Magnesium in PDB 4tuq: Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B).

All present enzymatic activity of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B).:
2.7.7.7;

The structure of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B)., PDB code: 4tuq was solved by M.C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.85 / 2.37
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.820, 80.542, 55.535, 90.00, 107.69, 90.00
R / Rfree (%)	19.8 / 25.9

The structure of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B). also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B). (pdb code 4tuq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B)., PDB code: 4tuq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:18.5 occ:1.00 OD2 A:ASP192 1.9 18.5 1.0 O1A A:0KX405 2.0 17.2 1.0 O1G A:0KX405 2.1 17.6 1.0 O2B A:0KX405 2.1 15.3 1.0 OD1 A:ASP190 2.1 18.1 1.0 O A:HOH565 2.1 17.5 1.0 CG A:ASP192 3.0 20.2 1.0 PB A:0KX405 3.1 15.6 1.0 PA A:0KX405 3.2 17.4 1.0 CG A:ASP190 3.2 22.7 1.0 OD1 A:ASP192 3.4 23.9 1.0 PG A:0KX405 3.4 17.3 1.0 MG A:MG402 3.4 23.3 1.0 N3A A:0KX405 3.6 16.8 1.0 O3B A:0KX405 3.7 16.9 1.0 OD2 A:ASP190 3.7 23.9 1.0 O A:ASP190 4.0 23.1 1.0 C5' A:0KX405 4.0 16.0 1.0 O3G A:0KX405 4.0 16.6 1.0 O5' A:0KX405 4.2 17.7 1.0 O A:HOH566 4.2 16.7 1.0 C A:ASP190 4.3 21.2 1.0 CB A:ASP192 4.3 20.8 1.0 N A:ASP190 4.4 19.6 1.0 O2A A:0KX405 4.4 19.8 1.0 O A:HOH583 4.5 23.7 1.0 CB A:ASP190 4.5 18.4 1.0 O2G A:0KX405 4.5 19.3 1.0 OG A:SER180 4.5 21.1 1.0 N A:SER180 4.5 22.3 1.0 CA A:ASP190 4.6 18.3 1.0 O1B A:0KX405 4.6 15.0 1.0 CA A:GLY179 4.6 18.2 1.0 N A:ASP192 4.9 21.8 1.0 N A:MET191 4.9 19.4 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:23.3 occ:1.00 OD2 A:ASP190 2.1 23.9 1.0 OD2 A:ASP256 2.1 29.5 1.0 O A:HOH583 2.2 23.7 1.0 OD1 A:ASP192 2.3 23.9 1.0 O1A A:0KX405 2.4 17.2 1.0 O3' P:DC10 2.4 26.9 1.0 CG A:ASP190 3.0 22.7 1.0 OD1 A:ASP190 3.1 18.1 1.0 CG A:ASP256 3.3 28.3 1.0 CG A:ASP192 3.3 20.2 1.0 MG A:MG401 3.4 18.5 1.0 C3' P:DC10 3.4 23.6 1.0 PA A:0KX405 3.5 17.4 1.0 OD2 A:ASP192 3.6 18.5 1.0 O5' A:0KX405 3.8 17.7 1.0 CB A:ASP256 3.9 26.9 1.0 O2A A:0KX405 3.9 19.8 1.0 C5' A:0KX405 3.9 16.0 1.0 C4' P:DC10 4.2 28.8 1.0 C5' P:DC10 4.3 24.5 1.0 OD1 A:ASP256 4.3 30.2 1.0 CB A:ASP190 4.4 18.4 1.0 O A:MET191 4.6 20.3 1.0 OP1 P:DC10 4.6 34.5 1.0 CB A:ASP192 4.6 20.8 1.0 O A:HOH525 4.7 34.3 1.0 O5' P:DC10 4.7 27.0 1.0 C2' P:DC10 4.7 27.3 1.0 O1G A:0KX405 4.8 17.6 1.0 CZ A:PHE272 4.8 33.1 1.0 NH2 A:ARG254 4.8 31.2 1.0 O2B A:0KX405 4.9 15.3 1.0

M.C.Koag, L.Lai, S.Lee. Structural Basis For the Inefficient Nucleotide Incorporation Opposite Cisplatin-Dna Lesion By Human Dna Polymerase Beta J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25237188
DOI: 10.1074/JBC.M114.605451