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Zinc 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:

Samarium (Sm) 7 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Zinc 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 Zinc atom.
In total 15 binding sites of Zinc where determined in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus, PDB code: 5zb8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in 5zb8

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Zinc binding site 1 out of 15 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
A:Zn501

b:32.0
occ:1.00
ND1 A:HIS84 2.1 34.0 1.0
OE2 A:GLU76 2.2 34.7 1.0
NE2 A:HIS139 2.2 39.3 1.0
CE1 A:HIS84 3.0 28.0 1.0
CD A:GLU76 3.0 36.3 1.0
CE1 A:HIS139 3.1 37.6 1.0
CD2 A:HIS139 3.2 36.1 1.0
ZN A:ZN502 3.2 26.3 1.0
OE1 A:GLU76 3.2 32.2 1.0
CG A:HIS84 3.2 31.2 1.0
NH1 A:ARG114 3.5 48.3 1.0
CB A:HIS84 3.7 23.0 1.0
OD2 A:ASP193 3.9 32.5 1.0
NE2 A:HIS84 4.1 30.3 1.0
CE1 A:HIS8 4.2 28.0 1.0
ND1 A:HIS139 4.2 36.2 1.0
CD2 A:HIS84 4.3 29.9 1.0
CG A:HIS139 4.3 33.5 1.0
OG1 A:THR145 4.3 33.8 1.0
CG A:GLU76 4.4 41.2 1.0
NE2 A:HIS8 4.6 27.1 1.0
CZ A:ARG114 4.6 55.1 1.0
CG A:ASP193 4.6 26.4 1.0
OD1 A:ASP193 4.8 31.5 1.0
CB A:ALA138 4.8 20.2 1.0
CD A:ARG114 4.9 51.2 1.0
NE2 A:HIS10 4.9 33.2 1.0

Zinc binding site 2 out of 15 in 5zb8

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Zinc binding site 2 out of 15 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
A:Zn502

b:26.3
occ:1.00
NE2 A:HIS10 2.1 33.2 1.0
OE1 A:GLU76 2.2 32.2 1.0
NE2 A:HIS8 2.3 27.1 1.0
OD1 A:ASP193 2.4 31.5 1.0
CE1 A:HIS8 2.8 28.0 1.0
CD A:GLU76 2.9 36.3 1.0
CG A:ASP193 3.0 26.4 1.0
OE2 A:GLU76 3.0 34.7 1.0
CD2 A:HIS10 3.1 31.2 1.0
CE1 A:HIS10 3.1 33.3 1.0
OD2 A:ASP193 3.2 32.5 1.0
ZN A:ZN501 3.2 32.0 1.0
CD2 A:HIS8 3.4 27.3 1.0
NH1 A:ARG114 3.6 48.3 1.0
ND1 A:HIS8 4.0 26.0 1.0
CG A:GLU76 4.2 41.2 1.0
CG A:HIS10 4.2 33.9 1.0
ND1 A:HIS10 4.2 34.0 1.0
CB A:ASP193 4.3 20.8 1.0
CG A:HIS8 4.3 27.5 1.0
CB A:GLU76 4.5 39.6 1.0
NE2 A:HIS139 4.6 39.3 1.0
CE1 A:HIS195 4.7 31.0 1.0
CZ A:ARG114 4.8 55.1 1.0
CA A:ASP193 4.8 24.6 1.0
CD2 A:HIS139 4.8 36.1 1.0
ND1 A:HIS84 4.9 34.0 1.0

Zinc binding site 3 out of 15 in 5zb8

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Zinc binding site 3 out of 15 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
A:Zn503

b:39.4
occ:1.00
SG A:CYS271 2.4 39.6 1.0
SG A:CYS252 2.4 35.5 1.0
SG A:CYS249 2.4 37.7 1.0
SG A:CYS268 2.5 42.0 1.0
CB A:CYS249 3.1 27.5 1.0
CB A:CYS268 3.2 32.4 1.0
CB A:CYS252 3.3 27.3 1.0
CB A:CYS271 3.6 36.9 1.0
N A:CYS252 3.7 27.2 1.0
N A:CYS271 3.9 43.0 1.0
CA A:CYS252 4.0 26.9 1.0
CA A:CYS271 4.2 42.0 1.0
N A:GLY273 4.3 37.2 1.0
CB A:LYS270 4.5 44.7 1.0
CA A:CYS249 4.6 30.4 1.0
CA A:GLY273 4.6 35.0 1.0
CB A:ARG251 4.7 28.7 1.0
CA A:CYS268 4.7 35.5 1.0
C A:CYS252 4.7 27.4 1.0
C A:CYS271 4.7 43.9 1.0
C A:ARG251 4.8 35.4 1.0
N A:GLY272 4.8 44.2 1.0
N A:TYR253 4.8 25.5 1.0
OH A:TYR256 4.8 45.5 1.0
C A:LYS270 4.8 49.9 1.0
OG1 A:THR254 4.9 48.6 1.0
N A:ARG251 5.0 32.0 1.0

Zinc binding site 4 out of 15 in 5zb8

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Zinc binding site 4 out of 15 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn501

b:34.1
occ:1.00
NE2 B:HIS139 2.0 35.8 1.0
ND1 B:HIS84 2.1 32.7 1.0
OE2 B:GLU76 2.1 37.9 1.0
CE1 B:HIS139 2.8 35.3 1.0
CD B:GLU76 2.9 33.3 1.0
CE1 B:HIS84 3.0 29.7 1.0
OE1 B:GLU76 3.0 32.2 1.0
CG B:HIS84 3.1 28.6 1.0
CD2 B:HIS139 3.1 31.2 1.0
ZN B:ZN502 3.3 33.2 1.0
CB B:HIS84 3.6 25.8 1.0
NH1 B:ARG114 3.7 25.9 1.0
ND1 B:HIS139 4.0 28.6 1.0
NE2 B:HIS84 4.1 31.4 1.0
CG B:HIS139 4.2 30.1 1.0
CD2 B:HIS84 4.2 28.3 1.0
CG B:GLU76 4.2 28.8 1.0
OD2 B:ASP193 4.2 33.6 1.0
CE1 B:HIS8 4.3 27.4 1.0
CZ B:ARG114 4.5 32.6 1.0
NE2 B:HIS8 4.5 31.6 1.0
OG1 B:THR145 4.5 33.0 1.0
CD B:ARG114 4.7 31.6 1.0
CB B:ALA138 4.8 23.3 1.0
CG B:ASP193 4.8 29.5 1.0
OD1 B:ASP193 4.9 34.4 1.0
NE B:ARG114 4.9 40.3 1.0
NE2 B:HIS10 5.0 31.1 1.0

Zinc binding site 5 out of 15 in 5zb8

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Zinc binding site 5 out of 15 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn502

b:33.2
occ:1.00
NE2 B:HIS10 2.2 31.1 1.0
OE1 B:GLU76 2.3 32.2 1.0
OD1 B:ASP193 2.3 34.4 1.0
NE2 B:HIS8 2.3 31.6 1.0
CE1 B:HIS8 3.0 27.4 1.0
CD B:GLU76 3.0 33.3 1.0
CD2 B:HIS10 3.0 31.4 1.0
CG B:ASP193 3.0 29.5 1.0
OE2 B:GLU76 3.2 37.9 1.0
ZN B:ZN501 3.3 34.1 1.0
OD2 B:ASP193 3.3 33.6 1.0
CE1 B:HIS10 3.3 31.6 1.0
CD2 B:HIS8 3.4 30.2 1.0
NH1 B:ARG114 3.7 25.9 1.0
ND1 B:HIS8 4.1 30.3 1.0
CG B:HIS10 4.2 33.1 1.0
CB B:ASP193 4.3 26.0 1.0
CG B:GLU76 4.3 28.8 1.0
ND1 B:HIS10 4.4 33.0 1.0
CG B:HIS8 4.4 30.4 1.0
NE2 B:HIS139 4.4 35.8 1.0
CE1 B:HIS195 4.5 35.3 1.0
CB B:GLU76 4.6 28.3 1.0
CD2 B:HIS139 4.7 31.2 1.0
CA B:ASP193 4.8 29.6 1.0
ND1 B:HIS84 5.0 32.7 1.0

Zinc binding site 6 out of 15 in 5zb8

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Zinc binding site 6 out of 15 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn503

b:40.5
occ:1.00
SG B:CYS271 2.3 44.3 1.0
SG B:CYS252 2.3 40.5 1.0
SG B:CYS268 2.4 49.9 1.0
SG B:CYS249 2.4 40.4 1.0
CB B:CYS268 3.0 46.3 1.0
CB B:CYS249 3.1 37.6 1.0
CB B:CYS252 3.3 38.2 1.0
CB B:CYS271 3.6 46.0 1.0
N B:CYS252 3.6 40.7 1.0
N B:CYS271 3.9 57.0 1.0
CA B:CYS252 4.0 38.6 1.0
CA B:CYS271 4.2 53.0 1.0
N B:GLY273 4.3 45.9 1.0
CB B:ARG251 4.5 36.1 1.0
CA B:CYS268 4.5 55.2 1.0
CB B:LYS270 4.6 67.1 1.0
CA B:CYS249 4.6 39.5 1.0
CA B:GLY273 4.6 43.0 1.0
N B:GLY272 4.6 51.3 1.0
C B:CYS271 4.7 50.4 1.0
C B:ARG251 4.7 42.1 1.0
C B:CYS252 4.7 41.2 1.0
N B:TYR253 4.8 39.9 1.0
C B:LYS270 4.9 62.9 1.0
CG B:ARG251 4.9 37.3 1.0
CA B:ARG251 4.9 37.8 1.0
N B:ARG251 4.9 39.0 1.0
CG B:LYS270 5.0 74.2 1.0

Zinc binding site 7 out of 15 in 5zb8

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Zinc binding site 7 out of 15 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
C:Zn501

b:34.4
occ:1.00
OE2 C:GLU76 2.1 36.7 1.0
ND1 C:HIS84 2.1 35.8 1.0
NE2 C:HIS139 2.2 33.9 1.0
CD C:GLU76 2.9 30.4 1.0
CE1 C:HIS84 2.9 34.0 1.0
ZN C:ZN502 3.1 27.0 1.0
OE1 C:GLU76 3.1 42.9 1.0
CD2 C:HIS139 3.1 34.2 1.0
CE1 C:HIS139 3.2 34.0 1.0
CG C:HIS84 3.2 28.7 1.0
CB C:HIS84 3.7 28.5 1.0
OD2 C:ASP193 3.9 29.1 1.0
NH1 C:ARG114 4.0 30.5 1.0
CE1 C:HIS8 4.1 31.9 1.0
NE2 C:HIS84 4.1 34.2 1.0
CD2 C:HIS84 4.3 31.1 1.0
ND1 C:HIS139 4.3 34.5 1.0
CG C:HIS139 4.3 32.2 1.0
CG C:GLU76 4.3 25.1 1.0
NE2 C:HIS8 4.5 32.0 1.0
CG C:ASP193 4.5 26.2 1.0
OD1 C:ASP193 4.6 33.8 1.0
OG1 C:THR145 4.6 37.2 1.0
CZ C:ARG114 4.8 45.1 1.0
CB C:ALA138 4.8 30.8 1.0
NE2 C:HIS10 4.9 36.4 1.0
CD C:ARG114 5.0 38.7 1.0

Zinc binding site 8 out of 15 in 5zb8

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Zinc binding site 8 out of 15 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 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:Zn502

b:27.0
occ:1.00
OE1 C:GLU76 2.2 42.9 1.0
NE2 C:HIS10 2.2 36.4 1.0
OD1 C:ASP193 2.2 33.8 1.0
NE2 C:HIS8 2.2 32.0 1.0
CE1 C:HIS8 2.8 31.9 1.0
CD C:GLU76 2.9 30.4 1.0
CG C:ASP193 2.9 26.2 1.0
OE2 C:GLU76 3.0 36.7 1.0
ZN C:ZN501 3.1 34.4 1.0
CE1 C:HIS10 3.1 32.3 1.0
OD2 C:ASP193 3.2 29.1 1.0
CD2 C:HIS10 3.2 32.0 1.0
CD2 C:HIS8 3.4 31.7 1.0
NH1 C:ARG114 3.8 30.5 1.0
ND1 C:HIS8 4.0 28.9 1.0
CG C:GLU76 4.2 25.1 1.0
ND1 C:HIS10 4.2 33.3 1.0
CB C:ASP193 4.3 20.4 1.0
CG C:HIS10 4.3 34.2 1.0
CG C:HIS8 4.3 30.9 1.0
CB C:GLU76 4.4 27.6 1.0
CE1 C:HIS195 4.6 30.6 1.0
NE2 C:HIS139 4.7 33.9 1.0
ND1 C:HIS84 4.8 35.8 1.0
CA C:ASP193 4.8 28.8 1.0
CD2 C:HIS139 4.9 34.2 1.0

Zinc binding site 9 out of 15 in 5zb8

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Zinc binding site 9 out of 15 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 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:Zn503

b:31.5
occ:1.00
SG C:CYS271 2.3 31.9 1.0
SG C:CYS252 2.3 32.9 1.0
SG C:CYS268 2.4 29.6 1.0
SG C:CYS249 2.4 33.7 1.0
CB C:CYS249 3.1 24.1 1.0
CB C:CYS268 3.1 26.3 1.0
CB C:CYS252 3.3 25.0 1.0
CB C:CYS271 3.5 31.5 1.0
N C:CYS252 3.7 30.1 1.0
N C:CYS271 3.9 28.8 1.0
CA C:CYS252 4.1 29.6 1.0
CA C:CYS271 4.2 31.6 1.0
N C:GLY273 4.3 24.0 1.0
CA C:CYS268 4.6 29.2 1.0
CA C:CYS249 4.6 23.8 1.0
CB C:LYS270 4.6 30.1 1.0
N C:GLY272 4.7 29.5 1.0
C C:CYS271 4.7 33.6 1.0
CA C:GLY273 4.7 26.3 1.0
CB C:ARG251 4.7 23.0 1.0
C C:CYS252 4.8 27.7 1.0
C C:ARG251 4.8 32.0 1.0
N C:TYR253 4.9 27.1 1.0
C C:LYS270 4.9 31.1 1.0
OH C:TYR256 5.0 33.0 1.0

Zinc binding site 10 out of 15 in 5zb8

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Zinc binding site 10 out of 15 in the Crystal Structure of the Novel Lesion-Specific Endonuclease Pfuendoq From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 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:Zn501

b:40.1
occ:1.00
OE2 D:GLU76 2.1 46.8 1.0
NE2 D:HIS139 2.2 40.1 1.0
ND1 D:HIS84 2.2 51.8 1.0
CD D:GLU76 2.9 41.6 1.0
CE1 D:HIS84 3.0 53.1 1.0
CE1 D:HIS139 3.1 41.6 1.0
OE1 D:GLU76 3.1 51.7 1.0
CD2 D:HIS139 3.2 38.7 1.0
ZN D:ZN502 3.2 35.0 1.0
CG D:HIS84 3.3 47.0 1.0
CB D:HIS84 3.7 32.9 1.0
NH1 D:ARG114 3.7 32.2 1.0
OD2 D:ASP193 4.0 48.5 1.0
NE2 D:HIS84 4.2 52.0 1.0
ND1 D:HIS139 4.2 38.7 1.0
CE1 D:HIS8 4.3 40.7 1.0
CG D:GLU76 4.3 35.2 1.0
CD2 D:HIS84 4.3 51.1 1.0
CG D:HIS139 4.3 35.8 1.0
OG1 D:THR145 4.5 45.5 1.0
NE2 D:HIS8 4.6 41.0 1.0
CZ D:ARG114 4.6 41.3 1.0
CG D:ASP193 4.7 42.0 1.0
CB D:ALA138 4.8 28.2 1.0
CD D:ARG114 4.8 42.4 1.0
OD1 D:ASP193 4.9 46.8 1.0
NE2 D:HIS10 5.0 45.5 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: Wed Dec 16 11:25:46 2020

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