 1; 2;

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 Dttp


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 Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:18.0 occ:1.00 O A:SER339 2.1 14.4 1.0 O A:ALA344 2.3 10.9 1.0 O A:HOH753 2.4 11.9 1.0 O A:ILE341 2.5 14.2 1.0 OP1 P:DA5 2.6 14.1 1.0 O P:HOH221 2.7 18.7 1.0 C A:SER339 3.3 12.7 1.0 C A:ALA344 3.5 9.9 1.0 P P:DA5 3.6 13.5 1.0 C A:ILE341 3.6 12.8 1.0 OP2 P:DA5 3.7 14.1 1.0 N A:ALA344 4.0 6.4 1.0 N A:ILE341 4.0 9.6 1.0 CA A:SER339 4.1 9.3 1.0 N A:ASN340 4.2 9.6 1.0 O P:HOH219 4.2 14.3 1.0 C A:ASN340 4.3 12.2 1.0 N A:GLY343 4.3 8.2 1.0 CA A:ALA344 4.3 5.1 1.0 CA A:ASN340 4.3 9.2 1.0 CA A:TRP342 4.3 8.9 1.0 N A:TRP342 4.4 8.9 1.0 N A:GLY345 4.5 5.6 1.0 O3' P:DT4 4.5 12.2 1.0 CA A:ILE341 4.6 8.8 1.0 CA A:GLY345 4.6 5.8 1.0 C A:TRP342 4.7 9.7 1.0 CB A:SER339 4.7 13.7 1.0 CB A:ALA344 4.8 5.8 1.0 O5' P:DA5 4.8 13.7 1.0 C A:GLY343 4.9 9.6 1.0 O A:ASN340 4.9 12.9 1.0 O A:HOH846 4.9 32.9 1.0

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 Dttp


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 Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:16.6 occ:1.00 OD2 A:ASP429 1.9 32.4 1.0 O A:HOH761 2.1 13.8 1.0 OD1 A:ASP427 2.1 14.1 1.0 O2A A:TTP601 2.2 19.9 1.0 O2B A:TTP601 2.4 9.2 1.0 O2G A:TTP601 2.4 22.4 1.0 CG A:ASP429 2.9 21.6 1.0 OD1 A:ASP429 3.3 19.8 1.0 CG A:ASP427 3.3 14.1 1.0 PB A:TTP601 3.3 14.8 1.0 PA A:TTP601 3.5 15.2 1.0 PG A:TTP601 3.6 24.9 1.0 O3A A:TTP601 3.7 15.8 1.0 O3B A:TTP601 3.7 20.9 1.0 O A:HOH766 3.9 14.5 1.0 O A:ASP427 3.9 10.8 1.0 OD2 A:ASP427 3.9 20.7 1.0 O A:HOH740 4.0 3.6 1.0 O1G A:TTP601 4.1 28.9 1.0 O A:HOH749 4.2 11.3 1.0 CB A:ASP429 4.2 13.7 1.0 N A:ASP427 4.2 9.8 1.0 OG A:SER417 4.2 13.9 1.0 C5' A:TTP601 4.3 13.8 1.0 O5' A:TTP601 4.3 13.8 1.0 C A:ASP427 4.3 10.9 1.0 CB A:ASP427 4.4 8.8 1.0 CA A:GLY416 4.5 11.2 1.0 CA A:ASP427 4.6 8.3 1.0 N A:SER417 4.6 12.5 1.0 O1A A:TTP601 4.6 14.5 1.0 N A:ASP429 4.6 10.6 1.0 O1B A:TTP601 4.7 14.4 1.0 O3G A:TTP601 4.9 23.9 1.0 N A:VAL428 5.0 10.0 1.0

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