Magnesium in PDB 2dpj: Structure of Hpoli with Dna and Dttp

All present enzymatic activity of Structure of Hpoli with Dna and Dttp:
2.7.7.7;

The structure of Structure of Hpoli with Dna and Dttp, PDB code: 2dpj was solved by D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.76 / 2.30
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.059, 98.059, 203.102, 90.00, 90.00, 120.00
R / Rfree (%)	23.8 / 27.7

The binding sites of Magnesium atom in the Structure of Hpoli with Dna and Dttp (pdb code 2dpj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Hpoli with Dna and Dttp, PDB code: 2dpj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Hpoli with Dna and Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Hpoli with Dna and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg871 b:18.8 occ:1.00 O2B A:TTP875 2.1 17.9 1.0 O A:LEU35 2.2 11.8 1.0 OD1 A:ASP126 2.2 13.7 1.0 O1G A:TTP875 2.3 19.1 1.0 O1A A:TTP875 2.3 22.6 1.0 OD2 A:ASP34 2.4 15.2 1.0 PB A:TTP875 3.2 20.6 1.0 MG A:MG872 3.3 78.1 1.0 CG A:ASP126 3.3 14.6 1.0 C A:LEU35 3.4 14.8 1.0 PG A:TTP875 3.4 18.2 1.0 CG A:ASP34 3.5 13.4 1.0 PA A:TTP875 3.5 21.7 1.0 O A:HOH929 3.6 49.0 1.0 O3A A:TTP875 3.7 20.7 1.0 O A:HOH932 3.7 50.5 1.0 OD2 A:ASP126 3.8 18.4 1.0 O3B A:TTP875 3.8 21.1 1.0 N A:LEU35 3.8 12.2 1.0 OD1 A:ASP34 3.9 12.0 1.0 O3G A:TTP875 4.1 18.5 1.0 CA A:LEU35 4.1 17.0 1.0 C A:ASP34 4.3 13.7 1.0 C5' A:TTP875 4.3 24.4 1.0 N A:ASP36 4.4 14.1 1.0 O5' A:TTP875 4.4 19.6 1.0 N A:CYS37 4.5 13.2 1.0 O1B A:TTP875 4.5 22.1 1.0 O2A A:TTP875 4.5 20.6 1.0 O2G A:TTP875 4.6 22.2 1.0 CB A:ASP126 4.6 14.0 1.0 CA A:ASP36 4.6 14.1 1.0 CB A:LEU35 4.7 17.9 1.0 C A:ASP36 4.7 14.1 1.0 CB A:ASP34 4.7 13.2 1.0 O A:ASP34 4.7 15.5 1.0 N A:PHE38 4.7 14.3 1.0 CA A:ASP34 4.9 11.8 1.0

Magnesium binding site 2 out of 2 in the Structure of Hpoli with Dna and Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Hpoli with Dna and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg872 b:78.1 occ:1.00 O1A A:TTP875 2.2 22.6 1.0 OE2 A:GLU127 2.5 15.8 1.0 OD1 A:ASP34 2.6 12.0 1.0 O A:HOH932 2.8 50.5 1.0 OD2 A:ASP34 3.0 15.2 1.0 CG A:ASP34 3.1 13.4 1.0 PA A:TTP875 3.2 21.7 1.0 MG A:MG871 3.3 18.8 1.0 O2A A:TTP875 3.3 20.6 1.0 OD2 A:ASP126 3.3 18.4 1.0 CD A:GLU127 3.4 16.2 1.0 CG A:GLU127 3.6 9.5 1.0 C3' P:DOC873 3.8 26.6 1.0 OD1 A:ASP126 3.9 13.7 1.0 O1G A:TTP875 4.0 19.1 1.0 CG A:ASP126 4.1 14.6 1.0 O5' A:TTP875 4.1 19.6 1.0 O3A A:TTP875 4.4 20.7 1.0 OE1 A:GLU127 4.5 17.3 1.0 CB A:ASP34 4.6 13.2 1.0 O A:HOH904 4.6 33.1 1.0 C5' A:TTP875 4.7 24.4 1.0 O2B A:TTP875 4.8 17.9 1.0 C2' P:DOC873 4.8 21.1 1.0 C4' P:DOC873 4.9 27.1 1.0

D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal. Hoogsteen Base Pair Formation Promotes Synthesis Opposite the 1,N(6)-Ethenodeoxyadenosine Lesion By Human Dna Polymerase Iota. Nat.Struct.Mol.Biol. V. 13 619 2006.
ISSN: ISSN 1545-9993
PubMed: 16819516
DOI: 10.1038/NSMB1118