Magnesium in PDB 4elu: Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines

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

The structure of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines, PDB code: 4elu 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)	46.86 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.209, 108.209, 90.397, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 18.2

The binding sites of Magnesium atom in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines (pdb code 4elu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines, PDB code: 4elu:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines


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 Modified Pyrimidines within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:18.5 occ:1.00 O3G A:0R6901 2.0 17.5 1.0 OD1 A:ASP610 2.1 20.4 1.0 O1B A:0R6901 2.1 17.7 1.0 OD2 A:ASP785 2.1 18.3 1.0 O1A A:0R6901 2.1 17.3 1.0 O A:TYR611 2.1 17.0 1.0 CG A:ASP785 3.1 17.6 1.0 PB A:0R6901 3.1 19.9 1.0 CG A:ASP610 3.2 24.3 1.0 PA A:0R6901 3.3 18.6 1.0 C A:TYR611 3.3 17.4 1.0 PG A:0R6901 3.4 19.6 1.0 OD1 A:ASP785 3.5 17.7 1.0 MG A:MG903 3.6 22.4 1.0 O3A A:0R6901 3.6 20.5 1.0 O3B A:0R6901 3.6 18.2 1.0 OD2 A:ASP610 3.8 21.5 1.0 O A:HOH1050 3.8 21.4 1.0 O A:HOH1030 3.9 24.1 1.0 N A:TYR611 3.9 18.9 1.0 C5' A:0R6901 4.0 17.0 1.0 CA A:TYR611 4.1 17.6 1.0 O1G A:0R6901 4.2 19.3 1.0 O5' A:0R6901 4.2 18.1 1.0 C A:ASP610 4.3 17.1 1.0 N A:SER612 4.3 19.9 1.0 N A:GLN613 4.4 21.0 1.0 CB A:ASP785 4.4 17.7 1.0 CB A:ASP610 4.4 19.2 1.0 O2G A:0R6901 4.5 21.7 1.0 O2A A:0R6901 4.5 18.9 1.0 CA A:SER612 4.5 21.1 1.0 CB A:TYR611 4.5 18.8 1.0 O2B A:0R6901 4.5 18.4 1.0 CG2 A:ILE614 4.6 17.8 1.0 C A:SER612 4.7 21.7 1.0 O A:ASP610 4.7 21.1 1.0 N A:ILE614 4.8 19.7 1.0 CA A:ASP610 4.8 16.8 1.0 O A:ASP785 4.9 17.8 1.0 CB A:ILE614 5.0 17.9 1.0

Magnesium binding site 2 out of 3 in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines


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 Modified Pyrimidines within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:22.4 occ:1.00 OD1 A:ASP785 2.2 17.7 1.0 OD2 A:ASP610 2.3 21.5 1.0 O A:HOH1003 2.4 19.4 1.0 O1A A:0R6901 2.4 17.3 1.0 O A:HOH1001 2.4 20.1 1.0 CG A:ASP610 3.0 24.3 1.0 OD1 A:ASP610 3.2 20.4 1.0 CG A:ASP785 3.2 17.6 1.0 PA A:0R6901 3.4 18.6 1.0 OD2 A:ASP785 3.5 18.3 1.0 MG A:MG902 3.6 18.5 1.0 C3' B:DDG112 3.6 16.7 1.0 O A:HOH1050 3.7 21.4 1.0 O2A A:0R6901 3.8 18.9 1.0 O5' A:0R6901 4.0 18.1 1.0 NZ A:LYS831 4.1 22.4 1.0 C4' B:DDG112 4.2 16.7 1.0 C5' A:0R6901 4.2 17.0 1.0 CB A:GLU786 4.3 19.1 1.0 C5' B:DDG112 4.3 13.1 1.0 OE1 A:GLU786 4.3 23.6 1.0 CB A:ASP610 4.4 19.2 1.0 O A:VAL783 4.5 18.8 1.0 CB A:ASP785 4.6 17.7 1.0 O3G A:0R6901 4.6 17.5 1.0 C A:ASP785 4.6 16.3 1.0 N A:GLU786 4.7 15.8 1.0 C2' B:DDG112 4.8 15.8 1.0 O A:ASP785 4.8 17.8 1.0 N A:ASP785 4.8 16.7 1.0 O3A A:0R6901 4.9 20.5 1.0 O5' B:DDG112 4.9 17.4 1.0 OP1 B:DDG112 4.9 19.6 1.0 CA A:ASP785 4.9 15.2 1.0

Magnesium binding site 3 out of 3 in the Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Snapshot of the Large Fragment of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:50.0 occ:1.00 O B:HOH330 2.2 26.2 1.0 O C:HOH440 2.2 43.4 1.0 O B:HOH331 2.2 36.0 1.0 O B:HOH329 2.2 31.2 1.0 O B:HOH327 2.7 45.5 1.0 O6 B:DG108 4.0 22.3 1.0 O C:HOH434 4.1 37.1 1.0 O B:HOH305 4.2 32.0 1.0 O C:HOH429 4.2 28.1 1.0 O B:HOH323 4.3 44.9 1.0 O6 B:DG107 4.3 20.1 1.0 N7 B:DG107 4.3 21.6 1.0 N4 C:DC209 4.4 21.8 1.0 O B:HOH317 4.4 35.0 1.0 CH3 C:ACT301 4.7 54.6 1.0 C5 B:DC106 4.8 23.5 1.0 C6 B:DG108 5.0 21.9 1.0

S.Obeid, H.Busskamp, W.Welte, K.Diederichs, A.Marx. Interactions of Non-Polar and "Click-Able" Nucleotides in the Confines of A Dna Polymerase Active Site. Chem.Commun.(Camb.) V. 48 8320 2012.
ISSN: ISSN 1359-7345
PubMed: 22766607
DOI: 10.1039/C2CC34181F