Magnesium in PDB 3ojs: Snapshots of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing C5 Modified Thymidines

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

The structure of Snapshots of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing C5 Modified Thymidines, PDB code: 3ojs 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)	46.69 / 1.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.829, 107.829, 90.197, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 21.2

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

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Snapshots of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing C5 Modified Thymidines within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg7 b:29.3 occ:1.00 O6 A:XJS1 2.1 29.6 1.0 OD2 A:ASP785 2.1 33.7 1.0 O11 A:XJS1 2.1 28.4 1.0 O9 A:XJS1 2.2 33.8 1.0 O A:TYR611 2.2 25.4 1.0 OD1 A:ASP610 2.2 32.8 1.0 CG A:ASP785 3.1 37.1 1.0 P2 A:XJS1 3.2 32.1 1.0 CG A:ASP610 3.3 37.6 1.0 C A:TYR611 3.3 30.0 1.0 P1 A:XJS1 3.4 31.1 1.0 P3 A:XJS1 3.4 34.7 1.0 OD1 A:ASP785 3.5 27.8 1.0 MG A:MG8 3.6 31.2 1.0 O1 A:XJS1 3.7 36.0 1.0 O3 A:XJS1 3.7 33.8 1.0 O A:HOH33 3.8 33.6 1.0 OD2 A:ASP610 3.8 32.5 1.0 H A:ILE614 3.8 34.9 1.0 HG22 A:ILE614 3.9 30.6 1.0 H A:GLN613 3.9 39.8 1.0 N A:TYR611 4.0 24.2 1.0 HA A:SER612 4.0 36.0 1.0 H A:TYR611 4.0 29.0 1.0 HB2 A:TYR611 4.0 29.8 1.0 O A:HOH120 4.1 36.2 1.0 C5' A:XJS1 4.1 33.8 1.0 CA A:TYR611 4.2 26.4 1.0 O5 A:XJS1 4.2 29.0 1.0 O5' A:XJS1 4.2 28.9 1.0 N A:GLN613 4.3 33.1 1.0 N A:SER612 4.3 30.2 1.0 C A:ASP610 4.4 27.9 1.0 HB A:ILE614 4.4 34.1 1.0 CB A:ASP785 4.5 23.6 1.0 HB2 A:ASP785 4.5 28.4 1.0 O8 A:XJS1 4.5 32.1 1.0 CA A:SER612 4.5 30.0 1.0 CB A:TYR611 4.5 24.8 1.0 O10 A:XJS1 4.5 28.6 1.0 CB A:ASP610 4.6 28.0 1.0 CG2 A:ILE614 4.6 25.5 1.0 O7 A:XJS1 4.6 40.8 1.0 HB3 A:TYR611 4.6 29.8 1.0 HG21 A:ILE614 4.6 30.6 1.0 C A:SER612 4.6 30.6 1.0 N A:ILE614 4.7 29.1 1.0 O A:ASP785 4.7 24.8 1.0 HB3 A:ASP610 4.8 33.6 1.0 O A:ASP610 4.8 28.1 1.0 HA A:ASP610 4.9 31.2 1.0 HZ2 A:LYS663 4.9 49.9 0.5 HB3 A:ASP785 4.9 28.4 1.0 HZ3 A:LYS663 4.9 52.8 0.5 CA A:ASP610 4.9 26.0 1.0 HA A:GLN613 5.0 38.5 1.0 CB A:ILE614 5.0 28.4 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Snapshots of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing C5 Modified Thymidines within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8 b:31.2 occ:1.00 OD1 A:ASP785 2.3 27.8 1.0 O11 A:XJS1 2.3 28.4 1.0 O A:HOH216 2.4 32.4 1.0 OD2 A:ASP610 2.4 32.5 1.0 O A:HOH833 2.6 41.8 1.0 H3'2 B:DOC112 2.7 32.3 1.0 CG A:ASP610 3.1 37.6 1.0 OD1 A:ASP610 3.2 32.8 1.0 CG A:ASP785 3.3 37.1 1.0 HB2 A:GLU786 3.4 29.3 1.0 P1 A:XJS1 3.5 31.1 1.0 H5' B:DOC112 3.5 39.9 1.0 MG A:MG7 3.6 29.3 1.0 C3' B:DOC112 3.6 26.9 1.0 OD2 A:ASP785 3.6 33.7 1.0 O10 A:XJS1 3.7 28.6 1.0 O A:HOH120 3.8 36.2 1.0 H4' B:DOC112 3.9 36.1 1.0 H3'1 B:DOC112 4.0 32.3 1.0 O5' A:XJS1 4.0 28.9 1.0 HZ2 A:LYS831 4.0 67.5 1.0 HZ3 A:LYS831 4.1 67.5 1.0 HB3 A:GLU786 4.1 29.3 1.0 C4' B:DOC112 4.1 30.1 1.0 CB A:GLU786 4.2 24.4 1.0 C5' B:DOC112 4.2 33.2 1.0 H A:ASP785 4.2 24.0 1.0 OE1 A:GLU786 4.3 32.9 1.0 C5' A:XJS1 4.3 33.8 1.0 NZ A:LYS831 4.4 56.3 1.0 O6 A:XJS1 4.5 29.6 1.0 O A:VAL783 4.5 21.6 1.0 CB A:ASP610 4.5 28.0 1.0 HZ1 A:LYS831 4.6 67.5 1.0 C A:ASP785 4.6 27.8 1.0 CB A:ASP785 4.7 23.6 1.0 O A:ASP785 4.7 24.8 1.0 H2'' B:DOC112 4.7 22.8 1.0 HB2 A:ASP610 4.7 33.6 1.0 C2' B:DOC112 4.7 19.0 1.0 N A:GLU786 4.8 22.9 1.0 O5' B:DOC112 4.8 24.6 1.0 HA A:ASP610 4.9 31.2 1.0 N A:ASP785 4.9 20.0 1.0 O1 A:XJS1 4.9 36.0 1.0 H5'' B:DOC112 5.0 39.9 1.0 HB3 A:ASP785 5.0 28.4 1.0 CA A:ASP785 5.0 22.0 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