Magnesium in PDB 5ugp: Dna Polymerase Beta Complex with A 1NT Gap and Dcmppnp

All present enzymatic activity of Dna Polymerase Beta Complex with A 1NT Gap and Dcmppnp:
2.7.7.7;

The structure of Dna Polymerase Beta Complex with A 1NT Gap and Dcmppnp, PDB code: 5ugp was solved by B.D.Freudenthal, S.H.Wilson, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.63 / 1.96
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.784, 79.966, 55.454, 90.00, 107.68, 90.00
R / Rfree (%)	18.3 / 23.3

The binding sites of Magnesium atom in the Dna Polymerase Beta Complex with A 1NT Gap and Dcmppnp (pdb code 5ugp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dna Polymerase Beta Complex with A 1NT Gap and Dcmppnp, PDB code: 5ugp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Beta Complex with A 1NT Gap and Dcmppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Beta Complex with A 1NT Gap and Dcmppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:21.7 occ:1.00 OD2 A:ASP190 2.0 22.5 1.0 OD1 A:ASP192 2.1 18.8 1.0 OD2 A:ASP256 2.2 23.4 1.0 O A:HOH550 2.3 28.1 1.0 O3' P:DC10 2.4 22.0 1.0 O2A A:8CP401 2.4 17.1 1.0 CG A:ASP190 2.9 18.8 1.0 CG A:ASP192 3.1 16.7 1.0 OD1 A:ASP190 3.3 17.5 1.0 CG A:ASP256 3.4 22.6 1.0 OD2 A:ASP192 3.5 17.0 1.0 PA A:8CP401 3.5 19.1 1.0 C3' P:DC10 3.5 23.3 1.0 MG A:MG403 3.6 16.0 1.0 O5' A:8CP401 3.8 17.9 1.0 O1A A:8CP401 3.9 17.8 1.0 CB A:ASP256 4.1 24.5 1.0 C5' A:8CP401 4.1 19.9 1.0 C4' P:DC10 4.2 26.0 1.0 C5' P:DC10 4.2 25.6 1.0 O P:HOH105 4.2 34.6 1.0 CB A:ASP190 4.3 15.4 1.0 OD1 A:ASP256 4.4 22.8 1.0 CB A:ASP192 4.5 20.1 1.0 O A:HOH660 4.5 27.9 1.0 OP1 P:DC10 4.6 25.5 1.0 O5' P:DC10 4.7 22.9 1.0 O3G A:8CP401 4.7 14.7 1.0 O A:MET191 4.7 18.5 1.0 C2' P:DC10 4.8 19.6 1.0 NH2 A:ARG254 4.9 24.7 1.0 O3A A:8CP401 4.9 21.1 1.0 CA A:ASP192 5.0 18.8 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Beta Complex with A 1NT Gap and Dcmppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase Beta Complex with A 1NT Gap and Dcmppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:16.0 occ:1.00 OD2 A:ASP192 2.0 17.0 1.0 OD1 A:ASP190 2.0 17.5 1.0 O1B A:8CP401 2.0 13.5 1.0 O3G A:8CP401 2.1 14.7 1.0 O2A A:8CP401 2.1 17.1 1.0 O A:HOH542 2.3 18.4 1.0 PB A:8CP401 3.1 15.7 1.0 CG A:ASP192 3.1 16.7 1.0 CG A:ASP190 3.1 18.8 1.0 PA A:8CP401 3.3 19.1 1.0 PG A:8CP401 3.3 20.0 1.0 O3A A:8CP401 3.5 21.1 1.0 OD1 A:ASP192 3.5 18.8 1.0 OD2 A:ASP190 3.5 22.5 1.0 MG A:MG402 3.6 21.7 1.0 N3B A:8CP401 3.6 14.2 1.0 O1G A:8CP401 3.9 17.0 1.0 O A:ASP190 4.0 19.3 1.0 C5' A:8CP401 4.1 19.9 1.0 O5' A:8CP401 4.2 17.9 1.0 O A:HOH660 4.2 27.9 1.0 O A:HOH607 4.2 19.1 1.0 C A:ASP190 4.3 20.2 1.0 OG A:SER180 4.4 19.5 1.0 O2B A:8CP401 4.4 15.0 1.0 CB A:ASP192 4.4 20.1 1.0 O1A A:8CP401 4.4 17.8 1.0 N A:SER180 4.4 19.7 1.0 CB A:ASP190 4.4 15.4 1.0 N A:ASP190 4.4 16.9 1.0 CA A:GLY179 4.4 14.9 1.0 O2G A:8CP401 4.5 25.4 1.0 CA A:ASP190 4.6 15.8 1.0 O A:HOH550 4.7 28.1 1.0 N A:ASP192 4.8 19.3 1.0 N A:MET191 4.9 16.3 1.0 C A:GLY179 5.0 16.0 1.0

D.D.Shock, B.D.Freudenthal, W.A.Beard, S.H.Wilson. Modulating the Dna Polymerase Beta Reaction Equilibrium to Dissect the Reverse Reaction. Nat. Chem. Biol. V. 13 1074 2017.
ISSN: ESSN 1552-4469
PubMed: 28759020
DOI: 10.1038/NCHEMBIO.2450