Magnesium in PDB 3snn: RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dg in the Presence of MG2+

All present enzymatic activity of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dg in the Presence of MG2+:
2.7.7.7;

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dg in the Presence of MG2+, PDB code: 3snn was solved by M.Wang, J.Wang, W.H.Konigsberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.327, 119.525, 130.740, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 22.2

The binding sites of Magnesium atom in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dg in the Presence of MG2+ (pdb code 3snn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dg in the Presence of MG2+, PDB code: 3snn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dg in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dg in the Presence of MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg905 b:19.7 occ:1.00 O2B A:DCP904 1.9 18.7 1.0 OD1 A:ASP623 2.0 18.7 1.0 OD1 A:ASP411 2.0 19.8 1.0 O1G A:DCP904 2.1 18.4 1.0 O A:LEU412 2.1 16.9 1.0 O2A A:DCP904 2.3 17.4 1.0 PB A:DCP904 3.1 18.8 1.0 CG A:ASP623 3.1 19.5 1.0 CG A:ASP411 3.2 22.8 1.0 C A:LEU412 3.3 19.1 1.0 PG A:DCP904 3.3 19.9 1.0 PA A:DCP904 3.4 21.3 1.0 OD2 A:ASP623 3.6 21.6 1.0 O3A A:DCP904 3.6 20.9 1.0 O3B A:DCP904 3.6 20.7 1.0 MG A:MG906 3.7 29.4 1.0 OD2 A:ASP411 3.7 24.6 1.0 O A:HOH1104 3.7 30.8 1.0 O A:HOH1090 3.8 23.1 1.0 N A:LEU412 3.9 19.4 1.0 CA A:LEU412 4.0 18.6 1.0 C5' A:DCP904 4.1 16.2 1.0 O2G A:DCP904 4.1 20.1 1.0 O5' A:DCP904 4.2 18.8 1.0 N A:THR413 4.3 17.9 1.0 C A:ASP411 4.3 20.1 1.0 N A:SER414 4.4 18.9 1.0 CB A:ASP623 4.4 17.9 1.0 CB A:ASP411 4.4 20.0 1.0 O1B A:DCP904 4.5 20.8 1.0 O3G A:DCP904 4.5 20.1 1.0 N A:LEU415 4.5 17.5 1.0 CB A:LEU412 4.5 18.0 1.0 CA A:THR413 4.6 18.9 1.0 C A:THR413 4.6 18.6 1.0 O1A A:DCP904 4.7 20.6 1.0 O A:HOH938 4.7 27.6 1.0 CB A:LEU415 4.8 17.5 1.0 O A:ASP411 4.8 21.7 1.0 CA A:ASP411 4.9 20.2 1.0 O A:ASP623 4.9 20.7 1.0

Magnesium binding site 2 out of 2 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dg in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dg in the Presence of MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg906 b:29.4 occ:1.00 O A:HOH1366 2.1 10.8 1.0 OD2 A:ASP411 2.1 24.6 1.0 O A:HOH938 2.2 27.6 1.0 O2A A:DCP904 2.3 17.4 1.0 OD2 A:ASP623 2.4 21.6 1.0 CG A:ASP411 3.0 22.8 1.0 OD1 A:ASP411 3.3 19.8 1.0 CG A:ASP623 3.3 19.5 1.0 PA A:DCP904 3.4 21.3 1.0 OD1 A:ASP623 3.6 18.7 1.0 C3' P:DOC115 3.7 25.2 1.0 MG A:MG905 3.7 19.7 1.0 O1A A:DCP904 3.7 20.6 1.0 O A:HOH1090 3.8 23.1 1.0 O5' A:DCP904 3.9 18.8 1.0 C5' A:DCP904 4.2 16.2 1.0 CB A:SER624 4.2 21.1 1.0 O A:ASP621 4.4 17.9 1.0 CB A:ASP411 4.4 20.0 1.0 O A:HOH961 4.4 7.7 1.0 N A:SER624 4.6 20.2 1.0 O1G A:DCP904 4.6 18.4 1.0 C5' P:DOC115 4.6 26.5 1.0 C A:ASP623 4.6 18.9 1.0 OG A:SER624 4.6 19.6 1.0 O5' P:DOC115 4.7 28.4 1.0 C4' P:DOC115 4.7 26.6 1.0 CB A:ASP623 4.7 17.9 1.0 O3A A:DCP904 4.8 20.9 1.0 O A:ASP623 4.8 20.7 1.0 C2' P:DOC115 4.8 26.6 1.0 N A:ASP623 4.9 18.2 1.0 O2B A:DCP904 4.9 18.7 1.0 CA A:SER624 4.9 20.0 1.0 CA A:ASP623 5.0 20.0 1.0

S.Xia, M.Wang, G.Blaha, W.H.Konigsberg, J.Wang. Structural Insights Into Complete Metal Ion Coordination From Ternary Complexes of B Family RB69 Dna Polymerase. Biochemistry V. 50 9114 2011.
ISSN: ISSN 0006-2960
PubMed: 21923197
DOI: 10.1021/BI201260H