Magnesium in PDB 3c5g: Structure of A Ternary Complex of the R517K Pol Lambda Mutant

All present enzymatic activity of Structure of A Ternary Complex of the R517K Pol Lambda Mutant:
2.7.7.7;

The structure of Structure of A Ternary Complex of the R517K Pol Lambda Mutant, PDB code: 3c5g was solved by M.Garcia-Diaz, K.Bebenek, M.C.Foley, L.C.Pedersen, T.Schlick, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.335, 150.819, 85.822, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23.6

The structure of Structure of A Ternary Complex of the R517K Pol Lambda Mutant also contains other interesting chemical elements:

Sodium

(Na)

8 atoms

The binding sites of Magnesium atom in the Structure of A Ternary Complex of the R517K Pol Lambda Mutant (pdb code 3c5g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of A Ternary Complex of the R517K Pol Lambda Mutant, PDB code: 3c5g:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of A Ternary Complex of the R517K Pol Lambda Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Ternary Complex of the R517K Pol Lambda Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:14.9 occ:1.00 O1A A:D3T576 2.0 14.9 1.0 OD2 A:ASP427 2.0 16.5 1.0 O A:HOH976 2.0 11.8 1.0 O3G A:D3T576 2.1 16.0 1.0 O1B A:D3T576 2.1 11.3 1.0 OD2 A:ASP429 2.2 15.1 1.0 CG A:ASP427 3.0 16.3 1.0 CG A:ASP429 3.1 18.8 1.0 PB A:D3T576 3.2 18.1 1.0 PA A:D3T576 3.3 17.2 1.0 PG A:D3T576 3.3 17.9 1.0 OD1 A:ASP429 3.4 17.1 1.0 NA A:NA803 3.5 21.4 1.0 OD1 A:ASP427 3.5 18.1 1.0 O3A A:D3T576 3.5 17.7 1.0 O3B A:D3T576 3.7 17.5 1.0 O A:ASP427 3.7 15.4 1.0 O1G A:D3T576 3.9 15.3 1.0 O A:HOH1126 4.0 27.9 1.0 C A:ASP427 4.1 15.0 1.0 O A:HOH846 4.1 21.7 1.0 C5' A:D3T576 4.2 15.8 1.0 N A:ASP427 4.2 12.9 1.0 O5' A:D3T576 4.2 18.9 1.0 OG A:SER417 4.2 15.1 1.0 CB A:ASP427 4.3 14.0 1.0 O2A A:D3T576 4.3 20.5 1.0 O2G A:D3T576 4.4 23.0 1.0 CA A:ASP427 4.4 12.4 1.0 CB A:ASP429 4.5 17.1 1.0 N A:SER417 4.5 15.7 1.0 O2B A:D3T576 4.6 16.0 1.0 CA A:GLY416 4.7 15.3 1.0 N A:VAL428 4.7 14.3 1.0 N A:ASP429 4.7 16.2 1.0 O P:HOH671 4.9 33.9 1.0 C A:VAL428 5.0 18.3 1.0

Magnesium binding site 2 out of 2 in the Structure of A Ternary Complex of the R517K Pol Lambda Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Ternary Complex of the R517K Pol Lambda Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:16.2 occ:1.00 O1A B:D3T577 2.0 12.8 1.0 O B:HOH1067 2.0 12.6 1.0 O1B B:D3T577 2.0 12.1 1.0 O3G B:D3T577 2.1 17.0 1.0 OD2 B:ASP427 2.1 16.2 1.0 OD2 B:ASP429 2.2 18.1 1.0 CG B:ASP427 3.1 16.6 1.0 PB B:D3T577 3.2 18.6 1.0 CG B:ASP429 3.2 21.3 1.0 PA B:D3T577 3.2 18.9 1.0 PG B:D3T577 3.3 19.6 1.0 O3A B:D3T577 3.5 17.6 1.0 OD1 B:ASP427 3.5 18.1 1.0 OD1 B:ASP429 3.6 19.6 1.0 O3B B:D3T577 3.6 17.7 1.0 NA B:NA802 3.6 22.0 1.0 O1G B:D3T577 3.8 15.8 1.0 O B:ASP427 3.9 14.0 1.0 C B:ASP427 4.2 14.5 1.0 C5' B:D3T577 4.2 14.5 1.0 OG B:SER417 4.2 15.7 1.0 O5' B:D3T577 4.2 18.1 1.0 O B:HOH830 4.3 16.3 1.0 O2A B:D3T577 4.3 16.7 1.0 O B:HOH855 4.3 31.1 1.0 N B:SER417 4.3 17.8 1.0 N B:ASP427 4.4 14.6 1.0 O2G B:D3T577 4.4 19.0 1.0 CB B:ASP427 4.4 14.1 1.0 O2B B:D3T577 4.5 16.8 1.0 CA B:GLY416 4.5 15.8 1.0 CB B:ASP429 4.6 19.7 1.0 CA B:ASP427 4.6 14.2 1.0 N B:VAL428 4.8 14.1 1.0 N B:ASP429 4.8 15.2 1.0 CB B:SER417 4.9 15.2 1.0 O Q:HOH16 4.9 29.5 1.0 C B:GLY416 5.0 17.5 1.0

K.Bebenek, M.Garcia-Diaz, M.C.Foley, L.C.Pedersen, T.Schlick, T.A.Kunkel. Substrate-Induced Dna Strand Misalignment During Catalytic Cycling By Dna Polymerase Lambda. Embo Rep. V. 9 459 2008.
ISSN: ISSN 1469-221X
PubMed: 18369368
DOI: 10.1038/EMBOR.2008.33