Magnesium in PDB 7m0c: Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound Mismatched Dsb Substrate

All present enzymatic activity of Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound Mismatched Dsb Substrate:
2.7.7.7;

The structure of Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound Mismatched Dsb Substrate, PDB code: 7m0c was solved by A.M.Kaminski, K.Bebenek, 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)	39.37 / 2.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.205, 60.023, 139.824, 90, 90, 90
R / Rfree (%)	18 / 22.9

The structure of Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound Mismatched Dsb Substrate also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound Mismatched Dsb Substrate (pdb code 7m0c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound Mismatched Dsb Substrate, PDB code: 7m0c:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound Mismatched Dsb Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound Mismatched Dsb Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:16.9 occ:1.00 OD2 A:ASP427 1.8 28.8 1.0 OD1 A:ASP429 1.8 19.3 1.0 OP1 P:DT7 2.1 28.2 1.0 OD2 A:ASP490 2.2 29.7 1.0 O3' P:DC6 2.7 26.2 1.0 CG A:ASP427 2.9 30.4 1.0 CG A:ASP429 2.9 25.1 1.0 P P:DT7 2.9 33.1 1.0 CG A:ASP490 3.1 27.3 1.0 OD2 A:ASP429 3.3 26.9 1.0 OD1 A:ASP427 3.3 26.1 1.0 CB A:ASP490 3.7 16.5 1.0 MG A:MG602 3.7 29.6 1.0 C3' P:DC6 4.0 27.4 1.0 O5' P:DT7 4.0 27.5 1.0 OP2 P:DT7 4.1 30.4 1.0 C5' P:DT7 4.1 25.1 1.0 OD1 A:ASP490 4.1 30.8 1.0 CB A:ASP427 4.2 25.7 1.0 CB A:ASP429 4.2 21.9 1.0 C4' P:DC6 4.3 21.8 1.0 C5' P:DC6 4.4 21.7 1.0 NH2 A:ARG488 4.7 24.9 1.0 CA A:ASP429 4.8 19.3 1.0 O A:VAL428 4.9 19.6 1.0 CA A:ASP490 5.0 19.9 1.0 N A:ASP490 5.0 22.2 1.0 N A:ASP429 5.0 18.6 1.0

Magnesium binding site 2 out of 2 in the Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound Mismatched Dsb Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound Mismatched Dsb Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:29.6 occ:1.00 O12 A:PPV607 2.1 26.0 0.8 OD1 A:ASP427 2.1 26.1 1.0 OD2 A:ASP429 2.2 26.9 1.0 O11 A:PPV607 2.2 33.1 0.8 O A:HOH752 2.5 25.2 1.0 OP1 P:DT7 2.5 28.2 1.0 P2 A:PPV607 3.2 34.5 0.8 CG A:ASP427 3.2 30.4 1.0 CG A:ASP429 3.3 25.1 1.0 O32 A:PPV607 3.4 43.2 0.8 P1 A:PPV607 3.4 43.5 0.8 OD2 A:ASP427 3.6 28.8 1.0 OD1 A:ASP429 3.7 19.3 1.0 OPP A:PPV607 3.7 36.9 0.8 MG A:MG601 3.7 16.9 1.0 P P:DT7 3.8 33.1 1.0 O5' P:DT7 4.0 27.5 1.0 O31 A:PPV607 4.1 28.9 0.8 N A:SER417 4.1 16.8 1.0 CA A:GLY416 4.2 19.1 1.0 C5' P:DT7 4.2 25.1 1.0 N A:ASP427 4.4 20.6 1.0 O A:ASP427 4.4 27.1 1.0 O22 A:PPV607 4.5 26.8 0.8 CB A:ASP427 4.5 25.7 1.0 O A:HOH745 4.5 22.4 1.0 CB A:ASP429 4.6 21.9 1.0 C A:ASP427 4.6 25.7 1.0 OG A:SER417 4.6 22.1 1.0 O21 A:PPV607 4.6 48.5 0.8 OP2 P:DT7 4.6 30.4 1.0 C A:GLY416 4.7 19.4 1.0 CA A:ASP427 4.7 23.6 1.0 O3' P:DC6 4.9 26.2 1.0 CB A:SER417 5.0 22.2 1.0

A.M.Kaminski, K.Bebenek, T.A.Kunkel, L.C.Pedersen. Comprehensive Structural Survey of Dna Double-Strand Break Synapsis By Dna Polymerase Lambda To Be Published.