Samarium in PDB 5zb8: Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus

The structure of Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus, PDB code: 5zb8 was solved by K.Miyazono, T.Ito, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.12 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	257.354, 82.245, 116.581, 90.00, 109.13, 90.00
R / Rfree (%)	17.6 / 20.9

The structure of Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus also contains other interesting chemical elements:

Zinc

(Zn)

15 atoms

The binding sites of Samarium atom in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus (pdb code 5zb8). This binding sites where shown within 5.0 Angstroms radius around Samarium atom.
In total 7 binding sites of Samarium where determined in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus, PDB code: 5zb8:
Jump to Samarium binding site number: 1; 2; 3; 4; 5; 6; 7;

Samarium binding site 1 out of 7 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 1 of Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Sm504 b:0.2 occ:0.66 OE2 B:GLU122 3.1 51.3 1.0 O B:HOH606 3.3 55.0 1.0 OE1 B:GLU126 3.3 53.4 1.0 CD B:GLU122 3.7 48.2 1.0 CB B:ASP160 3.8 47.4 1.0 OD2 B:ASP160 4.0 63.7 1.0 O A:HOH678 4.0 39.1 1.0 CG B:GLU122 4.2 38.7 1.0 CG B:ASP160 4.4 59.5 1.0 OE1 B:GLU122 4.5 52.9 1.0 CD B:GLU126 4.5 54.7 1.0 N B:ASP160 4.7 33.4 1.0 CA B:ASP160 4.7 39.2 1.0 OE2 B:GLU126 4.9 57.6 1.0

Samarium binding site 2 out of 7 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 2 of Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ C:Sm504 b:97.4 occ:0.78 OE1 C:GLU122 3.0 43.1 1.0 OE2 C:GLU122 3.2 44.5 1.0 CD C:GLU122 3.5 39.9 1.0 OD2 C:ASP160 4.0 65.8 1.0 CG C:ASP160 4.8 58.5 1.0 N C:ASP160 5.0 49.6 1.0 CG C:GLU122 5.0 37.4 1.0

Samarium binding site 3 out of 7 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 3 of Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ C:Sm505 b:81.8 occ:0.80 OD2 C:ASP156 3.1 75.4 1.0 OD1 C:ASP156 3.2 80.2 1.0 CG C:ASP156 3.4 72.3 1.0 CB C:ASP152 4.2 53.6 1.0 OD2 C:ASP152 4.5 78.8 1.0 CB C:ASP156 4.7 59.6 1.0 CG C:ASP152 4.8 70.2 1.0 OG C:SER153 4.9 43.7 1.0

Samarium binding site 4 out of 7 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 4 of Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ D:Sm504 b:64.3 occ:0.99 OD1 D:ASP132 3.0 54.3 1.0 OD2 D:ASP132 3.2 58.0 1.0 CG D:ASP132 3.4 53.2 1.0 O D:HOH657 4.2 40.4 1.0 O D:ASN129 4.8 55.2 1.0 CB D:ASP132 4.8 50.2 1.0 O D:GLU130 5.0 48.9 1.0

Samarium binding site 5 out of 7 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 5 of Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ E:Sm504 b:84.2 occ:0.93 OD2 E:ASP156 3.1 64.4 1.0 OD1 E:ASP156 3.3 69.7 1.0 CG E:ASP156 3.4 62.3 1.0 CB E:ASP156 4.7 56.9 1.0

Samarium binding site 6 out of 7 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 6 of Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ E:Sm505 b:0.9 occ:0.98 OE2 E:GLU122 3.0 69.1 1.0 OD2 E:ASP160 3.4 90.7 1.0 OE1 E:GLU126 3.8 82.0 1.0 O E:HOH647 4.0 57.4 1.0 CB E:ASP160 4.0 74.0 1.0 CD E:GLU122 4.1 60.9 1.0 CG E:ASP160 4.2 85.1 1.0 OE2 E:GLU126 4.6 85.3 1.0 CD E:GLU126 4.6 82.4 1.0 O E:HOH667 4.6 52.8 1.0 CG E:GLU122 4.8 45.3 1.0 N E:ASP160 4.8 58.2 1.0

Samarium binding site 7 out of 7 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 7 of Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ E:Sm506 b:0.6 occ:0.76 OD1 E:ASP156 3.2 69.7 1.0 CG E:ASP156 3.3 62.3 1.0 OD2 E:ASP156 3.3 64.4 1.0 CB E:ASP156 4.3 56.9 1.0 OG E:SER153 4.4 44.4 1.0 CB E:ASP152 4.5 52.0 1.0 OD2 E:ASP152 4.8 66.7 1.0

K.I.Miyazono, S.Ishino, N.Makita, T.Ito, Y.Ishino, M.Tanokura. Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus. Nucleic Acids Res. V. 46 4807 2018.
ISSN: ESSN 1362-4962
PubMed: 29660024
DOI: 10.1093/NAR/GKY261