Magnesium in PDB 3k57: Crystal Structure of E.Coli Pol II-Normal Dna-Datp Ternary Complex

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

The structure of Crystal Structure of E.Coli Pol II-Normal Dna-Datp Ternary Complex, PDB code: 3k57 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)	20.00 / 2.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.425, 99.888, 125.745, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 21.6

The binding sites of Magnesium atom in the Crystal Structure of E.Coli Pol II-Normal Dna-Datp Ternary Complex (pdb code 3k57). 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-Datp Ternary Complex, PDB code: 3k57:
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-Datp 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-Datp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:20.1 occ:1.00 OD2 A:ASP547 2.0 23.5 1.0 OD2 A:ASP419 2.1 22.4 1.0 O A:TYR420 2.2 18.7 1.0 O1A A:DTP914 2.2 22.0 1.0 O1G A:DTP914 2.3 24.9 1.0 O1B A:DTP914 2.3 19.2 1.0 CG A:ASP547 3.1 21.9 1.0 CG A:ASP419 3.2 22.2 1.0 C A:TYR420 3.3 20.1 1.0 PB A:DTP914 3.4 21.1 1.0 PA A:DTP914 3.5 22.6 1.0 PG A:DTP914 3.5 24.5 1.0 OD1 A:ASP547 3.5 20.5 1.0 MG A:MG1002 3.6 33.5 1.0 O A:HOH967 3.6 28.3 1.0 O A:HOH805 3.7 22.1 1.0 OD1 A:ASP419 3.7 21.7 1.0 N A:TYR420 3.9 18.8 1.0 O3A A:DTP914 3.9 23.4 1.0 O3B A:DTP914 4.0 24.4 1.0 C5' A:DTP914 4.0 23.3 1.0 CA A:TYR420 4.0 19.0 1.0 O2G A:DTP914 4.1 23.1 1.0 C A:ASP419 4.3 19.6 1.0 N A:SER422 4.3 17.8 1.0 CB A:ASP547 4.3 21.6 1.0 N A:LYS421 4.4 19.5 1.0 O5' A:DTP914 4.4 22.2 1.0 CB A:ASP419 4.4 20.1 1.0 CB A:TYR420 4.5 18.8 1.0 CA A:LYS421 4.5 19.5 1.0 O2A A:DTP914 4.6 22.5 1.0 N A:LEU423 4.7 17.4 1.0 O A:ASP419 4.7 19.5 1.0 C A:LYS421 4.7 18.6 1.0 O2B A:DTP914 4.7 19.1 1.0 O3G A:DTP914 4.8 25.4 1.0 CA A:ASP419 4.8 20.1 1.0 O A:HOH814 4.9 18.0 1.0 O A:ASP547 5.0 20.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of E.Coli Pol II-Normal Dna-Datp 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-Datp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:33.5 occ:1.00 O A:HOH835 2.2 16.0 1.0 OD1 A:ASP547 2.3 20.5 1.0 OD1 A:ASP419 2.3 21.7 1.0 O A:HOH814 2.4 18.0 1.0 O1A A:DTP914 2.5 22.0 1.0 CG A:ASP419 3.2 22.2 1.0 CG A:ASP547 3.2 21.9 1.0 PA A:DTP914 3.4 22.6 1.0 OD2 A:ASP419 3.4 22.4 1.0 C3' P:DOC913 3.5 20.0 1.0 OD2 A:ASP547 3.5 23.5 1.0 O5' A:DTP914 3.6 22.2 1.0 MG A:MG1001 3.6 20.1 1.0 O A:HOH967 3.7 28.3 1.0 O2A A:DTP914 3.7 22.5 1.0 O A:HOH940 3.8 36.5 1.0 C5' A:DTP914 4.0 23.3 1.0 C5' P:DOC913 4.2 20.0 1.0 C4' P:DOC913 4.2 20.5 1.0 O A:ASP545 4.4 16.9 1.0 CB A:SER548 4.5 17.7 1.0 O A:HOH802 4.5 19.3 1.0 CB A:ASP419 4.5 20.1 1.0 CB A:ASP547 4.6 21.6 1.0 O1G A:DTP914 4.7 24.9 1.0 C A:ASP547 4.7 20.9 1.0 O P:HOH224 4.8 29.6 1.0 C2' P:DOC913 4.8 19.6 1.0 N A:ASP547 4.8 19.4 1.0 N A:SER548 4.9 19.6 1.0 O A:ASP547 4.9 20.0 1.0 O3A A:DTP914 4.9 23.4 1.0 O5' P:DOC913 5.0 20.7 1.0 CA A:ASP547 5.0 21.3 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