Calcium in PDB 3k5m: Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex

All present enzymatic activity of Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex:
2.7.7.7;

The structure of Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex, PDB code: 3k5m 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)	28.43 / 2.04
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.109, 95.228, 144.735, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 26

The binding sites of Calcium atom in the Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex (pdb code 3k5m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex, PDB code: 3k5m:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:32.6 occ:1.00 OD2 A:ASP547 1.9 40.3 1.0 O1G A:DG3914 2.3 39.9 1.0 OD2 A:ASP419 2.4 39.2 1.0 O1B A:DG3914 2.5 42.3 1.0 O A:TYR420 2.5 30.1 1.0 O1A A:DG3914 2.5 40.2 1.0 CG A:ASP547 3.0 34.0 1.0 PA A:DG3914 3.3 36.8 1.0 PB A:DG3914 3.3 43.2 1.0 CG A:ASP419 3.4 36.7 1.0 O3A A:DG3914 3.4 40.7 1.0 PG A:DG3914 3.5 40.1 1.0 C A:TYR420 3.6 28.4 1.0 O5' A:DG3914 3.7 40.2 1.0 OD1 A:ASP419 3.7 39.7 1.0 OD1 A:ASP547 3.8 31.5 1.0 O3B A:DG3914 3.9 42.5 1.0 O A:HOH1115 4.0 39.7 1.0 CB A:ASP547 4.0 31.7 1.0 N A:SER422 4.0 27.1 1.0 O A:HOH826 4.1 35.5 1.0 O2G A:DG3914 4.2 41.6 1.0 C5' A:DG3914 4.2 34.2 1.0 CA A:LYS421 4.2 28.3 1.0 CA A:CA1002 4.3 59.1 1.0 N A:LYS421 4.3 28.9 1.0 N A:TYR420 4.4 27.4 1.0 C A:LYS421 4.5 27.4 1.0 CA A:TYR420 4.6 28.0 1.0 C A:ASP419 4.7 30.4 1.0 CB A:ASP419 4.7 35.3 1.0 O2B A:DG3914 4.8 44.7 1.0 N A:LEU423 4.8 24.4 1.0 O3G A:DG3914 4.8 43.7 1.0 O2A A:DG3914 4.8 38.6 1.0 CA A:SER422 4.9 27.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:59.1 occ:1.00 OD1 A:ASP419 2.8 39.7 1.0 OD1 A:ASP547 2.9 31.5 1.0 O1B A:DG3914 3.3 42.3 1.0 C3' P:DG913 3.5 27.7 1.0 OD2 A:ASP547 3.7 40.3 1.0 CG A:ASP547 3.7 34.0 1.0 O3' P:DG913 3.7 26.6 1.0 CG A:ASP419 3.9 36.7 1.0 C2' P:DG913 4.1 27.0 1.0 O A:HOH1115 4.1 39.7 1.0 O5' P:DG913 4.2 24.0 1.0 OD2 A:ASP419 4.3 39.2 1.0 CA A:CA1001 4.3 32.6 1.0 C5' A:DG3914 4.4 34.2 1.0 PB A:DG3914 4.6 43.2 1.0 C4' P:DG913 4.7 26.8 1.0 CB A:SER548 4.8 31.1 1.0 C5' P:DG913 4.8 23.4 1.0 O5' A:DG3914 4.8 40.2 1.0 O2B A:DG3914 4.8 44.7 1.0 OP2 P:DG913 4.9 21.4 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