Magnesium in PDB 2ihm: Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide

All present enzymatic activity of Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide:
2.7.7.7;

The structure of Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide, PDB code: 2ihm was solved by A.F.Moon, L.C.Pedersen, T.A.Kunkel, 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 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.028, 96.085, 73.090, 90.00, 106.55, 90.00
R / Rfree (%)	23 / 27.7

The structure of Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Magnesium atom in the Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide (pdb code 2ihm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide, PDB code: 2ihm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg700 b:34.5 occ:1.00 O1B A:D3T538 2.1 28.9 1.0 O1A A:D3T538 2.2 30.3 1.0 O A:HOH903 2.3 25.8 1.0 OD1 A:ASP330 2.4 44.5 1.0 O3G A:D3T538 2.5 36.0 1.0 OD2 A:ASP332 2.8 48.8 1.0 PB A:D3T538 3.2 32.6 1.0 PA A:D3T538 3.4 34.8 1.0 CG A:ASP330 3.5 43.1 1.0 PG A:D3T538 3.5 38.0 1.0 O3B A:D3T538 3.5 35.3 1.0 O3A A:D3T538 3.6 35.0 1.0 O A:ASP330 3.8 37.9 1.0 O A:HOH905 3.8 33.6 1.0 OD2 A:ASP330 3.9 46.0 1.0 CG A:ASP332 3.9 48.8 1.0 O1G A:D3T538 4.0 39.9 1.0 NA A:NA902 4.1 40.4 0.5 ND1 A:HIS329 4.2 40.4 1.0 O A:HOH907 4.2 28.6 1.0 C5' A:D3T538 4.2 30.2 1.0 O5' A:D3T538 4.2 32.0 1.0 CE1 A:HIS329 4.3 39.0 1.0 C A:ASP330 4.3 39.5 1.0 N A:GLY320 4.3 28.1 1.0 OD1 A:ASP332 4.4 47.9 1.0 N A:ASP330 4.5 35.8 1.0 O2B A:D3T538 4.5 30.8 1.0 CA A:GLY319 4.5 29.5 1.0 O2A A:D3T538 4.6 34.1 1.0 CB A:ASP330 4.7 41.0 1.0 O2G A:D3T538 4.7 38.9 1.0 CA A:ASP330 4.7 39.5 1.0 N A:HIS329 4.9 35.4 1.0 C A:GLY319 5.0 30.1 1.0

Magnesium binding site 2 out of 2 in the Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Polymerase Mu in Ternary Complex with Gapped 11MER Dna Duplex and Bound Incoming Nucleotide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg800 b:57.1 occ:1.00 O1B A:D3T638 2.0 38.7 1.0 OD1 B:ASP330 2.3 58.2 1.0 O B:HOH902 2.4 46.5 1.0 O1A A:D3T638 2.4 41.8 1.0 OD2 B:ASP332 2.4 54.2 1.0 O3G A:D3T638 2.8 46.7 1.0 PB A:D3T638 3.1 41.1 1.0 CG B:ASP330 3.4 56.9 1.0 O3B A:D3T638 3.4 42.3 1.0 PG A:D3T638 3.4 43.7 1.0 PA A:D3T638 3.5 43.9 1.0 O3A A:D3T638 3.5 43.3 1.0 CG B:ASP332 3.6 56.9 1.0 O1G A:D3T638 3.6 49.2 1.0 OD2 B:ASP330 3.9 57.6 1.0 O B:ASP330 3.9 50.5 1.0 N B:GLY320 4.1 48.3 1.0 ND1 B:HIS329 4.1 49.5 1.0 OD1 B:ASP332 4.1 58.5 1.0 C5' A:D3T638 4.1 40.9 1.0 O5' A:D3T638 4.2 45.4 1.0 CE1 B:HIS329 4.3 48.8 1.0 C B:ASP330 4.3 53.1 1.0 O2B A:D3T638 4.4 35.7 1.0 CA B:GLY319 4.5 51.2 1.0 N B:ASP330 4.6 52.3 1.0 CB B:ASP330 4.7 53.6 1.0 CB B:ASP332 4.8 54.8 1.0 O2A A:D3T638 4.8 45.3 1.0 CA B:ASP330 4.8 53.5 1.0 O2G A:D3T638 4.8 50.0 1.0 C B:GLY319 4.8 49.9 1.0 N B:ASP332 4.9 54.4 1.0 N B:VAL331 4.9 53.2 1.0 CA B:GLY320 5.0 47.9 1.0 N B:HIS329 5.0 49.7 1.0

A.F.Moon, M.Garcia-Diaz, K.Bebenek, B.J.Davis, X.Zhong, D.A.Ramsden, T.A.Kunkel, L.C.Pedersen. Structural Insight Into the Substrate Specificity of Dna Polymerase Mu. Nat.Struct.Mol.Biol. V. 14 45 2007.
ISSN: ISSN 1545-9993
PubMed: 17159995
DOI: 10.1038/NSMB1180