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Magnesium in PDB 6ozg: Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (E89Q) 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 (E89Q) 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 (E89Q) 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 (E89Q) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine, PDB code: 6ozg 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) 33.14 / 1.93
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.495, 82.487, 108.569, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (E89Q) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine (pdb code 6ozg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (E89Q) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine, PDB code: 6ozg:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6ozg

Go back to Magnesium Binding Sites List in 6ozg
Magnesium binding site 1 out of 3 in the Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (E89Q) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (E89Q) 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:Mg301

b:53.0
occ:1.00
 OP1 C:DG7 2.0 79.5 1.0
ND1 A:HIS214 2.5 47.3 1.0
OD1 A:ASP43 2.7 53.2 1.0
OD2 A:ASP43 3.2 56.1 1.0
CG A:ASP43 3.3 49.8 1.0
CG A:HIS214 3.3 45.8 1.0
P C:DG7 3.4 57.4 1.0
CB A:HIS214 3.5 39.3 1.0
OD2 A:ASP110 3.5 60.5 1.0
CE1 A:HIS214 3.5 51.3 1.0
OP2 C:DG7 3.9 53.4 1.0
O5' C:DG7 4.1 57.1 1.0
CA A:HIS214 4.3 33.5 1.0
CD2 A:HIS214 4.5 49.2 1.0
C5' C:DG7 4.5 55.3 1.0
O3' C:A6 4.5 43.8 1.0
NE2 A:HIS214 4.5 52.2 1.0
CG A:ASP110 4.7 55.3 1.0
CB A:ASP43 4.7 38.0 1.0
O C:HOH210 4.9 35.4 1.0
O A:LEU44 4.9 51.4 1.0

Magnesium binding site 2 out of 3 in 6ozg

Go back to Magnesium Binding Sites List in 6ozg
Magnesium binding site 2 out of 3 in the Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (E89Q) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (E89Q) 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:Mg301

b:55.8
occ:1.00
 OP1 D:DG7 2.0 83.8 1.0
OD1 B:ASP43 2.3 65.2 1.0
ND1 B:HIS214 2.4 64.3 1.0
CG B:ASP43 3.1 61.8 1.0
OD2 B:ASP43 3.2 69.6 1.0
CE1 B:HIS214 3.3 69.1 1.0
CG B:HIS214 3.3 62.8 1.0
P D:DG7 3.4 68.0 1.0
CB B:HIS214 3.6 53.6 1.0
OD2 B:ASP110 3.8 75.6 1.0
O5' D:DG7 3.9 72.3 1.0
C5' D:DG7 4.0 77.8 1.0
OP2 D:DG7 4.2 66.3 1.0
CA B:HIS214 4.4 52.0 1.0
NE2 B:HIS214 4.4 71.3 1.0
CD2 B:HIS214 4.4 68.1 1.0
CB B:ASP43 4.5 54.4 1.0
O3' D:A6 4.5 57.9 1.0
CG B:ASP110 4.6 66.8 1.0
O B:HOH468 4.8 44.4 1.0
NZ B:LYS139 4.8 63.2 1.0
O B:LEU44 4.9 70.3 1.0
OD1 B:ASP110 4.9 75.2 1.0

Magnesium binding site 3 out of 3 in 6ozg

Go back to Magnesium Binding Sites List in 6ozg
Magnesium binding site 3 out of 3 in the Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (E89Q) in Complex with A 12MER Dna Containing An Inosine Followed By A Ribo- Adenosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Thermotoga Maritima (Tm) Endonuclease V (E89Q) 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:Mg101

b:44.3
occ:1.00
 O C:HOH206 2.0 41.1 1.0
O6 C:DG7 2.1 77.3 1.0
O C:HOH201 2.1 43.7 1.0
O C:HOH208 2.2 45.1 1.0
O C:HOH205 2.2 44.2 1.0
O C:HOH203 2.3 32.9 1.0
C6 C:DG7 3.2 65.1 1.0
N7 C:A6 3.9 38.3 1.0
C5 C:DG7 3.9 59.2 1.0
OP2 C:DT3 3.9 89.9 1.0
N7 C:DG7 4.0 54.4 1.0
OP1 C:DA5 4.1 41.2 1.0
N1 C:DG7 4.3 62.6 1.0
N6 C:DA8 4.4 71.3 1.0
N1 C:DA8 4.4 73.6 1.0
OP2 C:A6 4.5 39.7 1.0
C8 C:A6 4.6 36.1 1.0
OP2 C:DA5 4.7 37.6 1.0
C6 C:DA8 4.8 73.1 1.0
P C:DA5 4.8 37.7 1.0
N6 C:A6 4.9 48.2 1.0
C5 C:A6 4.9 40.9 1.0
OG A:SER140 5.0 45.1 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 Oct 1 13:43:14 2024

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