Magnesium in PDB 2dpi: Ternary Complex of Hpoli with Dna and Dctp

All present enzymatic activity of Ternary Complex of Hpoli with Dna and Dctp:
2.7.7.7;

The structure of Ternary Complex of Hpoli with Dna and Dctp, PDB code: 2dpi 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)	42.64 / 2.30
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.148, 98.148, 203.112, 90.00, 90.00, 120.00
R / Rfree (%)	22.8 / 27.8

The binding sites of Magnesium atom in the Ternary Complex of Hpoli with Dna and Dctp (pdb code 2dpi). 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 of Hpoli with Dna and Dctp, PDB code: 2dpi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Complex of Hpoli with Dna and 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 of Hpoli with Dna and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg871 b:20.7 occ:1.00 O2B A:DCP875 2.2 13.7 1.0 O A:LEU35 2.3 8.7 1.0 OD1 A:ASP126 2.3 18.1 1.0 O1A A:DCP875 2.3 25.5 1.0 OD2 A:ASP34 2.3 10.9 1.0 O1G A:DCP875 2.3 22.1 1.0 PB A:DCP875 3.2 24.3 1.0 MG A:MG872 3.2 68.3 1.0 CG A:ASP126 3.4 14.6 1.0 PG A:DCP875 3.4 21.8 1.0 C A:LEU35 3.4 9.9 1.0 O A:HOH929 3.4 46.1 1.0 CG A:ASP34 3.4 9.7 1.0 PA A:DCP875 3.5 24.1 1.0 O3A A:DCP875 3.7 25.1 1.0 O3B A:DCP875 3.7 24.8 1.0 OD2 A:ASP126 3.8 16.3 1.0 O A:HOH932 3.8 52.6 1.0 N A:LEU35 3.8 6.0 1.0 OD1 A:ASP34 3.9 16.3 1.0 O3G A:DCP875 4.0 24.1 1.0 CA A:LEU35 4.1 10.8 1.0 C A:ASP34 4.2 7.9 1.0 C5' A:DCP875 4.3 20.9 1.0 O5' A:DCP875 4.4 17.8 1.0 N A:ASP36 4.4 10.2 1.0 N A:CYS37 4.5 8.3 1.0 O1B A:DCP875 4.5 25.6 1.0 O2A A:DCP875 4.6 26.6 1.0 CB A:ASP126 4.6 11.0 1.0 CB A:ASP34 4.6 7.8 1.0 O2G A:DCP875 4.7 24.0 1.0 O A:ASP34 4.7 9.2 1.0 CA A:ASP36 4.7 9.8 1.0 CB A:LEU35 4.7 12.7 1.0 C A:ASP36 4.8 9.2 1.0 CA A:ASP34 4.8 6.4 1.0 N A:PHE38 4.8 9.7 1.0 O A:ASP126 5.0 8.7 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex of Hpoli with Dna and 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 of Hpoli with Dna and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg872 b:68.3 occ:1.00 O1A A:DCP875 2.4 25.5 1.0 OE2 A:GLU127 2.4 11.3 1.0 OD1 A:ASP34 2.5 16.3 1.0 O A:HOH932 2.8 52.6 1.0 OD2 A:ASP34 2.9 10.9 1.0 CG A:ASP34 3.0 9.7 1.0 MG A:MG871 3.2 20.7 1.0 PA A:DCP875 3.3 24.1 1.0 CD A:GLU127 3.3 13.6 1.0 O2A A:DCP875 3.4 26.6 1.0 OD2 A:ASP126 3.5 16.3 1.0 CG A:GLU127 3.6 3.4 1.0 O1G A:DCP875 4.0 22.1 1.0 C3' P:DOC873 4.0 26.9 1.0 OD1 A:ASP126 4.0 18.1 1.0 CG A:ASP126 4.2 14.6 1.0 O5' A:DCP875 4.3 17.8 1.0 CB A:ASP34 4.4 7.8 1.0 OE1 A:GLU127 4.4 13.5 1.0 O3A A:DCP875 4.5 25.1 1.0 O2B A:DCP875 4.8 13.7 1.0 C5' A:DCP875 4.9 20.9 1.0 O A:HOH904 4.9 32.8 1.0 C4' P:DOC873 4.9 26.5 1.0 O A:HOH929 4.9 46.1 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