Magnesium in PDB 3ktq: Crystal Structure of An Active Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus

All present enzymatic activity of Crystal Structure of An Active Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus:
2.7.7.7;

The structure of Crystal Structure of An Active Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus, PDB code: 3ktq was solved by Y.Li, G.Waksman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.028, 108.028, 90.167, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 27.5

The binding sites of Magnesium atom in the Crystal Structure of An Active Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus (pdb code 3ktq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of An Active Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus, PDB code: 3ktq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of An Active Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of An Active Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:2.0 occ:1.00 OD1 A:ASP610 2.1 12.5 1.0 OD2 A:ASP785 2.1 7.5 1.0 O2B A:DCT113 2.2 70.3 1.0 O A:TYR611 2.2 15.2 1.0 O1G A:DCT113 2.3 59.9 1.0 O2A A:DCT113 2.4 51.8 1.0 PB A:DCT113 3.0 74.1 1.0 CG A:ASP785 3.0 9.0 1.0 O3B A:DCT113 3.1 86.1 1.0 PG A:DCT113 3.2 64.2 1.0 CG A:ASP610 3.2 10.8 1.0 O3A A:DCT113 3.3 83.6 1.0 OD1 A:ASP785 3.3 11.7 1.0 PA A:DCT113 3.4 54.3 1.0 C A:TYR611 3.5 13.2 1.0 OD2 A:ASP610 3.8 9.8 1.0 MG A:MG902 3.8 22.8 1.0 O A:HOH3102 4.0 30.7 1.0 N A:TYR611 4.1 12.5 1.0 C5' A:DCT113 4.1 28.2 1.0 O A:HOH3111 4.2 28.3 1.0 O2G A:DCT113 4.2 58.6 1.0 O5' A:DCT113 4.3 43.8 1.0 CA A:TYR611 4.3 11.9 1.0 C A:ASP610 4.3 12.4 1.0 CG2 A:ILE614 4.4 13.7 1.0 O3G A:DCT113 4.4 59.2 1.0 O1B A:DCT113 4.4 68.1 1.0 CB A:ASP785 4.4 8.4 1.0 N A:SER612 4.4 14.9 1.0 CB A:ASP610 4.4 11.9 1.0 N A:GLN613 4.5 13.8 1.0 CA A:SER612 4.5 15.9 1.0 O1A A:DCT113 4.6 51.1 1.0 N A:ILE614 4.6 15.0 1.0 O A:ASP785 4.7 9.7 1.0 CB A:ILE614 4.7 14.8 1.0 CB A:TYR611 4.7 11.8 1.0 O A:ASP610 4.7 14.9 1.0 C A:SER612 4.8 14.7 1.0 CA A:ASP610 4.8 11.3 1.0 O A:HOH3003 4.9 12.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of An Active Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of An Active Ternary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:22.8 occ:1.00 O A:HOH3125 2.2 37.3 1.0 O2A A:DCT113 2.2 51.8 1.0 OD2 A:ASP610 2.4 9.8 1.0 OD1 A:ASP785 2.5 11.7 1.0 O A:HOH3003 2.5 12.2 1.0 CG A:ASP610 3.1 10.8 1.0 OD1 A:ASP610 3.2 12.5 1.0 PA A:DCT113 3.4 54.3 1.0 CG A:ASP785 3.6 9.0 1.0 C3' B:DOC112 3.6 9.2 1.0 MG A:MG901 3.8 2.0 1.0 OE1 A:GLU786 3.8 14.6 1.0 CB A:GLU786 3.8 11.3 1.0 O1A A:DCT113 3.8 51.1 1.0 O5' A:DCT113 4.0 43.8 1.0 OD2 A:ASP785 4.0 7.5 1.0 O A:HOH3111 4.1 28.3 1.0 C4' B:DOC112 4.1 12.2 1.0 O A:VAL783 4.1 10.6 1.0 C5' B:DOC112 4.1 15.0 1.0 C5' A:DCT113 4.2 28.2 1.0 CB A:ASP610 4.5 11.9 1.0 NZ A:LYS831 4.5 29.4 1.0 N A:GLU786 4.5 11.0 1.0 C A:ASP785 4.5 10.0 1.0 OP1 B:DOC112 4.6 17.0 1.0 O5' B:DOC112 4.7 17.1 1.0 CD A:GLU786 4.7 13.6 1.0 O3A A:DCT113 4.7 83.6 1.0 O1G A:DCT113 4.7 59.9 1.0 CA A:GLU786 4.8 10.9 1.0 O A:ASP785 4.8 9.7 1.0 CB A:ASP785 4.8 8.4 1.0 CG A:GLU786 4.8 12.3 1.0 N A:ASP785 4.8 10.9 1.0 C2' B:DOC112 4.9 9.8 1.0 O A:HOH3026 4.9 21.0 1.0 CA A:ASP785 5.0 9.4 1.0

Y.Li, S.Korolev, G.Waksman. Crystal Structures of Open and Closed Forms of Binary and Ternary Complexes of the Large Fragment of Thermus Aquaticus Dna Polymerase I: Structural Basis For Nucleotide Incorporation. Embo J. V. 17 7514 1998.
ISSN: ISSN 0261-4189
PubMed: 9857206
DOI: 10.1093/EMBOJ/17.24.7514