Magnesium in PDB 3k59: Crystal Structure of E.Coli Pol II-Normal Dna-Dctp Ternary Complex

All present enzymatic activity of Crystal Structure of E.Coli Pol II-Normal Dna-Dctp Ternary Complex:
2.7.7.7;

The structure of Crystal Structure of E.Coli Pol II-Normal Dna-Dctp Ternary Complex, PDB code: 3k59 was solved by W.Yang, F.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.726, 100.656, 126.030, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 20.2

The binding sites of Magnesium atom in the Crystal Structure of E.Coli Pol II-Normal Dna-Dctp Ternary Complex (pdb code 3k59). 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 E.Coli Pol II-Normal Dna-Dctp Ternary Complex, PDB code: 3k59:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of E.Coli Pol II-Normal Dna-Dctp Ternary Complex


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 E.Coli Pol II-Normal Dna-Dctp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:20.7 occ:1.00 OD2 A:ASP547 2.1 19.6 1.0 OD2 A:ASP419 2.1 18.5 1.0 O A:TYR420 2.2 15.6 1.0 O1G A:DCP914 2.2 18.1 1.0 O2A A:DCP914 2.3 14.2 1.0 O2B A:DCP914 2.3 14.2 1.0 CG A:ASP547 3.1 19.2 1.0 CG A:ASP419 3.2 17.8 1.0 PB A:DCP914 3.3 17.3 1.0 O3A A:DCP914 3.3 19.2 1.0 C A:TYR420 3.4 16.8 1.0 PA A:DCP914 3.4 16.4 1.0 PG A:DCP914 3.4 14.6 1.0 OD1 A:ASP547 3.4 18.7 1.0 MG A:MG1002 3.6 21.6 1.0 O A:HOH1168 3.7 22.2 1.0 O3B A:DCP914 3.7 20.6 1.0 O A:HOH798 3.7 17.9 1.0 OD1 A:ASP419 3.8 17.6 1.0 N A:TYR420 3.9 15.0 1.0 O5' A:DCP914 4.1 18.1 1.0 CA A:TYR420 4.1 15.3 1.0 O2G A:DCP914 4.1 17.7 1.0 N A:SER422 4.3 15.2 1.0 C A:ASP419 4.3 16.1 1.0 O1A A:DCP914 4.4 18.8 1.0 C5' A:DCP914 4.4 19.2 1.0 N A:LYS421 4.4 15.3 1.0 CB A:ASP547 4.4 17.8 1.0 CB A:ASP419 4.5 15.6 1.0 CA A:LYS421 4.6 15.4 1.0 N A:LEU423 4.6 13.8 1.0 O3G A:DCP914 4.6 19.1 1.0 CB A:TYR420 4.6 15.3 1.0 O1B A:DCP914 4.6 19.9 1.0 C A:LYS421 4.7 15.6 1.0 O A:ASP419 4.7 16.6 1.0 O A:HOH873 4.8 18.8 1.0 CA A:ASP419 4.8 16.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of E.Coli Pol II-Normal Dna-Dctp Ternary Complex


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 E.Coli Pol II-Normal Dna-Dctp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:21.6 occ:1.00 O2A A:DCP914 2.3 14.2 1.0 OD1 A:ASP419 2.3 17.6 1.0 OD1 A:ASP547 2.3 18.7 1.0 O A:HOH1169 2.4 15.9 1.0 O A:HOH873 2.4 18.8 1.0 CG A:ASP419 3.2 17.8 1.0 CG A:ASP547 3.4 19.2 1.0 OD2 A:ASP419 3.4 18.5 1.0 PA A:DCP914 3.5 16.4 1.0 C3' P:DOC913 3.6 18.1 1.0 MG A:MG1001 3.6 20.7 1.0 O5' A:DCP914 3.7 18.1 1.0 OD2 A:ASP547 3.7 19.6 1.0 O1A A:DCP914 3.8 18.8 1.0 O A:HOH922 3.9 33.3 1.0 O A:HOH1168 3.9 22.2 1.0 O A:ASP545 4.3 16.8 1.0 C5' P:DOC913 4.3 21.0 1.0 C5' A:DCP914 4.4 19.2 1.0 C4' P:DOC913 4.4 18.9 1.0 CB A:SER548 4.4 17.1 1.0 CB A:ASP419 4.5 15.6 1.0 O A:HOH785 4.5 17.8 1.0 O P:HOH131 4.6 22.7 1.0 C A:ASP547 4.7 17.7 1.0 CB A:ASP547 4.7 17.8 1.0 O3A A:DCP914 4.8 19.2 1.0 N A:SER548 4.8 18.1 1.0 O1G A:DCP914 4.8 18.1 1.0 N A:ASP547 4.8 17.4 1.0 OG A:SER548 4.8 17.9 1.0 O A:ASP547 4.9 17.3 1.0 C2' P:DOC913 4.9 19.3 1.0 O5' P:DOC913 4.9 22.6 1.0 CA A:ASP547 5.0 18.0 1.0

F.Wang, W.Yang. Structural Insight Into Translesion Synthesis By Dna Pol II Cell(Cambridge,Mass.) V. 139 1279 2009.
ISSN: ISSN 0092-8674
PubMed: 20064374
DOI: 10.1016/J.CELL.2009.11.043