Sodium in PDB 3isc: Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna

All present enzymatic activity of Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna:
2.7.7.7;

The structure of Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna, PDB code: 3isc was solved by W.A.Beard, D.D.Shock, V.K.Batra, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.81 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.410, 79.300, 54.950, 90.00, 105.80, 90.00
R / Rfree (%)	18.6 / 22.7

The binding sites of Sodium atom in the Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna (pdb code 3isc). 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 of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna, PDB code: 3isc:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:12.4 occ:1.00 O A:THR101 2.3 13.7 1.0 OP1 P:DG9 2.4 10.0 1.0 O A:ILE106 2.4 13.1 1.0 O A:VAL103 2.4 12.0 1.0 O P:HOH11 2.5 12.9 1.0 O A:HOH507 2.6 21.0 1.0 C A:THR101 3.2 15.8 1.0 NA A:NA403 3.2 28.6 1.0 C A:VAL103 3.4 13.1 1.0 C A:ILE106 3.4 12.2 1.0 P P:DG9 3.5 13.4 1.0 OP2 P:DG9 3.7 13.8 1.0 N A:ILE106 3.8 11.4 1.0 CA A:THR101 3.8 14.4 1.0 CA A:SER104 3.9 12.9 1.0 N A:GLY105 4.0 10.6 1.0 N A:SER104 4.0 13.0 1.0 N A:VAL103 4.1 13.0 1.0 CA A:ILE106 4.1 12.4 1.0 N A:ARG102 4.3 16.4 1.0 C A:ARG102 4.3 15.4 1.0 CB A:THR101 4.3 13.2 1.0 C A:SER104 4.3 11.7 1.0 N A:GLY107 4.3 12.5 1.0 CA A:VAL103 4.4 12.7 1.0 O3' P:DC8 4.5 13.5 1.0 CB A:ILE106 4.5 13.8 1.0 CA A:GLY107 4.6 12.2 1.0 O5' P:DG9 4.6 13.7 1.0 CA A:ARG102 4.6 15.5 1.0 C A:GLY105 4.6 12.1 1.0 O A:ARG102 4.8 13.2 1.0 O A:HOH655 4.9 30.4 1.0 O A:LEU100 4.9 14.2 1.0 CA A:GLY105 5.0 10.2 1.0

Sodium binding site 2 out of 4 in the Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:24.8 occ:1.00 O A:VAL65 2.2 23.9 1.0 O D:HOH280 2.4 23.1 1.0 O A:LYS60 2.5 28.4 1.0 OP1 D:DC3 2.5 23.6 1.0 O A:LEU62 2.6 25.3 1.0 O A:HOH687 2.7 30.0 1.0 C A:VAL65 3.3 20.5 1.0 C A:LYS60 3.5 28.6 1.0 C A:LEU62 3.6 26.6 1.0 P D:DC3 3.6 20.4 1.0 N A:VAL65 3.7 20.6 1.0 OP2 D:DC3 3.8 16.2 1.0 O D:HOH279 3.9 38.6 1.0 CA A:VAL65 4.0 20.1 1.0 N A:GLY64 4.1 23.4 1.0 CA A:LYS60 4.2 26.2 1.0 N A:LEU62 4.2 28.3 1.0 CA A:PRO63 4.2 25.3 1.0 N A:PRO63 4.3 26.0 1.0 CB A:VAL65 4.3 20.6 1.0 CG A:LYS60 4.3 29.1 1.0 C A:LYS61 4.3 30.0 1.0 N A:GLY66 4.3 19.6 1.0 O3' D:DT2 4.5 21.0 1.0 N A:LYS61 4.5 29.4 1.0 C A:PRO63 4.5 23.1 1.0 CA A:LEU62 4.5 27.2 1.0 CA A:GLY66 4.6 17.9 1.0 C A:GLY64 4.7 21.0 1.0 O A:LYS61 4.7 30.9 1.0 CA A:LYS61 4.7 30.1 1.0 O5' D:DC3 4.9 20.9 1.0 CB A:LYS60 4.9 26.7 1.0 O A:ALA59 4.9 22.9 1.0 CA A:GLY64 5.0 20.7 1.0

Sodium binding site 3 out of 4 in the Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:28.6 occ:1.00 O A:HOH399 2.4 17.9 1.0 O A:HOH638 2.5 43.1 1.0 O P:HOH11 2.5 12.9 1.0 O A:THR101 2.6 13.7 1.0 O A:HOH507 2.7 21.0 1.0 O A:HOH627 2.8 30.4 1.0 NA A:NA401 3.2 12.4 1.0 C A:THR101 3.6 15.8 1.0 O A:HOH655 4.2 30.4 1.0 CA A:ARG102 4.2 15.5 1.0 N A:ARG102 4.3 16.4 1.0 NZ A:LYS27 4.3 24.4 1.0 OG1 A:THR101 4.4 13.3 1.0 CB A:THR101 4.4 13.2 1.0 CA A:THR101 4.6 14.4 1.0 C A:ARG102 4.7 15.4 1.0 O A:HOH675 4.7 32.7 1.0 OP1 P:DG9 4.7 10.0 1.0 O P:HOH130 4.8 22.8 1.0 O A:HOH689 4.8 27.3 1.0 OP2 P:DG9 4.8 13.8 1.0 O A:HOH548 4.9 23.1 1.0 O A:ARG102 5.0 13.2 1.0

Sodium binding site 4 out of 4 in the Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:20.6 occ:1.00 OG A:SER171 2.2 13.6 1.0 O A:HOH586 2.3 30.8 1.0 O A:HOH497 2.5 18.3 1.0 O A:HOH557 2.5 19.7 1.0 O A:HOH486 2.7 21.8 1.0 CB A:SER171 3.4 13.9 1.0 N A:SER171 3.9 13.7 1.0 O A:HOH504 4.1 17.4 1.0 CA A:SER171 4.2 14.7 1.0 O A:HOH397 4.3 34.6 1.0 O A:HOH692 4.6 35.9 1.0 OD1 A:ASP170 4.6 15.5 1.0 C A:SER171 4.9 15.5 1.0 N A:GLU172 4.9 13.1 1.0 C A:ASP170 5.0 14.9 1.0

W.A.Beard, D.D.Shock, V.K.Batra, L.C.Pedersen, S.H.Wilson. Dna Polymerase Beta Substrate Specificity: Side Chain Modulation of the "A-Rule". J.Biol.Chem. V. 284 31680 2009.
ISSN: ISSN 0021-9258
PubMed: 19759017
DOI: 10.1074/JBC.M109.029843