Magnesium in PDB 6bem: Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp:
2.7.7.7;

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp, PDB code: 6bem was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.64 / 1.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.806, 79.995, 55.521, 90.00, 107.68, 90.00
R / Rfree (%)	18.7 / 22.6

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	3 atoms

The binding sites of Magnesium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp (pdb code 6bem). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp, PDB code: 6bem:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:46.4 occ:1.00 O T:HOH127 2.0 34.8 1.0 O D:HOH214 2.5 33.0 1.0 O T:HOH149 2.9 35.5 1.0 O D:HOH208 3.9 27.2 1.0 OE1 A:GLU288 4.3 35.7 1.0 O D:HOH217 4.3 40.7 1.0 O T:HOH114 4.3 29.3 1.0 O2 D:DC3 4.5 33.6 1.0 O A:HOH705 4.6 29.7 1.0 N3 T:DA4 4.8 28.6 1.0 C5' D:DG4 4.9 37.8 1.0 O4' T:DC5 5.0 26.4 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:14.1 occ:1.00 OD1 A:ASP190 2.0 14.0 1.0 OD2 A:ASP192 2.1 14.4 1.0 O A:HOH562 2.1 14.0 1.0 O1A A:DJJ408 2.1 13.5 1.0 O1G A:DJJ408 2.1 13.7 1.0 O1B A:DJJ408 2.1 13.3 1.0 CG A:ASP192 3.1 13.3 1.0 CG A:ASP190 3.1 17.1 1.0 PB A:DJJ408 3.2 14.0 1.0 PG A:DJJ408 3.3 18.5 1.0 PA A:DJJ408 3.3 13.6 1.0 OD1 A:ASP192 3.5 15.5 1.0 NA A:NA404 3.5 15.6 1.0 O3G A:DJJ408 3.6 21.0 1.0 OD2 A:ASP190 3.6 17.9 1.0 O3A A:DJJ408 3.6 16.6 1.0 O A:HOH573 3.8 24.4 1.0 O A:ASP190 3.9 15.3 1.0 C3B A:DJJ408 3.9 16.1 1.0 C5' A:DJJ408 4.1 17.1 1.0 C A:ASP190 4.2 18.0 1.0 O A:HOH701 4.2 14.6 1.0 O5' A:DJJ408 4.3 15.6 1.0 N A:ASP190 4.3 13.7 1.0 CB A:ASP192 4.4 12.6 1.0 CB A:ASP190 4.4 15.0 1.0 O2A A:DJJ408 4.4 17.0 1.0 CA A:GLY179 4.5 10.2 1.0 O2B A:DJJ408 4.5 14.1 1.0 O2G A:DJJ408 4.5 20.0 1.0 CA A:ASP190 4.5 13.9 1.0 O A:HOH580 4.7 24.4 1.0 N A:ASP192 4.7 14.8 1.0 N A:SER180 4.8 17.2 1.0 N A:MET191 4.8 12.8 1.0 C A:MET191 5.0 13.7 1.0

V.K.Batra, K.Oertell, W.A.Beard, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson. Mapping Functional Substrate-Enzyme Interactions in the Pol Beta Active Site Through Chemical Biology: Structural Responses to Acidity Modification of Incoming Dntps. Biochemistry V. 57 3934 2018.
ISSN: ISSN 1520-4995
PubMed: 29874056
DOI: 10.1021/ACS.BIOCHEM.8B00418