Sodium in PDB 9icv: 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: 9icv 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 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 179.972, 57.628, 48.334, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / n/a

Other elements in 9icv:

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) 3 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 9icv). 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: 9icv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 9icv

Go back to Sodium Binding Sites List in 9icv
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:15.2
occ:1.00
O A:VAL103 2.3 8.2 1.0
O A:THR101 2.3 30.7 1.0
OP1 P:DT6 2.4 16.2 1.0
O A:ILE106 2.5 8.8 1.0
O A:HOH601 3.0 69.8 1.0
C A:VAL103 3.0 6.8 1.0
C A:THR101 3.3 19.7 1.0
N A:VAL103 3.5 25.6 1.0
C A:ILE106 3.6 3.4 1.0
C A:ARG102 3.7 28.5 1.0
N A:SER104 3.7 6.5 1.0
P P:DT6 3.7 17.0 1.0
CA A:SER104 3.7 9.5 1.0
N A:ILE106 3.8 5.8 1.0
N A:GLY105 3.9 8.7 1.0
CA A:VAL103 3.9 17.6 1.0
CA A:ARG102 4.0 27.6 1.0
N A:ARG102 4.0 23.1 1.0
CA A:ILE106 4.2 3.3 1.0
O A:ARG102 4.2 29.9 1.0
C A:SER104 4.2 9.0 1.0
CA A:THR101 4.2 11.2 1.0
OP2 P:DT6 4.3 26.2 1.0
CB A:ILE106 4.4 8.5 1.0
O5' P:DT6 4.6 13.8 1.0
C A:GLY105 4.7 11.2 1.0
N A:GLY107 4.7 5.5 1.0
O A:LEU100 4.7 16.9 1.0
O3' P:DA5 4.7 17.8 1.0
CB A:VAL103 4.8 18.2 1.0
CA A:GLY105 4.9 9.0 1.0

Sodium binding site 2 out of 2 in 9icv

Go back to Sodium Binding Sites List in 9icv
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:58.7
occ:1.00
O A:LEU62 2.5 35.5 1.0
O A:LYS60 2.8 37.9 1.0
O A:VAL65 3.2 30.3 1.0
C A:LEU62 3.6 37.7 1.0
C A:LYS60 4.0 35.3 1.0
C A:LYS61 4.0 37.4 1.0
O A:LYS61 4.2 42.5 1.0
C A:VAL65 4.2 18.6 1.0
N A:LEU62 4.2 33.3 1.0
N A:PRO63 4.4 40.5 1.0
N A:VAL65 4.4 16.9 1.0
CA A:LYS61 4.5 40.6 1.0
CA A:LEU62 4.5 28.7 1.0
CA A:PRO63 4.6 44.1 1.0
N A:LYS61 4.7 33.9 1.0
N A:GLY64 4.7 51.3 1.0
CA A:VAL65 4.8 11.4 1.0
CE A:LYS60 4.9 57.1 1.0
CG A:LYS60 4.9 40.7 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 18:47:20 2020

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