Magnesium in PDB 4elt: 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: 4elt 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)	47.14 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.860, 108.860, 91.004, 90.00, 90.00, 120.00
R / Rfree (%)	16 / 20.9

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 4elt). 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: 4elt:
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:24.2 occ:1.00 O2G A:0R5901 2.0 30.7 1.0 O A:TYR611 2.1 20.3 1.0 OD2 A:ASP785 2.2 27.9 1.0 OD1 A:ASP610 2.2 20.6 1.0 O2B A:0R5901 2.2 20.2 1.0 O1A A:0R5901 2.2 20.2 1.0 PB A:0R5901 3.2 28.6 1.0 CG A:ASP785 3.2 27.8 1.0 PG A:0R5901 3.2 33.6 1.0 C A:TYR611 3.3 27.2 1.0 PA A:0R5901 3.3 30.0 1.0 CG A:ASP610 3.4 30.6 1.0 OD1 A:ASP785 3.6 21.4 1.0 O3A A:0R5901 3.6 42.8 1.0 O3B A:0R5901 3.6 31.9 1.0 O A:HOH1066 3.7 25.6 1.0 MG A:MG903 3.7 31.5 1.0 O A:HOH1067 3.7 24.9 1.0 O3G A:0R5901 4.0 29.7 1.0 OD2 A:ASP610 4.0 31.9 1.0 N A:TYR611 4.1 19.1 1.0 C5' A:0R5901 4.2 23.7 1.0 CA A:TYR611 4.2 24.0 1.0 O5' A:0R5901 4.2 28.3 1.0 N A:SER612 4.3 28.3 1.0 N A:GLN613 4.3 22.5 1.0 C A:ASP610 4.4 19.9 1.0 O1G A:0R5901 4.4 24.2 1.0 CA A:SER612 4.4 29.1 1.0 O2A A:0R5901 4.5 27.2 1.0 CG2 A:ILE614 4.5 17.9 1.0 O1B A:0R5901 4.5 23.3 1.0 CB A:ASP785 4.5 16.3 1.0 CB A:ASP610 4.5 25.2 1.0 C A:SER612 4.6 31.2 1.0 CB A:TYR611 4.6 18.7 1.0 O A:ASP610 4.7 21.0 1.0 N A:ILE614 4.7 23.0 1.0 CA A:ASP610 4.9 19.4 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:31.5 occ:1.00 OD1 A:ASP785 2.2 21.4 1.0 O1A A:0R5901 2.4 20.2 1.0 OD2 A:ASP610 2.5 31.9 1.0 O A:HOH1001 2.5 26.6 1.0 O A:HOH1002 2.8 25.6 1.0 OD1 A:ASP610 3.1 20.6 1.0 CG A:ASP610 3.1 30.6 1.0 CG A:ASP785 3.2 27.8 1.0 PA A:0R5901 3.5 30.0 1.0 OD2 A:ASP785 3.6 27.9 1.0 C3' B:DOC112 3.6 13.0 1.0 MG A:MG902 3.7 24.2 1.0 O2A A:0R5901 3.7 27.2 1.0 O A:HOH1067 3.7 24.9 1.0 O5' A:0R5901 4.0 28.3 1.0 C4' B:DOC112 4.2 22.6 1.0 OE1 A:GLU786 4.2 22.8 1.0 CB A:GLU786 4.2 23.3 1.0 NZ A:LYS831 4.3 30.6 1.0 C5' A:0R5901 4.3 23.7 1.0 C5' B:DOC112 4.4 19.0 1.0 O A:VAL783 4.5 14.5 1.0 CB A:ASP610 4.6 25.2 1.0 CB A:ASP785 4.6 16.3 1.0 O2G A:0R5901 4.6 30.7 1.0 C A:ASP785 4.6 22.1 1.0 C2' B:DOC112 4.7 13.3 1.0 N A:GLU786 4.7 21.9 1.0 N A:ASP785 4.8 16.7 1.0 O A:ASP785 4.9 19.7 1.0 O5' B:DOC112 4.9 27.4 1.0 CA A:ASP785 4.9 17.2 1.0 O3A A:0R5901 4.9 42.8 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 C:Mg302 b:76.0 occ:1.00 O C:HOH432 2.1 64.7 1.0 O C:HOH435 2.1 65.3 1.0 O C:HOH433 2.2 56.9 1.0 O C:HOH434 2.2 56.9 1.0 N7 C:DG213 3.7 34.0 1.0 O6 C:DG214 3.9 38.2 1.0 O6 C:DG213 4.2 30.3 1.0 C7 C:DT212 4.5 17.7 1.0 O B:HOH325 4.5 43.9 1.0 N7 C:DG214 4.6 42.3 1.0 C5 C:DG213 4.6 25.7 1.0 C8 C:DG213 4.7 35.6 1.0 C6 C:DG213 4.7 28.2 1.0 C6 C:DG214 4.8 33.1 1.0 C5 C:DT212 5.0 25.8 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