Sodium in PDB 9icb: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and COCL2

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 COCL2, PDB code: 9icb 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 / 3.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 178.884, 57.712, 48.421, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / n/a

Other elements in 9icb:

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 COCL2 also contains other interesting chemical elements:

Cobalt (Co) 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 COCL2 (pdb code 9icb). 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 COCL2, PDB code: 9icb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 9icb

Go back to Sodium Binding Sites List in 9icb
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 COCL2


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 COCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:1.0
occ:1.00
O A:THR101 2.1 3.2 1.0
O P:HOH601 2.2 0.0 1.0
O A:VAL103 2.7 6.5 1.0
OP1 P:DT6 2.8 17.5 1.0
O A:ILE106 2.9 1.0 1.0
C A:ARG102 3.1 25.3 1.0
C A:VAL103 3.1 9.1 1.0
C A:THR101 3.2 8.1 1.0
O A:ARG102 3.2 26.6 1.0
N A:VAL103 3.4 19.6 1.0
CA A:ARG102 3.5 27.9 1.0
N A:SER104 3.7 9.3 1.0
N A:ARG102 3.8 18.2 1.0
P P:DT6 3.8 14.5 1.0
CA A:VAL103 3.8 13.8 1.0
CA A:SER104 3.9 7.6 1.0
OP2 P:DT6 4.0 17.1 1.0
C A:ILE106 4.0 1.0 1.0
N A:ILE106 4.1 1.0 1.0
N A:GLY105 4.4 3.3 1.0
CA A:THR101 4.4 3.4 1.0
CA A:ILE106 4.5 1.0 1.0
C A:SER104 4.6 7.6 1.0
O5' P:DT6 4.6 11.2 1.0
CB A:ILE106 4.7 1.0 1.0
O A:LEU100 4.9 10.1 1.0
CB A:ARG102 5.0 39.7 1.0

Sodium binding site 2 out of 2 in 9icb

Go back to Sodium Binding Sites List in 9icb
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 COCL2


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 COCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:33.3
occ:1.00
O A:LEU62 2.0 29.3 1.0
O A:LYS60 3.0 9.8 1.0
C A:LEU62 3.1 28.1 1.0
O A:HOH656 3.3 17.9 1.0
O A:VAL65 3.3 9.9 1.0
N A:PRO63 3.9 28.1 1.0
O A:LYS61 3.9 26.2 1.0
CA A:PRO63 4.0 28.2 1.0
C A:LYS61 4.0 29.1 1.0
N A:LEU62 4.1 24.4 1.0
C A:LYS60 4.1 21.0 1.0
CA A:LEU62 4.1 25.4 1.0
C A:VAL65 4.2 5.6 1.0
N A:VAL65 4.3 5.5 1.0
N A:GLY64 4.3 28.6 1.0
CG2 A:VAL65 4.6 7.2 1.0
CD A:PRO63 4.6 29.4 1.0
C A:PRO63 4.7 25.2 1.0
CA A:VAL65 4.7 1.4 1.0
CA A:LYS61 4.7 39.2 1.0
N A:LYS61 4.9 31.6 1.0

Reference:

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
Page generated: Tue Dec 15 18:35:21 2020

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