Sodium in PDB 9icf: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2

Protein crystallography data

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 ZNCL2, PDB code: 9icf 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 / 3.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 179.962, 57.615, 48.380, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / n/a

Other elements in 9icf:

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 ZNCL2 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

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 ZNCL2 (pdb code 9icf). 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 ZNCL2, PDB code: 9icf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 9icf

Go back to Sodium Binding Sites List in 9icf
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 ZNCL2


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 ZNCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:9.5
occ:1.00
O A:HOH601 1.9 83.0 1.0
OP1 P:DT6 2.2 24.6 1.0
O A:THR101 2.3 26.1 1.0
O A:VAL103 2.5 9.2 1.0
O A:ILE106 2.6 1.0 1.0
C A:VAL103 3.3 11.2 1.0
C A:THR101 3.4 14.0 1.0
P P:DT6 3.4 16.4 1.0
C A:ILE106 3.5 1.0 1.0
N A:ILE106 3.5 7.4 1.0
C A:ARG102 3.8 24.8 1.0
CA A:SER104 3.9 6.3 1.0
OP2 P:DT6 3.9 17.6 1.0
N A:GLY105 3.9 1.0 1.0
N A:SER104 3.9 12.3 1.0
CA A:ILE106 3.9 3.1 1.0
N A:VAL103 3.9 23.3 1.0
O A:ARG102 4.0 24.8 1.0
N A:ARG102 4.2 10.7 1.0
C A:SER104 4.2 1.7 1.0
CA A:ARG102 4.2 19.6 1.0
CA A:VAL103 4.2 15.6 1.0
CB A:ILE106 4.2 6.3 1.0
CA A:THR101 4.3 5.9 1.0
O5' P:DT6 4.3 12.5 1.0
N A:GLY107 4.6 1.0 1.0
C A:GLY105 4.6 6.7 1.0
O3' P:DA5 4.6 11.4 1.0
CA A:GLY105 4.8 3.4 1.0
O A:LEU100 4.9 15.6 1.0
CB A:VAL103 4.9 14.7 1.0

Sodium binding site 2 out of 2 in 9icf

Go back to Sodium Binding Sites List in 9icf
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 ZNCL2


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 ZNCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:26.6
occ:1.00
O A:LEU62 2.4 17.4 1.0
O A:LYS60 2.9 18.0 1.0
O A:VAL65 3.4 17.5 1.0
C A:LEU62 3.5 17.7 1.0
O A:LYS61 4.0 30.9 1.0
C A:LYS61 4.0 27.4 1.0
C A:LYS60 4.1 19.0 1.0
N A:LEU62 4.2 18.2 1.0
CG2 A:VAL65 4.3 13.4 1.0
N A:PRO63 4.4 23.3 1.0
C A:VAL65 4.4 7.3 1.0
CA A:LEU62 4.4 15.2 1.0
CA A:PRO63 4.5 28.5 1.0
CA A:LYS61 4.5 36.7 1.0
N A:LYS61 4.7 27.2 1.0
N A:VAL65 4.8 10.7 1.0
CG A:LYS60 4.9 22.5 1.0

Reference:

H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, J.Kraut. A Structural Basis For Metal Ion Mutagenicity and Nucleotide Selectivity in Human Dna Polymerase Beta Biochemistry V. 35 12762 1996.
ISSN: ISSN 0006-2960
PubMed: 8841119
DOI: 10.1021/BI9529566
Page generated: Tue Dec 15 18:37:06 2020

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