Magnesium in PDB 2bdp: Crystal Structure of Bacillus Dna Polymerase I Fragment Complexed to 9 Base Pairs of Duplex Dna

The structure of Crystal Structure of Bacillus Dna Polymerase I Fragment Complexed to 9 Base Pairs of Duplex Dna, PDB code: 2bdp was solved by J.R.Kiefer, C.Mao, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.241, 93.275, 106.374, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 27.6

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Dna Polymerase I Fragment Complexed to 9 Base Pairs of Duplex Dna (pdb code 2bdp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Bacillus Dna Polymerase I Fragment Complexed to 9 Base Pairs of Duplex Dna, PDB code: 2bdp:

Magnesium binding site 1 out of 1 in the Crystal Structure of Bacillus Dna Polymerase I Fragment Complexed to 9 Base Pairs of Duplex Dna


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 Bacillus Dna Polymerase I Fragment Complexed to 9 Base Pairs of Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg950 b:27.4 occ:1.00 O A:TYR654 2.8 13.3 1.0 OD2 A:ASP653 2.8 16.0 1.0 OD2 A:ASP830 2.9 14.6 1.0 O A:HOH1427 3.0 37.5 1.0 O A:HOH1018 3.1 19.8 1.0 O A:HOH1019 3.1 20.5 1.0 O A:HOH1190 3.6 26.6 1.0 O A:HOH1012 3.7 14.7 1.0 CG A:ASP653 3.7 16.1 1.0 CG A:ASP830 3.8 13.5 1.0 CB A:ASP653 3.8 13.9 1.0 C A:TYR654 4.0 13.0 1.0 OD1 A:ASP830 4.1 12.4 1.0 O A:HOH1191 4.2 22.6 1.0 N A:TYR654 4.6 12.9 1.0 O A:HOH1022 4.7 32.2 1.0 C A:ASP653 4.7 13.2 1.0 CA A:SER655 4.7 13.7 1.0 N A:SER655 4.8 13.5 1.0 OD1 A:ASP653 4.9 16.8 1.0 CA A:ASP653 4.9 13.3 1.0 CA A:TYR654 4.9 13.0 1.0 CB A:ASP830 5.0 12.7 1.0

J.R.Kiefer, C.Mao, J.C.Braman, L.S.Beese. Visualizing Dna Replication in A Catalytically Active Bacillus Dna Polymerase Crystal. Nature V. 391 304 1998.
ISSN: ISSN 0028-0836
PubMed: 9440698
DOI: 10.1038/34693