Zinc in PDB 3af6: The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii Complexed with Rna-Analog

The structure of The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii Complexed with Rna-Analog, PDB code: 3af6 was solved by Y.Nishida, H.Ishikawa, N.Nakagawa, R.Masui, S.Kuramitsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.59 / 2.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	86.438, 86.438, 237.501, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 25.8

The binding sites of Zinc atom in the The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii Complexed with Rna-Analog (pdb code 3af6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii Complexed with Rna-Analog, PDB code: 3af6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii Complexed with Rna-Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii Complexed with Rna-Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn657 b:91.7 occ:1.00 NE2 A:HIS256 2.2 39.6 1.0 NE2 A:HIS344 2.5 36.4 1.0 ND1 A:HIS258 2.5 50.3 1.0 OD1 A:ASP367 2.9 45.5 1.0 CD2 A:HIS256 3.1 37.0 1.0 CD2 A:HIS344 3.2 34.0 1.0 CE1 A:HIS256 3.2 40.2 1.0 CE1 A:HIS258 3.4 51.0 1.0 CG A:HIS258 3.5 46.2 1.0 CE1 A:HIS344 3.6 36.1 1.0 CB A:HIS258 3.8 43.1 1.0 O2 A:SO4655 3.8 0.1 1.0 ZN A:ZN658 3.9 0.5 1.0 CG A:ASP367 3.9 43.0 1.0 CB A:ASP367 4.2 41.4 1.0 CG A:HIS256 4.3 38.0 1.0 ND1 A:HIS256 4.3 40.5 1.0 OD2 A:ASP260 4.4 51.6 1.0 CG A:HIS344 4.4 36.3 1.0 NE2 A:HIS258 4.5 51.1 1.0 CD2 A:HIS258 4.5 48.7 1.0 CD2 A:HIS261 4.5 29.5 1.0 O4 A:SO4655 4.6 0.7 1.0 ND1 A:HIS344 4.6 36.6 1.0 NE2 A:HIS261 4.7 30.0 1.0 OD1 A:ASP260 4.7 52.8 1.0 S A:SO4655 4.7 0.8 1.0 O A:HOH685 5.0 50.3 1.0

Zinc binding site 2 out of 2 in the The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii Complexed with Rna-Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii Complexed with Rna-Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn658 b:0.5 occ:1.00 NE2 A:HIS261 2.2 30.0 1.0 NE2 A:HIS618 2.5 36.3 1.0 OD1 A:ASP367 2.5 45.5 1.0 OD1 A:ASP260 2.5 52.8 1.0 O2 A:SO4655 2.6 0.1 1.0 CD2 A:HIS261 2.8 29.5 1.0 CG A:ASP260 3.1 48.8 1.0 CE1 A:HIS261 3.3 31.4 1.0 CE1 A:HIS618 3.4 35.4 1.0 OD2 A:ASP260 3.4 51.6 1.0 CG A:ASP367 3.4 43.0 1.0 CD2 A:HIS618 3.5 36.2 1.0 OD2 A:ASP367 3.7 47.0 1.0 ZN A:ZN657 3.9 91.7 1.0 S A:SO4655 3.9 0.8 1.0 CG A:HIS261 4.1 31.1 1.0 CE1 A:HIS256 4.2 40.2 1.0 CB A:ASP260 4.2 40.1 1.0 O1 A:SO4655 4.3 0.5 1.0 NE2 A:HIS256 4.3 39.6 1.0 ND1 A:HIS261 4.3 32.5 1.0 ND1 A:HIS618 4.5 38.6 1.0 O3 A:SO4655 4.6 0.4 1.0 O A:ASP260 4.6 37.2 1.0 CG A:HIS618 4.6 37.2 1.0 CB A:ASP367 4.8 41.4 1.0 O4 A:SO4655 4.9 0.7 1.0 C A:ASP260 4.9 34.4 1.0 CE1 A:HIS594 5.0 39.0 1.0

Y.Nishida, H.Ishikawa, S.Baba, N.Nakagawa, S.Kuramitsu, R.Masui. Crystal Structure of An Archaeal Cleavage and Polyadenylation Specificity Factor Subunit From Pyrococcus Horikoshii Proteins V. 78 2395 2010.
ISSN: ISSN 0887-3585
PubMed: 20544974
DOI: 10.1002/PROT.22748