Magnesium in PDB 3ht3: Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus V713P Mutant Bound to G:Dctp

All present enzymatic activity of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus V713P Mutant Bound to G:Dctp:
2.7.7.7;

The structure of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus V713P Mutant Bound to G:Dctp, PDB code: 3ht3 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)	46.98 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.280, 108.790, 152.090, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 24.7

The binding sites of Magnesium atom in the Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus V713P Mutant Bound to G:Dctp (pdb code 3ht3). 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 V713P Mutant Bound to G:Dctp, PDB code: 3ht3:
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 V713P Mutant Bound to G:Dctp


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 V713P Mutant Bound to G:Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg200 b:39.9 occ:1.00 O2A A:DCP201 1.9 37.1 1.0 O2G A:DCP201 1.9 39.5 1.0 O2B A:DCP201 1.9 38.0 1.0 O A:HOH1098 2.1 43.8 1.0 O A:HOH1099 2.1 43.5 1.0 O A:HOH1100 2.3 42.2 1.0 PB A:DCP201 2.9 36.7 1.0 PA A:DCP201 3.1 34.6 1.0 PG A:DCP201 3.1 38.0 1.0 O3B A:DCP201 3.1 38.4 1.0 O3A A:DCP201 3.3 36.6 1.0 O1A A:DCP201 4.0 33.7 1.0 O3G A:DCP201 4.1 38.3 1.0 O1G A:DCP201 4.2 38.3 1.0 O5' A:DCP201 4.3 33.1 1.0 O1B A:DCP201 4.3 36.2 1.0 O A:HOH279 4.4 25.6 1.0 C5' A:DCP201 4.6 30.5 1.0 NH1 A:ARG629 4.6 36.4 1.0 NH2 A:ARG629 4.6 36.7 1.0 O B:HOH834 4.7 34.5 1.0 NZ A:LYS706 4.7 30.5 1.0 O A:HOH1097 4.8 42.0 1.0 O A:HOH1059 4.9 32.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus V713P Mutant Bound to G:Dctp


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 V713P Mutant Bound to G:Dctp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg200 b:17.1 occ:1.00 O2G D:DCP202 1.9 17.5 1.0 O2B D:DCP202 1.9 18.0 1.0 O2A D:DCP202 1.9 20.0 1.0 O D:HOH1102 2.1 23.8 1.0 O D:HOH1103 2.2 17.6 1.0 O D:HOH1101 2.2 19.3 1.0 PB D:DCP202 3.0 17.7 1.0 PG D:DCP202 3.1 18.8 1.0 PA D:DCP202 3.2 19.0 1.0 O3A D:DCP202 3.4 17.5 1.0 O3B D:DCP202 3.5 17.7 1.0 O3G D:DCP202 3.7 18.6 1.0 O D:HOH899 4.0 25.4 1.0 O D:HOH173 4.0 23.6 1.0 O1A D:DCP202 4.2 17.7 1.0 OD2 D:ASP830 4.2 18.1 1.0 O D:HOH286 4.3 26.6 1.0 O D:TYR654 4.3 12.1 1.0 O5' D:DCP202 4.3 18.3 1.0 OD2 D:ASP653 4.3 17.3 0.5 O1B D:DCP202 4.4 18.2 1.0 C5' D:DCP202 4.4 19.4 1.0 O1G D:DCP202 4.4 21.0 1.0 N D:GLN656 4.4 9.2 1.0 O D:HOH1000 4.5 27.6 1.0 OD2 D:ASP653 4.5 15.3 0.5 OD1 D:ASP653 4.8 19.2 0.5 CG D:ASP653 4.9 13.7 0.5

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