Magnesium in PDB 6ctq: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Dctp

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Dctp:
2.7.7.7;

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Dctp, PDB code: 6ctq 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)	25.07 / 1.87
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.894, 79.789, 55.414, 90.00, 107.65, 90.00
R / Rfree (%)	17.5 / 22.8

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Dctp also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	3 atoms

The binding sites of Magnesium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Dctp (pdb code 6ctq). 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 A Dideoxy Terminated Primer with Dctp, PDB code: 6ctq:
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 A Dideoxy Terminated Primer with 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 A Dideoxy Terminated Primer with Dctp within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg101 b:41.8 occ:1.00 O D:HOH216 2.2 39.6 1.0 O T:HOH208 2.2 30.8 1.0 O D:HOH214 2.2 37.3 1.0 O A:HOH880 2.3 35.2 1.0 O T:HOH247 2.3 34.0 1.0 O A:HOH768 4.2 26.9 1.0 O D:HOH208 4.3 29.9 1.0 O T:HOH241 4.4 38.1 1.0 O2 D:DC3 4.4 36.1 1.0 O A:HOH854 4.4 39.9 1.0 O T:HOH222 4.5 28.4 1.0 OE1 A:GLU288 4.5 37.6 1.0 N3 T:DA4 4.5 30.2 1.0 O T:HOH240 4.6 39.2 1.0 O4' T:DC5 4.7 30.8 1.0 C4' T:DC5 4.8 31.9 1.0 C5' D:DG4 4.9 35.7 1.0 C5' T:DC5 4.9 30.3 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with 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 A Dideoxy Terminated Primer with Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:18.1 occ:1.00 O3G A:DCP404 2.0 18.3 1.0 O2A A:DCP404 2.0 18.5 1.0 OD1 A:ASP190 2.0 17.9 1.0 OD2 A:ASP192 2.0 20.7 1.0 O A:HOH569 2.1 19.7 1.0 O2B A:DCP404 2.1 16.9 1.0 CG A:ASP192 3.1 20.2 1.0 PB A:DCP404 3.1 18.8 1.0 CG A:ASP190 3.1 19.9 1.0 PA A:DCP404 3.2 18.8 1.0 PG A:DCP404 3.3 20.7 1.0 OD1 A:ASP192 3.5 18.5 1.0 O3A A:DCP404 3.5 20.4 1.0 NA A:NA401 3.5 18.4 1.0 OD2 A:ASP190 3.6 23.1 1.0 O3B A:DCP404 3.6 17.9 1.0 O A:HOH700 3.9 28.7 1.0 O A:ASP190 4.0 20.7 1.0 C5' A:DCP404 4.1 19.2 1.0 O1G A:DCP404 4.1 16.7 1.0 O5' A:DCP404 4.1 17.6 1.0 O A:HOH676 4.2 22.5 1.0 C A:ASP190 4.2 21.1 1.0 N A:ASP190 4.3 19.6 1.0 OG A:SER180 4.4 19.8 1.0 O1A A:DCP404 4.4 19.9 1.0 CB A:ASP190 4.4 19.4 1.0 CB A:ASP192 4.4 19.7 1.0 O2G A:DCP404 4.4 20.6 1.0 O1B A:DCP404 4.5 16.9 1.0 N A:SER180 4.5 20.0 1.0 CA A:ASP190 4.5 15.6 1.0 CA A:GLY179 4.5 18.0 1.0 N A:MET191 4.8 17.1 1.0 O P:HOH212 4.8 29.3 1.0 N A:ASP192 4.8 18.5 1.0 C A:MET191 5.0 18.6 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