Sodium in PDB 6btf: Dna Polymerase Beta I260Q Ternary Complex

All present enzymatic activity of Dna Polymerase Beta I260Q Ternary Complex:
2.7.7.7;

The structure of Dna Polymerase Beta I260Q Ternary Complex, PDB code: 6btf was solved by B.E.Eckenroth, S.Doublie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.55 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.610, 79.879, 55.382, 90.00, 107.40, 90.00
R / Rfree (%)	17.5 / 21.4

The structure of Dna Polymerase Beta I260Q Ternary Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Dna Polymerase Beta I260Q Ternary Complex (pdb code 6btf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dna Polymerase Beta I260Q Ternary Complex, PDB code: 6btf:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Beta I260Q Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Beta I260Q Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:19.2 occ:1.00 O A:THR101 2.3 17.1 1.0 O A:VAL103 2.4 14.8 1.0 O A:HOH720 2.4 23.4 1.0 O A:ILE106 2.4 19.5 1.0 OP1 P:DG9 2.5 22.1 1.0 O P:HOH105 2.6 25.8 1.0 C A:THR101 3.2 16.7 1.0 C A:VAL103 3.4 15.1 1.0 C A:ILE106 3.4 18.1 1.0 P P:DG9 3.5 19.6 1.0 O A:HOH582 3.7 35.0 1.0 OP2 P:DG9 3.7 19.1 1.0 N A:ILE106 3.8 18.3 1.0 CA A:THR101 3.8 19.0 1.0 N A:GLY105 3.9 14.0 1.0 CA A:SER104 4.0 22.1 1.0 N A:VAL103 4.0 14.9 1.0 N A:SER104 4.1 17.9 1.0 CA A:ILE106 4.1 19.2 1.0 C A:ARG102 4.3 26.1 1.0 N A:ARG102 4.3 19.1 1.0 O P:HOH123 4.3 51.8 1.0 C A:SER104 4.3 17.1 1.0 CA A:VAL103 4.3 14.9 1.0 CB A:THR101 4.4 19.0 1.0 N A:GLY107 4.4 19.1 1.0 O3' P:DC8 4.5 19.9 1.0 CB A:ILE106 4.5 19.1 1.0 CA A:ARG102 4.5 19.5 1.0 C A:GLY105 4.6 18.3 1.0 O5' P:DG9 4.6 22.4 1.0 CA A:GLY107 4.7 16.4 1.0 O A:LEU100 4.7 16.4 1.0 O A:ARG102 4.7 22.2 1.0 CA A:GLY105 4.9 18.0 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Beta I260Q Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Beta I260Q Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:36.6 occ:1.00 O A:VAL65 2.4 32.5 1.0 O A:LEU62 2.4 34.4 1.0 O A:LYS60 2.5 39.0 1.0 O A:HOH700 2.5 42.9 1.0 OP1 D:DC3 2.6 39.9 1.0 O A:HOH540 2.7 46.8 1.0 C A:LEU62 3.4 33.6 1.0 C A:VAL65 3.4 30.3 1.0 C A:LYS60 3.5 38.7 1.0 P D:DC3 3.7 42.3 1.0 OP2 D:DC3 3.8 42.4 1.0 N A:VAL65 3.9 24.5 1.0 O D:HOH107 3.9 45.1 1.0 N A:LEU62 4.0 33.8 1.0 CA A:VAL65 4.1 25.6 1.0 N A:PRO63 4.1 34.1 1.0 CA A:PRO63 4.1 35.7 1.0 C A:LYS61 4.2 38.2 1.0 N A:GLY64 4.2 34.7 1.0 CA A:LYS60 4.2 38.4 1.0 CG A:LYS60 4.3 47.6 1.0 CA A:LEU62 4.3 29.2 1.0 CB A:VAL65 4.4 24.5 1.0 O A:LYS61 4.4 36.8 1.0 N A:GLY66 4.5 28.9 1.0 N A:LYS61 4.5 36.6 1.0 C A:PRO63 4.5 36.4 1.0 NZ A:LYS60 4.6 61.3 1.0 O3' D:DT2 4.6 37.1 1.0 CA A:LYS61 4.6 34.4 1.0 CA A:GLY66 4.7 28.6 1.0 C A:GLY64 4.9 25.8 1.0 O5' D:DC3 4.9 41.6 1.0 CB A:LYS60 4.9 44.9 1.0 O A:ALA59 5.0 31.1 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Beta I260Q Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna Polymerase Beta I260Q Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:42.6 occ:1.00 O2A A:DUP405 2.2 22.6 1.0 OD1 A:ASP192 2.3 28.3 1.0 OD2 A:ASP190 2.4 36.2 1.0 O A:HOH533 3.1 36.2 1.0 OD2 A:ASP256 3.1 35.6 1.0 CG A:ASP190 3.1 28.1 1.0 OD1 A:ASP190 3.1 28.0 1.0 CG A:ASP192 3.2 24.9 1.0 C3' P:DC10 3.3 47.1 1.0 PA A:DUP405 3.3 25.9 1.0 OD2 A:ASP192 3.4 27.3 1.0 MG A:MG403 3.4 29.2 1.0 O3' P:DC10 3.5 56.4 1.0 O5' A:DUP405 3.6 22.8 1.0 O1A A:DUP405 3.8 28.9 1.0 C5' A:DUP405 3.8 21.4 1.0 CG A:ASP256 4.1 33.4 1.0 C2' P:DC10 4.3 44.9 1.0 C4' P:DC10 4.3 37.9 1.0 C5' P:DC10 4.3 45.6 1.0 CB A:ASP190 4.5 19.5 1.0 O5' P:DC10 4.5 47.0 1.0 O A:HOH549 4.5 36.4 1.0 O A:HOH505 4.5 47.2 1.0 CB A:ASP192 4.6 12.8 1.0 O A:HOH609 4.6 44.6 1.0 CB A:ASP256 4.7 15.7 1.0 N3A A:DUP405 4.8 40.4 1.0 O3G A:DUP405 4.9 32.1 1.0 O2B A:DUP405 4.9 20.9 1.0

C.Liptak, M.M.Mahmoud, B.E.Eckenroth, M.V.Moreno, K.East, K.S.Alnajjar, J.Huang, J.B.Towle-Weicksel, S.Doublie, J.P.Loria, J.B.Sweasy. I260Q Dna Polymerase Beta Highlights Precatalytic Conformational Rearrangements Critical For Fidelity. Nucleic Acids Res. V. 46 10740 2018.
ISSN: ESSN 1362-4962
PubMed: 30239932
DOI: 10.1093/NAR/GKY825