Magnesium in PDB 2pyl: PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex)

All present enzymatic activity of PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex):
2.7.7.7;

The structure of PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex), PDB code: 2pyl was solved by A.J.Berman, S.Kamtekar, J.L.Goodman, J.M.Lazaro, M.De Vega, L.Blanco, M.Salas, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.42 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.922, 78.199, 157.813, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 25.3

The binding sites of Magnesium atom in the PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex) (pdb code 2pyl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex), PDB code: 2pyl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3202 b:22.7 occ:1.00 O2B A:TTP3204 2.2 15.3 1.0 O1A A:TTP3204 2.5 18.2 1.0 O A:HOH3523 2.5 17.3 1.0 MG A:MG3203 2.6 19.9 1.0 O A:HOH3274 2.7 7.9 1.0 O1G A:TTP3204 2.7 18.7 1.0 OD1 A:ASP458 2.7 21.2 1.0 OD2 A:ASP249 2.8 22.9 1.0 O A:HOH3525 2.9 16.7 1.0 O A:VAL250 3.2 21.6 1.0 O A:HOH3501 3.5 20.7 1.0 PB A:TTP3204 3.5 16.9 1.0 PA A:TTP3204 3.7 14.2 1.0 CG A:ASP249 3.9 22.8 1.0 O3A A:TTP3204 3.9 15.6 1.0 CG A:ASP458 4.0 18.3 1.0 PG A:TTP3204 4.0 18.1 1.0 O3B A:TTP3204 4.2 20.0 1.0 O A:HOH3524 4.3 15.9 1.0 O5' A:TTP3204 4.4 11.7 1.0 C5' A:TTP3204 4.4 9.8 1.0 C A:VAL250 4.4 17.8 1.0 O A:HOH3409 4.5 14.8 1.0 N A:SER252 4.6 14.2 1.0 OD1 A:ASP249 4.6 25.7 1.0 OD2 A:ASP458 4.7 18.6 1.0 O1B A:TTP3204 4.7 17.4 1.0 CB A:ASP249 4.7 21.1 1.0 O A:HOH3233 4.8 18.5 1.0 O2G A:TTP3204 4.8 18.6 1.0 O2A A:TTP3204 4.9 14.2 1.0 O A:HOH3508 4.9 25.1 1.0 CB A:ASP458 4.9 16.9 1.0

Magnesium binding site 2 out of 2 in the PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PHI29 Dna Polymerase Complexed with Primer-Template Dna and Incoming Nucleotide Substrates (Ternary Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3203 b:19.9 occ:1.00 O1A A:TTP3204 2.2 18.2 1.0 O A:HOH3525 2.2 16.7 1.0 OD2 A:ASP249 2.3 22.9 1.0 OD1 A:ASP458 2.5 21.2 1.0 MG A:MG3202 2.6 22.7 1.0 CG A:ASP249 3.1 22.8 1.0 OD1 A:ASP249 3.2 25.7 1.0 OD2 A:ASP458 3.2 18.6 1.0 CG A:ASP458 3.2 18.3 1.0 O A:HOH3508 3.3 25.1 1.0 PA A:TTP3204 3.7 14.2 1.0 O A:HOH3523 3.7 17.3 1.0 O A:HOH3500 4.0 20.3 1.0 O A:HOH3233 4.0 18.5 1.0 O1G A:TTP3204 4.1 18.7 1.0 O2A A:TTP3204 4.2 14.2 1.0 O A:HOH3274 4.3 7.9 1.0 O2B A:TTP3204 4.3 15.3 1.0 C3' X:2DA11 4.4 18.5 1.0 C5' A:TTP3204 4.5 9.8 1.0 CB A:ASP249 4.5 21.1 1.0 O5' A:TTP3204 4.5 11.7 1.0 O A:HOH3524 4.7 15.9 1.0 O3A A:TTP3204 4.7 15.6 1.0 CB A:ASP458 4.7 16.9 1.0

A.J.Berman, S.Kamtekar, J.L.Goodman, J.M.Lazaro, M.De Vega, L.Blanco, M.Salas, T.A.Steitz. Structures of PHI29 Dna Polymerase Complexed with Substrate: the Mechanism of Translocation in B-Family Polymerases Embo J. V. 26 3494 2007.
ISSN: ISSN 0261-4189
PubMed: 17611604
DOI: 10.1038/SJ.EMBOJ.7601780