Zinc in PDB 4gem: Crystal Structure of Zucchini (K171A)

The structure of Crystal Structure of Zucchini (K171A), PDB code: 4gem was solved by H.Nishimasu, S.Fukuhara, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.85 / 2.21
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.883, 70.214, 56.938, 90.00, 108.76, 90.00
R / Rfree (%)	19 / 24.6

The binding sites of Zinc atom in the Crystal Structure of Zucchini (K171A) (pdb code 4gem). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Zucchini (K171A), PDB code: 4gem:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Zucchini (K171A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Zucchini (K171A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:33.8 occ:1.00 NE2 A:HIS67 2.4 31.4 1.0 SG A:CYS83 2.5 37.4 1.0 SG A:CYS63 2.6 32.4 1.0 SG A:CYS88 2.6 37.6 1.0 CD2 A:HIS67 3.0 30.5 1.0 CB A:CYS88 3.1 26.5 1.0 CB A:CYS63 3.3 26.1 1.0 CB A:CYS83 3.4 46.2 1.0 CE1 A:HIS67 3.5 43.0 1.0 O A:HOH427 3.5 50.4 1.0 CA A:CYS88 4.1 29.5 1.0 CG A:HIS67 4.2 43.1 1.0 O A:HOH431 4.3 30.8 1.0 CB A:ASN85 4.3 37.1 1.0 ND1 A:HIS67 4.4 39.4 1.0 O A:CYS63 4.6 31.0 1.0 CA A:CYS63 4.6 28.4 1.0 ND2 A:ASN85 4.7 23.9 1.0 CA A:CYS83 4.8 44.3 1.0 C A:CYS63 4.8 31.9 1.0 NH2 A:ARG91 4.9 52.3 1.0 C A:CYS88 4.9 34.2 1.0 O A:ASN85 5.0 39.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Zucchini (K171A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Zucchini (K171A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:32.8 occ:1.00 NE2 B:HIS67 2.5 36.8 1.0 SG B:CYS63 2.5 27.0 1.0 SG B:CYS83 2.6 31.8 1.0 SG B:CYS88 2.7 29.5 1.0 CB B:CYS88 3.1 24.5 1.0 CD2 B:HIS67 3.1 41.0 1.0 CB B:CYS83 3.2 39.3 1.0 CB B:CYS63 3.5 32.9 1.0 CE1 B:HIS67 3.5 37.6 1.0 O B:HOH443 3.9 23.1 1.0 O B:HOH419 4.0 34.7 1.0 CA B:CYS88 4.2 26.1 1.0 CG B:HIS67 4.4 51.8 1.0 O B:CYS63 4.4 38.0 1.0 CB B:ASN85 4.5 29.4 1.0 ND1 B:HIS67 4.5 50.6 1.0 CA B:CYS83 4.7 26.6 1.0 CG2 B:VAL66 4.7 47.4 1.0 CA B:CYS63 4.7 31.2 1.0 C B:CYS63 4.8 42.0 1.0 ND2 B:ASN85 4.8 28.3 1.0 O B:ASN85 5.0 23.0 1.0

H.Nishimasu, H.Ishizu, K.Saito, S.Fukuhara, M.K.Kamatani, L.Bonnefond, N.Matsumoto, T.Nishizawa, K.Nakanaga, J.Aoki, R.Ishitani, H.Siomi, M.C.Siomi, O.Nureki. Structure and Function of Zucchini Endoribonuclease in Pirna Biogenesis Nature V. 491 284 2012.
ISSN: ISSN 0028-0836
PubMed: 23064230
DOI: 10.1038/NATURE11509