Sodium in PDB 2p66: Human Dna Polymerase Beta Complexed with Tetrahydrofuran (Abasic Site) Containing Dna

All present enzymatic activity of Human Dna Polymerase Beta Complexed with Tetrahydrofuran (Abasic Site) Containing Dna:
2.7.7.7;

The structure of Human Dna Polymerase Beta Complexed with Tetrahydrofuran (Abasic Site) Containing Dna, PDB code: 2p66 was solved by R.Prasad, V.K.Batra, X.-P.Yang, J.M.Krahn, L.C.Pedersen, 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)	24.06 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.700, 81.100, 54.900, 90.00, 108.60, 90.00
R / Rfree (%)	21.7 / 28

The binding sites of Sodium atom in the Human Dna Polymerase Beta Complexed with Tetrahydrofuran (Abasic Site) Containing Dna (pdb code 2p66). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Human Dna Polymerase Beta Complexed with Tetrahydrofuran (Abasic Site) Containing Dna, PDB code: 2p66:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Human Dna Polymerase Beta Complexed with Tetrahydrofuran (Abasic Site) Containing Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dna Polymerase Beta Complexed with Tetrahydrofuran (Abasic Site) Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Na343 b:59.5 occ:1.00 OP1 C:DC11 2.1 68.8 1.0 O5' C:DC11 3.1 65.5 1.0 P C:DC11 3.1 68.5 1.0 OD1 A:ASP190 3.8 65.0 1.0 OD2 A:ASP190 3.9 64.7 1.0 OD2 A:ASP192 3.9 45.4 1.0 O3' C:DC10 4.2 60.9 1.0 OP2 C:DC11 4.2 65.3 1.0 CG A:ASP190 4.3 58.4 1.0 CB A:ASP192 4.4 35.4 1.0 C5' C:DC11 4.4 74.5 1.0 O2 A:PO4349 4.6 0.6 1.0 CG A:ASP192 4.6 42.5 1.0 O3 A:PO4349 4.7 0.8 1.0 CA A:GLY179 4.8 60.1 1.0 C4' C:DC11 4.8 79.4 1.0

Sodium binding site 2 out of 3 in the Human Dna Polymerase Beta Complexed with Tetrahydrofuran (Abasic Site) Containing Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Dna Polymerase Beta Complexed with Tetrahydrofuran (Abasic Site) Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:40.0 occ:1.00 O A:THR101 2.2 38.5 1.0 O C:HOH344 2.5 26.7 1.0 OP1 C:DG9 2.5 16.5 1.0 O A:VAL103 2.6 26.9 1.0 O C:HOH347 2.6 39.9 1.0 O A:ILE106 2.6 34.1 1.0 C A:THR101 3.2 24.7 1.0 C A:VAL103 3.5 27.7 1.0 O A:HOH389 3.5 39.9 1.0 P C:DG9 3.6 26.8 1.0 C A:ILE106 3.7 30.6 1.0 OP2 C:DG9 3.7 26.0 1.0 CA A:THR101 3.8 26.7 1.0 CA A:SER104 4.0 27.8 1.0 N A:ILE106 4.0 25.6 1.0 N A:SER104 4.1 31.8 1.0 N A:VAL103 4.1 20.6 1.0 C A:ARG102 4.2 28.4 1.0 N A:ARG102 4.2 22.6 1.0 N A:GLY105 4.2 27.4 1.0 CB A:THR101 4.2 21.5 1.0 CA A:ILE106 4.3 28.3 1.0 CA A:ARG102 4.4 28.6 1.0 CA A:VAL103 4.5 27.6 1.0 C A:SER104 4.5 22.9 1.0 O3' C:DC8 4.5 33.3 1.0 CB A:ILE106 4.6 22.1 1.0 O A:ARG102 4.7 36.4 1.0 N A:GLY107 4.7 28.1 1.0 O5' C:DG9 4.8 35.5 1.0 CA A:GLY107 4.9 24.6 1.0 O A:LEU100 4.9 34.2 1.0

Sodium binding site 3 out of 3 in the Human Dna Polymerase Beta Complexed with Tetrahydrofuran (Abasic Site) Containing Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Dna Polymerase Beta Complexed with Tetrahydrofuran (Abasic Site) Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:79.3 occ:1.00 O A:VAL65 2.0 46.7 1.0 O A:LYS60 2.4 59.4 1.0 O A:LEU62 2.5 55.0 1.0 C A:VAL65 3.1 42.5 1.0 OP1 D:DC3 3.2 59.1 1.0 C A:LYS60 3.5 56.0 1.0 C A:LEU62 3.7 57.7 1.0 N A:VAL65 3.8 53.1 1.0 CA A:VAL65 3.9 47.8 1.0 CA A:LYS60 4.1 53.5 1.0 N A:GLY66 4.1 33.0 1.0 N A:LEU62 4.1 55.7 1.0 P D:DC3 4.1 62.9 1.0 CB A:VAL65 4.2 49.5 1.0 CG A:LYS60 4.2 54.3 1.0 OP2 D:DC3 4.2 62.1 1.0 CA A:GLY66 4.3 39.1 1.0 CA A:LEU62 4.5 54.1 1.0 N A:GLY64 4.5 57.1 1.0 N A:LYS61 4.7 64.4 1.0 N A:PRO63 4.7 60.8 1.0 C A:LYS61 4.7 63.7 1.0 CB A:LYS60 4.7 53.4 1.0 CA A:PRO63 4.7 60.5 1.0 O3' D:DT2 4.9 60.7 1.0 O A:ALA59 4.9 48.7 1.0 CG1 A:VAL65 4.9 50.3 1.0 C A:GLY64 4.9 53.0 1.0

R.Prasad, V.K.Batra, X.-P.Yang, J.M.Krahn, L.C.Pedersen, W.A.Beard, S.H.Wilson. Structural Insight Into the Dna Polymerase Beta Deoxyribose Phosphate Lyase Mechanism Dna Repair V. 4 1347 2005.
ISSN: ISSN 1568-7864
PubMed: 16172026
DOI: 10.1016/J.DNAREP.2005.08.009