Magnesium in PDB 1d5a: Crystal Structure of An Archaebacterial Dna Polymerase D.Tok. Deposition of Second Native Structure at 2.4 Angstrom

All present enzymatic activity of Crystal Structure of An Archaebacterial Dna Polymerase D.Tok. Deposition of Second Native Structure at 2.4 Angstrom:
2.7.7.7;

The structure of Crystal Structure of An Archaebacterial Dna Polymerase D.Tok. Deposition of Second Native Structure at 2.4 Angstrom, PDB code: 1d5a was solved by Y.Zhao, D.Jeruzalmi, L.Leighton, R.Lasken, J.Kuriyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.800, 107.600, 153.200, 90.00, 90.00, 90.00
R / Rfree (%)	25.3 / 29.9

The binding sites of Magnesium atom in the Crystal Structure of An Archaebacterial Dna Polymerase D.Tok. Deposition of Second Native Structure at 2.4 Angstrom (pdb code 1d5a). 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 Archaebacterial Dna Polymerase D.Tok. Deposition of Second Native Structure at 2.4 Angstrom, PDB code: 1d5a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of An Archaebacterial Dna Polymerase D.Tok. Deposition of Second Native Structure at 2.4 Angstrom


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 Archaebacterial Dna Polymerase D.Tok. Deposition of Second Native Structure at 2.4 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg5030 b:57.5 occ:1.00 OD1 A:ASP141 2.2 66.9 1.0 OD1 A:ASP315 2.6 77.0 1.0 MG A:MG5031 2.9 59.4 1.0 CG A:ASP141 3.0 66.4 1.0 CG A:GLU143 3.2 92.1 1.0 OD2 A:ASP141 3.2 64.4 1.0 CG A:ASP315 3.8 80.1 1.0 O A:ILE142 4.0 82.9 1.0 CD A:GLU143 4.0 92.7 1.0 OE2 A:GLU143 4.1 93.6 1.0 C A:ILE142 4.4 82.5 1.0 CB A:GLU143 4.4 91.3 1.0 CB A:ASP141 4.4 66.9 1.0 CA A:GLU143 4.5 90.7 1.0 N A:GLU143 4.6 86.8 1.0 CB A:ASP315 4.6 81.5 1.0 OD2 A:ASP315 4.6 79.4 1.0 N A:ILE142 4.7 75.2 1.0 CE2 A:TYR311 4.8 91.4 1.0 OH A:TYR311 4.8 89.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of An Archaebacterial Dna Polymerase D.Tok. Deposition of Second Native Structure at 2.4 Angstrom


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 Archaebacterial Dna Polymerase D.Tok. Deposition of Second Native Structure at 2.4 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg5031 b:59.4 occ:1.00 OD2 A:ASP141 2.3 64.4 1.0 MG A:MG5030 2.9 57.5 1.0 CG A:ASP141 3.0 66.4 1.0 OD1 A:ASP141 3.2 66.9 1.0 OD1 A:ASP215 4.2 74.2 1.0 O A:ILE142 4.3 82.9 1.0 CB A:ASP141 4.4 66.9 1.0 OD2 A:ASP215 4.5 76.6 1.0 OD1 A:ASP315 4.5 77.0 1.0 N A:ILE142 4.7 75.2 1.0 O A:TYR209 4.7 62.5 1.0 CG A:ASP215 4.8 73.7 1.0

Y.Zhao, D.Jeruzalmi, I.Moarefi, L.Leighton, R.Lasken, J.Kuriyan. Crystal Structure of An Archaebacterial Dna Polymerase. Structure Fold.Des. V. 7 1189 1999.
ISSN: ISSN 0969-2126
PubMed: 10545321
DOI: 10.1016/S0969-2126(00)80053-2