Magnesium in PDB 2fll: Ternary Complex of Human Dna Polymerase Iota with Dna and Dttp

All present enzymatic activity of Ternary Complex of Human Dna Polymerase Iota with Dna and Dttp:
2.7.7.7;

The structure of Ternary Complex of Human Dna Polymerase Iota with Dna and Dttp, PDB code: 2fll 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)	50.00 / 2.60
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.329, 98.329, 202.186, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 27.7

The binding sites of Magnesium atom in the Ternary Complex of Human Dna Polymerase Iota with Dna and Dttp (pdb code 2fll). 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 Human Dna Polymerase Iota with Dna and Dttp, PDB code: 2fll:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Complex of Human Dna Polymerase Iota 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 Ternary Complex of Human Dna Polymerase Iota with Dna and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg871 b:3.3 occ:1.00 OD1 A:ASP126 2.0 29.2 1.0 OD2 A:ASP34 2.0 14.2 1.0 O A:LEU35 2.2 21.2 1.0 O2B A:TTP875 2.3 20.9 1.0 O1A A:TTP875 2.3 18.0 1.0 O1G A:TTP875 2.4 21.3 1.0 CG A:ASP126 3.1 33.4 1.0 CG A:ASP34 3.2 18.5 1.0 MG A:MG872 3.4 0.9 1.0 C A:LEU35 3.4 20.0 1.0 PB A:TTP875 3.5 21.6 1.0 O A:HOH908 3.5 58.0 1.0 OD2 A:ASP126 3.6 35.4 1.0 PA A:TTP875 3.6 23.6 1.0 PG A:TTP875 3.7 19.0 1.0 OD1 A:ASP34 3.7 23.8 1.0 N A:LEU35 3.8 21.1 1.0 O3B A:TTP875 4.0 24.3 1.0 O3A A:TTP875 4.0 24.4 1.0 O A:HOH923 4.1 64.7 1.0 CA A:LEU35 4.1 20.1 1.0 C A:ASP34 4.2 21.3 1.0 O3G A:TTP875 4.3 24.1 1.0 CB A:ASP34 4.4 21.0 1.0 CB A:ASP126 4.5 24.1 1.0 N A:ASP36 4.5 17.5 1.0 C5' A:TTP875 4.5 21.6 1.0 O5' A:TTP875 4.5 24.6 1.0 O A:ASP34 4.6 27.2 1.0 CA A:ASP34 4.6 19.8 1.0 O2A A:TTP875 4.6 27.0 1.0 CB A:LEU35 4.7 21.0 1.0 O1B A:TTP875 4.7 27.1 1.0 O A:ASP126 4.8 24.5 1.0 CA A:ASP36 4.8 16.7 1.0 N A:CYS37 4.9 17.9 1.0 O2G A:TTP875 4.9 21.8 1.0 C A:ASP36 5.0 16.0 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex of Human Dna Polymerase Iota 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 Ternary Complex of Human Dna Polymerase Iota with Dna and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg872 b:0.9 occ:1.00 OE2 A:GLU127 2.4 31.9 1.0 O1A A:TTP875 2.4 18.0 1.0 OD1 A:ASP34 2.7 23.8 1.0 OD2 A:ASP34 3.2 14.2 1.0 CG A:ASP34 3.2 18.5 1.0 O2A A:TTP875 3.3 27.0 1.0 PA A:TTP875 3.3 23.6 1.0 O A:HOH923 3.3 64.7 1.0 CD A:GLU127 3.3 29.4 1.0 MG A:MG871 3.4 3.3 1.0 C3' P:DOC873 3.6 43.5 1.0 CG A:GLU127 3.7 23.1 1.0 OD2 A:ASP126 3.7 35.4 1.0 O1G A:TTP875 4.2 21.3 1.0 O5' A:TTP875 4.2 24.6 1.0 OD1 A:ASP126 4.2 29.2 1.0 OE1 A:GLU127 4.4 25.7 1.0 CG A:ASP126 4.4 33.4 1.0 C4' P:DOC873 4.6 36.7 1.0 CB A:ASP34 4.6 21.0 1.0 O3A A:TTP875 4.6 24.4 1.0 O A:HOH954 4.7 42.5 1.0 C2' P:DOC873 4.8 41.1 1.0 O2B A:TTP875 4.8 20.9 1.0 C5' P:DOC873 5.0 34.0 1.0

D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal. An Incoming Nucleotide Imposes An Anti to Syn Conformational Change on the Templating Purine in the Human Dna Polymerase-Iota Active Site. Structure V. 14 749 2006.
ISSN: ISSN 0969-2126
PubMed: 16615915
DOI: 10.1016/J.STR.2006.01.010