Sodium in PDB 4r63: Binary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta

All present enzymatic activity of Binary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta:
2.7.7.7;

The structure of Binary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta, PDB code: 4r63 was solved by V.K.Batra, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.61 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.300, 79.320, 54.780, 90.00, 105.80, 90.00
R / Rfree (%)	18 / 23.2

The binding sites of Sodium atom in the Binary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta (pdb code 4r63). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Binary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta, PDB code: 4r63:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Binary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:9.9 occ:1.00 O A:ILE106 2.5 9.1 1.0 O A:THR101 2.5 11.4 1.0 O A:VAL103 2.5 9.7 1.0 OP1 P:DG9 2.5 9.7 1.0 O P:HOH101 2.6 11.2 1.0 O A:HOH503 2.7 14.0 1.0 C A:THR101 3.4 10.3 1.0 C A:VAL103 3.4 11.5 1.0 C A:ILE106 3.4 12.6 1.0 P P:DG9 3.5 10.4 1.0 NA A:NA403 3.5 22.4 1.0 N A:ILE106 3.7 8.7 1.0 OP2 P:DG9 3.8 10.6 1.0 CA A:THR101 4.0 10.5 1.0 CA A:SER104 4.0 11.3 1.0 N A:GLY105 4.0 9.8 1.0 N A:SER104 4.1 10.4 1.0 CA A:ILE106 4.1 9.1 1.0 N A:VAL103 4.1 9.2 1.0 O P:HOH117 4.3 31.3 1.0 C A:SER104 4.3 6.5 1.0 C A:ARG102 4.3 11.7 1.0 N A:GLY107 4.4 8.1 1.0 CB A:THR101 4.4 12.0 1.0 CA A:VAL103 4.4 9.5 1.0 O3' P:DC8 4.4 10.0 1.0 N A:ARG102 4.4 11.8 1.0 CB A:ILE106 4.5 9.5 1.0 C A:GLY105 4.6 8.8 1.0 CA A:GLY107 4.6 11.1 1.0 CA A:ARG102 4.7 11.8 1.0 O5' P:DG9 4.7 11.9 1.0 O A:ARG102 4.8 11.9 1.0 CA A:GLY105 4.9 9.7 1.0 O A:LEU100 4.9 11.0 1.0 O A:HOH598 4.9 17.1 1.0

Sodium binding site 2 out of 4 in the Binary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Binary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:20.3 occ:1.00 O A:VAL65 2.5 19.9 1.0 O A:LYS60 2.6 18.8 1.0 O A:LEU62 2.7 19.0 1.0 OP1 D:DC3 2.7 18.9 1.0 O A:HOH506 2.7 20.5 1.0 O A:HOH660 2.7 23.4 1.0 C A:LEU62 3.5 20.9 1.0 C A:VAL65 3.5 17.2 1.0 C A:LYS60 3.6 20.8 1.0 P D:DC3 3.7 16.6 1.0 N A:VAL65 3.7 15.8 1.0 O D:HOH123 3.8 29.2 1.0 OP2 D:DC3 3.8 13.2 1.0 N A:GLY64 3.9 19.0 1.0 CA A:PRO63 4.0 19.9 1.0 CA A:VAL65 4.1 17.2 1.0 N A:LEU62 4.1 17.9 1.0 N A:PRO63 4.1 20.7 1.0 C A:LYS61 4.2 22.6 1.0 C A:PRO63 4.3 18.1 1.0 CA A:LYS60 4.4 15.9 1.0 CB A:VAL65 4.4 16.5 1.0 CA A:LEU62 4.4 19.1 1.0 O A:LYS61 4.5 22.0 1.0 CG A:LYS60 4.5 23.0 1.0 N A:LYS61 4.5 24.1 1.0 N A:GLY66 4.6 13.0 1.0 O3' D:DT2 4.6 14.8 1.0 CA A:LYS61 4.7 19.7 1.0 C A:GLY64 4.7 16.9 1.0 CA A:GLY66 4.9 11.9 1.0 CA A:GLY64 4.9 16.8 1.0 NZ A:LYS60 4.9 26.0 1.0 O A:ALA59 4.9 17.1 1.0 O5' D:DC3 5.0 17.2 1.0

Sodium binding site 3 out of 4 in the Binary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Binary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:22.4 occ:1.00 O A:HOH537 2.6 17.1 1.0 O A:HOH503 2.7 14.0 1.0 O P:HOH101 2.7 11.2 1.0 O A:THR101 2.8 11.4 1.0 O A:HOH633 2.9 26.6 1.0 O A:HOH868 2.9 31.4 1.0 O A:HOH1009 3.1 34.6 1.0 O P:HOH117 3.5 31.3 1.0 NA A:NA401 3.5 9.9 1.0 C A:THR101 3.8 10.3 1.0 O A:HOH1015 4.0 35.9 1.0 CA A:ARG102 4.2 11.8 1.0 N A:ARG102 4.4 11.8 1.0 NZ A:LYS27 4.5 23.1 1.0 O A:HOH605 4.5 23.7 1.0 O A:HOH598 4.6 17.1 1.0 CB A:THR101 4.6 12.0 1.0 OG1 A:THR101 4.6 12.4 1.0 C A:ARG102 4.7 11.7 1.0 O A:HOH621 4.7 20.5 1.0 CA A:THR101 4.8 10.5 1.0 O A:ARG102 4.9 11.9 1.0

Sodium binding site 4 out of 4 in the Binary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Binary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:15.4 occ:1.00 OG A:SER171 2.5 13.9 1.0 O A:HOH556 2.6 18.0 1.0 O A:HOH609 2.6 19.2 1.0 CB A:SER171 3.6 12.8 1.0 N A:SER171 3.9 11.2 1.0 O A:HOH681 4.0 30.3 1.0 O A:HOH628 4.2 15.2 1.0 CA A:SER171 4.3 14.0 1.0 OD1 A:ASP170 4.5 16.4 1.0 C A:SER171 4.9 13.7 1.0

W.A.Beard, D.D.Shock, V.K.Batra, R.Prasad, S.H.Wilson. Substrate-Induced Dna Polymerase Beta Activation. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25261471
DOI: 10.1074/JBC.M114.607432