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Sodium in PDB 6ozf: Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine

Enzymatic activity of Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine

All present enzymatic activity of Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine:
3.1.21.7;

Protein crystallography data

The structure of Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine, PDB code: 6ozf was solved by N.L.Samara, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.09 / 1.80
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.129, 75.578, 106.397, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19.8

Other elements in 6ozf:

The structure of Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine (pdb code 6ozf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine, PDB code: 6ozf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6ozf

Go back to Sodium Binding Sites List in 6ozf
Sodium binding site 1 out of 2 in the Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:28.9
occ:1.00
 OD2 A:ASP43 2.4 27.2 0.5
O A:HOH412 2.8 27.6 1.0
O3' C:A6 3.1 16.2 1.0
N A:LEU44 3.1 14.5 1.0
OP1 C:DG7 3.2 23.9 1.0
OD1 A:ASP43 3.3 26.8 0.5
ND2 A:ASN110 3.4 28.7 0.6
CG A:ASP43 3.5 24.2 0.5
O2' C:A6 3.5 17.3 1.0
CB A:ASN110 3.5 26.0 0.6
CB A:ASN110 3.5 25.6 0.5
CA A:ASP43 3.7 14.2 0.5
CA A:ASP43 3.7 14.4 0.5
P C:DG7 3.8 19.8 1.0
C A:ASP43 3.9 12.7 1.0
CG A:ASP43 3.9 22.8 0.5
C5' C:DG7 4.0 17.4 1.0
CG A:ASN110 4.0 29.3 0.6
O A:LEU44 4.0 21.7 1.0
O A:HOH447 4.1 18.2 1.0
CA A:LEU44 4.1 22.7 1.0
CB A:LEU44 4.1 27.0 1.0
C3' C:A6 4.2 15.5 1.0
CB A:ASP43 4.2 16.7 0.5
CG A:ASN110 4.2 30.3 0.5
OE1 A:GLU89 4.4 48.0 1.0
O5' C:DG7 4.4 17.2 1.0
OD1 A:ASP43 4.4 22.1 0.5
CB A:ASP43 4.4 15.5 0.5
C2' C:A6 4.4 17.2 1.0
CD1 A:LEU44 4.5 35.3 1.0
C4' C:A6 4.5 15.3 1.0
C A:LEU44 4.6 23.6 1.0
O A:ASN110 4.6 24.4 1.0
OD2 A:ASP43 4.6 27.6 0.5
CA A:CA301 4.6 18.8 1.0
O A:VAL42 4.6 14.2 1.0
OE2 A:GLU89 4.6 43.5 1.0
ND2 A:ASN110 4.7 31.7 0.5
OD1 A:ASN110 4.8 35.2 0.5
N A:ASP43 4.8 13.7 1.0
CA A:ASN110 4.8 17.9 0.6
CA A:ASN110 4.8 18.9 0.5
CD A:GLU89 4.9 37.7 1.0
CG A:LEU44 4.9 38.3 1.0

Sodium binding site 2 out of 2 in 6ozf

Go back to Sodium Binding Sites List in 6ozf
Sodium binding site 2 out of 2 in the Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (D110N) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na306

b:36.8
occ:1.00
 O B:HOH435 2.8 28.3 1.0
O3' D:A6 2.9 20.8 1.0
OP1 D:DG7 3.0 22.1 1.0
N B:LEU44 3.2 19.3 1.0
ND2 B:ASN110 3.3 31.3 0.7
O2' D:A6 3.5 21.9 1.0
OD1 B:ASN110 3.5 31.6 0.3
CB B:ASN110 3.6 22.9 0.7
P D:DG7 3.6 22.6 1.0
CB B:ASN110 3.6 23.8 0.3
OD1 B:ASP43 3.7 28.7 1.0
O B:LEU44 3.8 23.9 1.0
CA B:ASP43 3.9 15.8 1.0
CG B:ASN110 3.9 26.6 0.7
C5' D:DG7 4.0 28.3 1.0
CG B:ASN110 4.0 26.8 0.3
CG B:ASP43 4.0 30.8 1.0
C B:ASP43 4.0 19.0 1.0
CA B:LEU44 4.0 19.8 1.0
C3' D:A6 4.0 17.8 1.0
CB B:LEU44 4.1 21.3 1.0
O B:HOH440 4.2 23.4 1.0
O5' D:DG7 4.3 19.8 1.0
C2' D:A6 4.3 24.3 1.0
C B:LEU44 4.3 24.5 1.0
OE2 B:GLU89 4.4 48.7 1.0
OD2 B:ASP43 4.4 40.0 1.0
CA B:CA301 4.4 19.3 1.0
C4' D:A6 4.5 16.8 1.0
CB B:ASP43 4.5 17.8 1.0
OE1 B:GLU89 4.6 46.3 1.0
CD1 B:LEU44 4.6 30.3 1.0
O B:ASN110 4.7 26.4 1.0
O B:VAL42 4.8 18.2 1.0
O B:HOH415 4.8 26.3 1.0
CD B:GLU89 4.9 40.8 1.0
OP2 D:DG7 4.9 23.9 1.0
CA B:ASN110 4.9 18.5 0.7
CA B:ASN110 4.9 22.0 0.3
CG B:LEU44 5.0 30.9 1.0

Reference:

J.Wu, N.L.Samara, I.Kuraoka, W.Yang. Evolution of Inosine-Specific Endonuclease V From Bacterial Dnase to Eukaryotic Rnase. Mol.Cell V. 76 44 2019.
ISSN: ISSN 1097-2765
PubMed: 31444105
DOI: 10.1016/J.MOLCEL.2019.06.046
Page generated: Mon Aug 18 06:32:26 2025

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