Sodium in PDB 9icc: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and CRCL3

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and CRCL3, PDB code: 9icc was solved by H.Pelletier, M.R.Sawaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.300, 57.603, 48.013, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / n/a

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and CRCL3 also contains other interesting chemical elements:

Chromium

(Cr)

1 atom

The binding sites of Sodium atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and CRCL3 (pdb code 9icc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and CRCL3, PDB code: 9icc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and CRCL3


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 (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and CRCL3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:12.1 occ:1.00 O A:HOH601 2.1 62.9 1.0 O A:THR101 2.3 13.8 1.0 OP1 P:DT6 2.4 14.2 1.0 O A:ILE106 2.4 7.1 1.0 O A:VAL103 2.6 3.7 1.0 P P:DT6 3.3 19.6 1.0 OP2 P:DT6 3.4 13.9 1.0 C A:VAL103 3.4 4.7 1.0 C A:THR101 3.5 16.7 1.0 C A:ILE106 3.6 4.7 1.0 C A:ARG102 3.9 29.5 1.0 CA A:SER104 4.0 16.6 1.0 O A:ARG102 4.0 30.8 1.0 N A:SER104 4.0 10.3 1.0 N A:ILE106 4.0 8.3 1.0 N A:GLY105 4.1 16.0 1.0 N A:VAL103 4.1 20.4 1.0 CA A:ILE106 4.3 4.1 1.0 CA A:ARG102 4.3 35.5 1.0 N A:ARG102 4.4 27.6 1.0 CA A:VAL103 4.4 9.2 1.0 O5' P:DT6 4.4 15.0 1.0 C A:SER104 4.5 19.0 1.0 CA A:THR101 4.5 7.6 1.0 CB A:ILE106 4.5 1.0 1.0 O3' P:DA5 4.5 20.3 1.0 CG2 A:THR101 4.6 3.6 1.0 N A:GLY107 4.6 4.9 1.0 C A:GLY105 4.9 8.9 1.0 CA A:GLY107 4.9 8.0 1.0 CG2 A:ILE106 5.0 1.0 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and CRCL3


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 (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and CRCL3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:35.7 occ:1.00 O A:LEU62 2.4 33.0 1.0 O A:LYS60 2.4 27.1 1.0 O A:VAL65 3.2 24.1 1.0 C A:LEU62 3.3 33.6 1.0 C A:LYS60 3.6 27.2 1.0 C A:LYS61 3.7 34.3 1.0 O A:LYS61 3.9 35.2 1.0 N A:LEU62 3.9 30.4 1.0 N A:PRO63 4.1 31.7 1.0 CA A:LEU62 4.2 29.2 1.0 C A:VAL65 4.2 21.7 1.0 CA A:LYS61 4.3 38.1 1.0 N A:VAL65 4.3 25.4 1.0 CA A:PRO63 4.4 29.0 1.0 N A:LYS61 4.4 29.9 1.0 CG2 A:VAL65 4.4 27.1 1.0 CG A:LYS60 4.5 36.7 1.0 CA A:VAL65 4.6 24.6 1.0 N A:GLY64 4.7 45.0 1.0 CA A:LYS60 4.8 25.1 1.0 C A:PRO63 4.9 35.0 1.0 CE A:LYS60 5.0 57.0 1.0

H.Pelletier, M.R.Sawaya. Characterization of the Metal Ion Binding Helix-Hairpin-Helix Motifs in Human Dna Polymerase Beta By X-Ray Structural Analysis. Biochemistry V. 35 12778 1996.
ISSN: ISSN 0006-2960
PubMed: 8841120
DOI: 10.1021/BI960790I