Zinc in PDB 3af5: The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii

The structure of The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii, PDB code: 3af5 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)	19.99 / 2.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	86.200, 86.200, 238.287, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.7

The binding sites of Zinc atom in the The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii (pdb code 3af5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii, PDB code: 3af5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn662 b:48.8 occ:1.00 ND1 A:HIS258 2.2 35.1 1.0 NE2 A:HIS256 2.3 26.8 1.0 NE2 A:HIS344 2.3 31.1 1.0 OD1 A:ASP367 2.6 38.3 1.0 CD2 A:HIS256 3.0 27.6 1.0 CD2 A:HIS344 3.1 25.7 1.0 CE1 A:HIS258 3.1 34.5 1.0 O2 A:SO4657 3.1 0.5 1.0 CG A:HIS258 3.3 35.5 1.0 CE1 A:HIS344 3.4 28.3 1.0 CE1 A:HIS256 3.4 29.2 1.0 O4 A:SO4657 3.4 0.1 1.0 CB A:HIS258 3.6 33.3 1.0 CG A:ASP367 3.6 34.1 1.0 ZN A:ZN665 3.7 44.3 1.0 S A:SO4657 3.9 0.1 1.0 CB A:ASP367 4.0 35.0 1.0 CG A:HIS256 4.2 28.2 1.0 O1 A:SO4654 4.2 0.1 1.0 NE2 A:HIS258 4.3 35.2 1.0 CD2 A:HIS261 4.3 27.1 1.0 CG A:HIS344 4.3 30.8 1.0 CD2 A:HIS258 4.3 35.4 1.0 ND1 A:HIS256 4.4 29.1 1.0 ND1 A:HIS344 4.4 30.8 1.0 NE2 A:HIS261 4.5 27.5 1.0 O3 A:SO4657 4.6 0.8 1.0 OD2 A:ASP367 4.7 34.9 1.0 CE1 A:HIS594 4.7 30.8 1.0 OD2 A:ASP260 4.7 39.6 1.0

Zinc binding site 2 out of 4 in the The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn663 b:0.1 occ:1.00 OE1 A:GLU387 2.0 49.2 1.0 OE2 A:GLU612 2.3 70.1 1.0 CD A:GLU387 3.2 48.3 1.0 CD A:GLU612 3.3 67.9 1.0 OE1 A:GLU612 3.7 69.9 1.0 CG A:GLU387 3.9 43.9 1.0 OXT A:ARG651 3.9 62.1 1.0 CE1 A:HIS360 4.1 57.3 1.0 ND1 A:HIS360 4.1 56.4 1.0 O A:LEU359 4.1 53.2 1.0 OE2 A:GLU387 4.2 49.5 1.0 O A:ARG651 4.6 64.6 1.0 CG A:GLU612 4.7 62.2 1.0 C A:ARG651 4.7 62.0 1.0 CB A:GLU387 4.8 39.7 1.0 CB A:GLU612 4.9 53.3 1.0

Zinc binding site 3 out of 4 in the The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn664 b:0.4 occ:1.00 OE2 A:GLU505 2.2 59.4 1.0 NE2 A:HIS498 2.4 61.9 1.0 CD A:GLU505 3.1 58.0 1.0 CE1 A:HIS498 3.2 62.5 1.0 OE1 A:GLU505 3.2 58.0 1.0 CD2 A:HIS498 3.3 61.1 1.0 O A:PRO499 4.2 48.6 1.0 ND1 A:HIS498 4.3 62.1 1.0 CG A:HIS498 4.4 60.4 1.0 CG A:GLU505 4.4 56.6 1.0

Zinc binding site 4 out of 4 in the The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of An Archaeal Cpsf Subunit, PH1404 From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn665 b:44.3 occ:1.00 NE2 A:HIS261 2.1 27.5 1.0 NE2 A:HIS618 2.2 29.9 1.0 OD1 A:ASP367 2.3 38.3 1.0 O3 A:SO4657 2.4 0.8 1.0 OD1 A:ASP260 2.8 40.7 1.0 CD2 A:HIS261 2.9 27.1 1.0 O2 A:SO4657 3.0 0.5 1.0 CE1 A:HIS618 3.0 30.6 1.0 CG A:ASP367 3.1 34.1 1.0 S A:SO4657 3.1 0.1 1.0 OD2 A:ASP367 3.2 34.9 1.0 CD2 A:HIS618 3.2 28.9 1.0 CE1 A:HIS261 3.3 27.2 1.0 OD2 A:ASP260 3.4 39.6 1.0 CG A:ASP260 3.5 37.0 1.0 O4 A:SO4657 3.5 0.1 1.0 ZN A:ZN662 3.7 48.8 1.0 CG A:HIS261 4.1 29.2 1.0 ND1 A:HIS618 4.2 29.8 1.0 NE2 A:HIS256 4.2 26.8 1.0 ND1 A:HIS261 4.3 27.9 1.0 CG A:HIS618 4.3 31.3 1.0 CE1 A:HIS256 4.3 29.2 1.0 O1 A:SO4657 4.5 1.0 1.0 CB A:ASP367 4.5 35.0 1.0 CE1 A:HIS594 4.5 30.8 1.0 CB A:ASP260 4.9 34.7 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