Magnesium in PDB 3hp6: Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus F710Y Mutant Bound to G:T Mismatch

All present enzymatic activity of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus F710Y Mutant Bound to G:T Mismatch:
2.7.7.7;

The structure of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus F710Y Mutant Bound to G:T Mismatch, PDB code: 3hp6 was solved by E.Y.Wu, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.84 / 1.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.170, 108.710, 152.210, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.7

The binding sites of Magnesium atom in the Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus F710Y Mutant Bound to G:T Mismatch (pdb code 3hp6). 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 Fragment Dna Polymerase I From Bacillus Stearothermophilus F710Y Mutant Bound to G:T Mismatch, PDB code: 3hp6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus F710Y Mutant Bound to G:T Mismatch


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 Fragment Dna Polymerase I From Bacillus Stearothermophilus F710Y Mutant Bound to G:T Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg200 b:35.3 occ:1.00 O2B A:D3T201 1.9 33.9 1.0 O2G A:D3T201 2.0 36.2 1.0 O A:HOH930 2.1 31.9 1.0 O2A A:D3T201 2.1 34.5 1.0 O A:HOH1064 2.3 43.8 1.0 O A:HOH249 2.5 36.1 1.0 PB A:D3T201 3.0 35.6 1.0 PG A:D3T201 3.2 36.8 1.0 PA A:D3T201 3.2 34.7 1.0 O3A A:D3T201 3.4 34.4 1.0 O3B A:D3T201 3.4 36.0 1.0 O3G A:D3T201 3.7 35.3 1.0 OD2 A:ASP653 4.2 39.2 1.0 O A:HOH82 4.2 21.5 1.0 O1A A:D3T201 4.3 32.6 1.0 O B:HOH865 4.3 46.9 1.0 O5' A:D3T201 4.4 30.6 1.0 O A:TYR654 4.4 32.2 1.0 N A:GLN656 4.4 27.8 1.0 O1B A:D3T201 4.4 35.2 1.0 C5' A:D3T201 4.4 27.8 1.0 O1G A:D3T201 4.5 36.2 1.0 O A:HOH988 4.6 35.7 1.0 CA A:SER655 4.8 30.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus F710Y Mutant Bound to G:T Mismatch


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 Fragment Dna Polymerase I From Bacillus Stearothermophilus F710Y Mutant Bound to G:T Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg200 b:30.3 occ:1.00 O2B D:D3T202 1.7 29.6 1.0 O D:HOH147 2.0 42.1 1.0 O2A D:D3T202 2.0 29.3 1.0 O D:HOH945 2.1 33.5 1.0 O1G D:D3T202 2.1 35.4 1.0 O D:HOH161 2.2 29.5 1.0 PB D:D3T202 2.8 30.6 1.0 PA D:D3T202 3.1 28.7 1.0 PG D:D3T202 3.2 36.2 1.0 O3A D:D3T202 3.3 31.4 1.0 O3B D:D3T202 3.4 32.9 1.0 O2G D:D3T202 3.8 33.7 1.0 O D:HOH30 4.0 30.4 1.0 O1A D:D3T202 4.2 30.0 1.0 O D:HOH915 4.2 45.5 1.0 O1B D:D3T202 4.2 29.9 1.0 C5' D:D3T202 4.3 24.8 1.0 O5' D:D3T202 4.3 27.0 1.0 OD2 D:ASP653 4.4 29.8 1.0 O D:HOH918 4.4 38.3 1.0 O3G D:D3T202 4.4 34.5 1.0 O D:HOH936 4.5 31.7 1.0 O D:HOH21 4.5 17.3 1.0 N D:GLN656 4.7 14.4 1.0 O D:TYR654 4.8 19.8 1.0 CA D:SER655 4.9 15.8 1.0

E.Y.Wu, L.S.Beese. The Structure of A High Fidelity Dna Polymerase Bound to A Mismatched Nucleotide Reveals An "Ajar" Intermediate Conformation in the Nucleotide Selection Mechanism. J.Biol.Chem. V. 286 19758 2011.
ISSN: ISSN 0021-9258
PubMed: 21454515
DOI: 10.1074/JBC.M110.191130