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

Enzymatic activity of 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;

Protein crystallography data

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

Sodium Binding Sites:

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 4r63

Go back to Sodium Binding Sites List in 4r63
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 4r63

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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 4r63

Go back to Sodium Binding Sites List in 4r63
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 4r63

Go back to Sodium Binding Sites List in 4r63
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

Reference:

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
Page generated: Sun Aug 17 21:35:20 2025

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