Sodium in PDB 6nkr: Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Dgtp

All present enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Dgtp:
2.7.7.7;

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Dgtp, PDB code: 6nkr was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.85 / 2.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.531, 80.125, 55.267, 90.00, 108.14, 90.00
R / Rfree (%)	20.7 / 29

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Dgtp also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Dgtp (pdb code 6nkr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Dgtp, PDB code: 6nkr:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Dgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:43.9 occ:1.00 OD1 A:ASP192 2.2 42.5 1.0 OD2 A:ASP190 2.5 37.5 1.0 O1A A:DGT407 2.5 37.8 1.0 OD1 A:ASP256 2.6 44.3 1.0 CG A:ASP190 3.2 38.0 1.0 CG A:ASP192 3.2 37.8 1.0 OD1 A:ASP190 3.2 34.0 1.0 PA A:DGT407 3.5 35.2 1.0 OD2 A:ASP192 3.5 42.0 1.0 MG A:MG401 3.5 35.1 1.0 O5' A:DGT407 3.7 36.2 1.0 CG A:ASP256 3.8 44.5 1.0 C5' P:DOC10 3.8 48.5 1.0 O2A A:DGT407 3.9 39.4 1.0 C5' A:DGT407 3.9 36.0 1.0 C4' P:DOC10 4.0 46.8 1.0 C3' P:DOC10 4.0 44.3 1.0 CB A:ASP256 4.4 41.6 1.0 O5' P:DOC10 4.5 38.9 1.0 CB A:ASP190 4.5 38.2 1.0 CB A:ASP192 4.5 33.1 1.0 O A:MET191 4.5 37.2 1.0 OD2 A:ASP256 4.7 43.0 1.0 O3A A:DGT407 4.9 38.5 1.0 O1G A:DGT407 5.0 40.4 1.0 NH2 A:ARG254 5.0 41.5 1.0

Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Dgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:36.7 occ:1.00 O A:ILE106 2.3 39.6 1.0 O A:HOH532 2.3 38.2 1.0 OP1 P:DG9 2.3 35.4 1.0 O A:THR101 2.5 39.7 1.0 O A:VAL103 2.7 38.9 1.0 P P:DG9 3.3 38.0 1.0 C A:ILE106 3.3 43.1 1.0 OP2 P:DG9 3.4 41.6 1.0 C A:VAL103 3.5 36.6 1.0 C A:THR101 3.5 40.2 1.0 N A:ILE106 3.8 37.1 1.0 CA A:SER104 3.9 30.1 1.0 N A:GLY105 3.9 38.1 1.0 N A:SER104 4.0 32.8 1.0 CA A:ILE106 4.1 33.4 1.0 CA A:THR101 4.1 38.5 1.0 O3' P:DC8 4.2 39.6 1.0 C A:SER104 4.2 40.5 1.0 N A:VAL103 4.3 39.0 1.0 N A:GLY107 4.3 38.9 1.0 C A:ARG102 4.5 38.1 1.0 O5' P:DG9 4.5 41.4 1.0 CA A:VAL103 4.5 36.8 1.0 C A:GLY105 4.5 36.9 1.0 CA A:GLY107 4.5 42.0 1.0 N A:ARG102 4.6 39.8 1.0 CB A:ILE106 4.6 38.1 1.0 CB A:THR101 4.7 34.7 1.0 CA A:GLY105 4.8 38.8 1.0 CA A:ARG102 4.8 37.7 1.0 O A:ARG102 4.9 42.9 1.0 O A:LEU100 5.0 38.6 1.0

Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Dgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:62.8 occ:1.00 O A:VAL65 2.4 57.1 1.0 O A:LYS60 2.5 55.2 1.0 O A:LEU62 2.6 53.7 1.0 OP1 D:DC3 2.7 51.9 1.0 C A:VAL65 3.4 51.4 1.0 C A:LYS60 3.5 54.5 1.0 C A:LEU62 3.6 55.5 1.0 P D:DC3 3.8 57.7 1.0 N A:VAL65 3.8 51.5 1.0 CA A:PRO63 3.9 57.4 1.0 OP2 D:DC3 3.9 58.1 1.0 N A:GLY64 4.0 51.7 1.0 CA A:VAL65 4.1 49.4 1.0 N A:PRO63 4.1 55.2 1.0 O A:LYS61 4.1 61.4 1.0 C A:LYS61 4.2 56.0 1.0 CA A:LYS60 4.2 55.8 1.0 C A:PRO63 4.3 52.9 1.0 CG A:LYS60 4.3 58.6 1.0 N A:LEU62 4.3 54.0 1.0 N A:GLY66 4.4 49.5 1.0 CB A:VAL65 4.5 47.6 1.0 N A:LYS61 4.5 55.4 1.0 CA A:LEU62 4.6 51.2 1.0 CA A:GLY66 4.7 51.5 1.0 O3' D:DT2 4.7 61.0 1.0 CA A:LYS61 4.7 54.6 1.0 C A:GLY64 4.7 51.9 1.0 O A:ALA59 4.8 53.7 1.0 CB A:LYS60 4.9 51.7 1.0 CA A:GLY64 4.9 50.5 1.0 O5' D:DC3 5.0 59.0 1.0

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure To Be Published.