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Calcium 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:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6ozf

Go back to Calcium Binding Sites List in 6ozf
Calcium binding site 1 out of 4 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 Calcium with other atoms in the Ca 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:Ca301

b:18.8
occ:1.00
 OP1 C:DG7 2.3 23.9 1.0
OD1 A:ASP43 2.4 22.1 0.5
O C:HOH227 2.4 25.3 1.0
O A:HOH496 2.4 23.4 1.0
O A:HOH419 2.4 21.9 1.0
OD1 A:ASP43 2.5 26.8 0.5
ND1 A:HIS214 2.6 21.0 1.0
OD2 A:ASP43 2.8 27.6 0.5
OD2 A:ASP43 2.9 27.2 0.5
CG A:ASP43 2.9 24.2 0.5
CG A:ASP43 3.0 22.8 0.5
CE1 A:HIS214 3.4 24.9 1.0
P C:DG7 3.6 19.8 1.0
CG A:HIS214 3.6 21.3 1.0
CB A:HIS214 3.9 13.8 1.0
O5' C:DG7 4.1 17.2 1.0
O A:LEU44 4.2 21.7 1.0
OP2 C:DG7 4.2 22.0 1.0
C5' C:DG7 4.3 17.4 1.0
ND2 A:ASN110 4.3 28.7 0.6
O A:HOH476 4.3 49.0 1.0
O C:HOH210 4.3 31.8 1.0
CB A:ASP43 4.4 16.7 0.5
O A:HOH474 4.5 41.9 1.0
CA A:HIS214 4.5 16.4 1.0
CB A:ASP43 4.5 15.5 0.5
O C:HOH201 4.6 29.8 1.0
NA A:NA302 4.6 28.9 1.0
OG1 A:THR217 4.6 27.6 1.0
NE2 A:HIS214 4.6 19.7 1.0
O3' C:A6 4.7 16.2 1.0
CD2 A:HIS214 4.7 21.8 1.0
O C:HOH206 4.7 31.9 1.0
NE2 A:GLN218 4.9 29.1 1.0
OP2 C:DA8 5.0 29.6 1.0

Calcium binding site 2 out of 4 in 6ozf

Go back to Calcium Binding Sites List in 6ozf
Calcium binding site 2 out of 4 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 Calcium with other atoms in the Ca 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:Ca301

b:19.3
occ:1.00
 OP1 D:DG7 2.3 22.1 1.0
O B:HOH415 2.3 26.3 1.0
OD1 B:ASP43 2.4 28.7 1.0
O B:HOH519 2.4 21.1 1.0
O D:HOH226 2.5 22.5 1.0
ND1 B:HIS214 2.5 19.4 1.0
OD2 B:ASP43 3.1 40.0 1.0
CG B:ASP43 3.1 30.8 1.0
CE1 B:HIS214 3.4 23.6 1.0
P D:DG7 3.5 22.6 1.0
CG B:HIS214 3.6 20.9 1.0
CB B:HIS214 3.9 21.1 1.0
ND2 B:ASN110 4.1 31.3 0.7
O5' D:DG7 4.1 19.8 1.0
OP2 D:DG7 4.2 23.9 1.0
OD1 B:ASN110 4.2 31.6 0.3
O B:HOH443 4.3 48.0 1.0
O B:LEU44 4.3 23.9 1.0
C5' D:DG7 4.4 28.3 1.0
NA B:NA306 4.4 36.8 1.0
CA B:HIS214 4.5 21.8 1.0
NE2 B:HIS214 4.5 23.0 1.0
CB B:ASP43 4.6 17.8 1.0
O D:HOH206 4.6 33.0 1.0
O B:HOH537 4.6 30.9 1.0
CD2 B:HIS214 4.7 21.1 1.0
O3' D:A6 4.7 20.8 1.0
NZ B:LYS139 4.8 46.4 1.0
OP2 D:DA8 4.9 37.0 1.0
OE1 B:GLN218 4.9 41.2 1.0

Calcium binding site 3 out of 4 in 6ozf

Go back to Calcium Binding Sites List in 6ozf
Calcium binding site 3 out of 4 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 Calcium with other atoms in the Ca binding site number 3 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
C:Ca101

b:21.9
occ:1.00
 O6 C:DG7 2.3 24.6 1.0
OP2 C:DT3 2.4 24.6 1.0
O C:HOH220 2.4 18.7 1.0
O C:HOH222 2.4 17.3 1.0
O C:HOH212 2.5 29.1 1.0
O C:HOH216 3.0 56.4 1.0
C6 C:DG7 3.5 25.0 1.0
P C:DT3 3.8 32.3 1.0
N7 C:A6 4.1 18.1 1.0
OP1 C:DI5 4.2 19.6 1.0
C5 C:DG7 4.3 23.3 1.0
O3' C:DA2 4.3 30.6 1.0
N7 C:DG7 4.3 22.8 1.0
N6 C:DA8 4.3 21.7 1.0
N1 C:DA8 4.4 26.1 1.0
O C:HOH223 4.5 34.3 1.0
N1 C:DG7 4.6 28.0 1.0
C3' C:DA2 4.6 33.9 1.0
OP2 C:A6 4.7 15.4 1.0
O5' C:DT3 4.7 31.4 1.0
C5' C:DT3 4.8 40.5 1.0
C6 C:DA8 4.8 27.9 1.0
OP1 C:DT3 4.8 43.6 1.0
N6 C:A6 4.8 27.5 1.0
OP2 C:DI5 4.9 16.3 1.0
C8 C:A6 4.9 20.7 1.0

Calcium binding site 4 out of 4 in 6ozf

Go back to Calcium Binding Sites List in 6ozf
Calcium binding site 4 out of 4 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 Calcium with other atoms in the Ca binding site number 4 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
D:Ca101

b:25.0
occ:1.00
 O D:HOH222 2.2 35.1 1.0
O6 D:DG7 2.3 27.8 1.0
O D:HOH215 2.3 21.6 1.0
O D:HOH218 2.3 17.3 1.0
O D:HOH210 2.4 20.2 1.0
OP2 D:DT3 2.5 29.6 1.0
O D:HOH219 2.9 36.5 1.0
C6 D:DG7 3.4 27.2 1.0
P D:DT3 4.0 34.9 1.0
OP1 D:DI5 4.0 21.7 1.0
N6 D:DA8 4.1 27.5 1.0
N7 D:A6 4.2 18.4 1.0
C5 D:DG7 4.2 21.4 1.0
N7 D:DG7 4.2 20.4 1.0
O D:HOH220 4.3 46.9 1.0
N1 D:DA8 4.5 30.9 1.0
O3' D:DA2 4.5 36.1 1.0
N1 D:DG7 4.5 28.4 1.0
OP2 D:DI5 4.7 19.8 1.0
C6 D:DA8 4.7 31.3 1.0
OG B:SER140 4.7 18.2 1.0
OP2 D:A6 4.8 16.6 1.0
C3' D:DA2 4.8 46.6 1.0
O5' D:DT3 4.8 37.3 1.0
P D:DI5 4.9 19.6 1.0
C8 D:A6 4.9 16.9 1.0
C5' D:DT3 4.9 31.3 1.0
OP1 D:DT3 4.9 32.9 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: Tue Jul 16 12:40:02 2024

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