Sodium 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:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound Mismatched Dsb Substrate, PDB code: 7m0c:
Jump to Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na 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:Na603 b:21.0 occ:1.00 O P:HOH104 2.2 19.3 1.0 OP1 P:DG5 2.3 20.9 1.0 O A:ILE341 2.4 20.6 1.0 O A:SER339 2.5 22.9 1.0 O A:ALA344 2.5 18.3 1.0 C A:ILE341 3.3 16.0 1.0 C A:SER339 3.4 17.1 1.0 P P:DG5 3.5 21.3 1.0 C A:ALA344 3.6 19.0 1.0 OP2 P:DG5 3.8 23.5 1.0 CA A:TRP342 3.9 17.3 1.0 N A:TRP342 3.9 17.8 1.0 N A:ILE341 4.0 18.7 1.0 N A:ALA344 4.0 17.5 1.0 C A:ASN340 4.0 22.0 1.0 N A:GLY343 4.0 18.4 1.0 N A:ASN340 4.2 21.4 1.0 CA A:SER339 4.2 20.2 1.0 CA A:ASN340 4.2 18.9 1.0 CA A:ILE341 4.3 15.6 1.0 CA A:ALA344 4.3 15.9 1.0 C A:TRP342 4.3 17.8 1.0 O5' P:DG5 4.5 19.2 1.0 O A:ASN340 4.5 20.9 1.0 O3' P:DT4 4.6 20.4 1.0 N A:GLY345 4.6 18.6 1.0 C A:GLY343 4.8 20.1 1.0 CB A:ALA344 4.8 14.0 1.0 CA A:GLY345 4.8 17.6 1.0 CB A:SER339 4.9 17.2 1.0 O A:PHE338 4.9 17.9 1.0 CA A:GLY343 5.0 14.0 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na604 b:42.9 occ:1.00 O A:ILE305 2.5 42.6 1.0 O D:HOH103 2.5 29.4 1.0 O A:CYS300 2.5 38.2 1.0 OP1 D:DC3 2.7 45.4 1.0 O A:ILE302 3.0 39.1 1.0 O A:HOH737 3.0 42.2 1.0 OP2 D:DC3 3.4 34.7 1.0 P D:DC3 3.5 38.1 1.0 C A:ILE305 3.6 34.9 1.0 C A:CYS300 3.7 40.2 1.0 C A:ILE302 3.8 35.0 1.0 N A:ILE305 4.1 34.1 1.0 CA A:PRO303 4.2 43.5 1.0 N A:PRO303 4.3 43.5 1.0 C A:SER301 4.3 40.4 1.0 N A:ILE302 4.4 41.6 1.0 CA A:ILE305 4.4 32.4 1.0 O3' D:DC2 4.5 34.5 1.0 N A:GLY306 4.5 34.5 1.0 O A:SER301 4.5 41.6 1.0 CA A:CYS300 4.5 39.5 1.0 N A:GLY304 4.6 32.7 1.0 CA A:GLY306 4.6 31.0 1.0 N A:SER301 4.7 39.9 1.0 O5' D:DC3 4.7 31.5 1.0 CA A:SER301 4.7 38.7 1.0 CA A:ILE302 4.8 36.8 1.0 C A:PRO303 4.8 34.4 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.