Magnesium in PDB 3oju: Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing C5 Modified Thymidies

All present enzymatic activity of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing C5 Modified Thymidies:
2.7.7.7;

The structure of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing C5 Modified Thymidies, PDB code: 3oju was solved by A.Marx, K.Diederichs, S.Obeid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.21 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.022, 109.022, 91.473, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 21.9

The binding sites of Magnesium atom in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing C5 Modified Thymidies (pdb code 3oju). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing C5 Modified Thymidies, PDB code: 3oju:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing C5 Modified Thymidies


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing C5 Modified Thymidies within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2 b:27.2 occ:1.00 O1G A:SSJ1 2.2 36.8 1.0 O A:TYR611 2.3 32.5 1.0 OD2 A:ASP785 2.3 51.6 1.0 O1B A:SSJ1 2.3 42.6 1.0 OD1 A:ASP610 2.3 40.8 1.0 O2A A:SSJ1 2.5 60.6 1.0 CG A:ASP785 3.4 41.4 1.0 C A:TYR611 3.4 26.8 1.0 PB A:SSJ1 3.5 46.0 1.0 CG A:ASP610 3.5 44.8 1.0 PG A:SSJ1 3.6 43.1 1.0 HA A:SER612 3.7 45.0 1.0 PA A:SSJ1 3.8 63.0 1.0 OD1 A:ASP785 3.8 38.0 1.0 MG A:MG3 3.9 59.9 1.0 H A:GLN613 3.9 35.4 1.0 O3B A:SSJ1 4.0 40.7 1.0 H A:ILE614 4.0 31.6 1.0 HG22 A:ILE614 4.1 33.0 1.0 O3A A:SSJ1 4.1 0.6 1.0 OD2 A:ASP610 4.2 44.7 1.0 N A:TYR611 4.2 26.1 1.0 O A:HOH126 4.2 48.6 1.0 H A:TYR611 4.3 31.3 1.0 N A:SER612 4.3 26.9 1.0 N A:GLN613 4.3 29.5 1.0 O2G A:SSJ1 4.3 45.9 1.0 C5' A:SSJ1 4.3 45.5 1.0 CA A:SER612 4.3 37.5 1.0 CA A:TYR611 4.4 26.1 1.0 HB2 A:TYR611 4.4 28.6 1.0 HB2 A:ASP785 4.5 33.2 1.0 C A:ASP610 4.5 30.8 1.0 CB A:ASP785 4.6 27.6 1.0 O5' A:SSJ1 4.6 56.1 1.0 HZ1 A:LYS663 4.6 64.9 1.0 CB A:ASP610 4.6 32.5 1.0 C A:SER612 4.6 31.1 1.0 HB3 A:ASP610 4.6 39.1 1.0 O3G A:SSJ1 4.7 45.3 1.0 HB A:ILE614 4.7 30.1 1.0 O2B A:SSJ1 4.8 48.0 1.0 HA A:ASP610 4.8 31.1 1.0 N A:ILE614 4.8 26.3 1.0 CB A:TYR611 4.8 23.9 1.0 CG2 A:ILE614 4.8 27.5 1.0 HG21 A:ILE614 4.9 33.0 1.0 O A:ASP610 4.9 33.7 1.0 O A:ASP785 4.9 28.6 1.0 CA A:ASP610 4.9 25.9 1.0 HB3 A:TYR611 5.0 28.6 1.0 O1A A:SSJ1 5.0 60.5 1.0

Magnesium binding site 2 out of 2 in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing C5 Modified Thymidies


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing C5 Modified Thymidies within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3 b:59.9 occ:1.00 OD2 A:ASP610 2.7 44.7 1.0 O A:HOH33 2.7 37.0 1.0 O2A A:SSJ1 3.1 60.6 1.0 H3'2 B:DOC112 3.2 38.7 1.0 H5' B:DOC112 3.2 43.4 1.0 OD1 A:ASP610 3.3 40.8 1.0 CG A:ASP610 3.3 44.8 1.0 OD1 A:ASP785 3.4 38.0 1.0 H3'1 B:DOC112 3.6 38.7 1.0 HZ1 A:LYS831 3.6 74.0 1.0 HB2 A:GLU786 3.7 33.9 1.0 C3' B:DOC112 3.8 32.3 1.0 MG A:MG2 3.9 27.2 1.0 C5' B:DOC112 4.1 36.1 1.0 O A:HOH126 4.1 48.6 1.0 PA A:SSJ1 4.2 63.0 1.0 OE1 A:GLU786 4.2 45.3 1.0 CG A:ASP785 4.2 41.4 1.0 O1A A:SSJ1 4.3 60.5 1.0 OD2 A:ASP785 4.3 51.6 1.0 C4' B:DOC112 4.4 34.4 1.0 NZ A:LYS831 4.5 61.6 1.0 O5' B:DOC112 4.5 41.7 1.0 CB A:GLU786 4.5 28.2 1.0 OP1 B:DOC112 4.6 55.4 1.0 H4' B:DOC112 4.6 41.3 1.0 HB3 A:GLU786 4.6 33.9 1.0 O1G A:SSJ1 4.6 36.8 1.0 HZ1 A:LYS663 4.7 64.9 1.0 HZ3 A:LYS831 4.8 74.0 1.0 CB A:ASP610 4.8 32.5 1.0 H5'' B:DOC112 4.8 43.4 1.0 HZ2 A:LYS831 4.9 74.0 1.0 HB2 A:ASP610 5.0 39.1 1.0

S.Obeid, A.Baccaro, W.Welte, K.Diederichs, A.Marx. Structural Basis For the Synthesis of Nucleobase Modified Dna By Thermus Aquaticus Dna Polymerase. Proc.Natl.Acad.Sci.Usa V. 107 21327 2010.
ISSN: ISSN 0027-8424
PubMed: 21123743
DOI: 10.1073/PNAS.1013804107