Atomistry » Samarium » PDB 5lxr-7ml9 » 5zb8
Atomistry »
  Samarium »
    PDB 5lxr-7ml9 »
      5zb8 »

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

Protein crystallography data

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

Other elements in 5zb8:

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

Samarium Binding Sites:

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 5zb8

Go back to Samarium Binding Sites List in 5zb8
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 5zb8

Go back to Samarium Binding Sites List in 5zb8
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 5zb8

Go back to Samarium Binding Sites List in 5zb8
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 5zb8

Go back to Samarium Binding Sites List in 5zb8
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 5zb8

Go back to Samarium Binding Sites List in 5zb8
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 5zb8

Go back to Samarium Binding Sites List in 5zb8
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 5zb8

Go back to Samarium Binding Sites List in 5zb8
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

Reference:

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
Page generated: Thu Oct 10 13:57:03 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy