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Zinc in PDB 4gel: Crystal Structure of Zucchini

Protein crystallography data

The structure of Crystal Structure of Zucchini, PDB code: 4gel 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) 42.81 / 1.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.994, 71.172, 56.318, 90.00, 107.90, 90.00
R / Rfree (%) 18.7 / 23

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Zucchini (pdb code 4gel). 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, PDB code: 4gel:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4gel

Go back to Zinc Binding Sites List in 4gel
Zinc binding site 1 out of 2 in the Crystal Structure of Zucchini


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:22.2
occ:1.00
NE2 A:HIS67 2.2 24.6 1.0
SG A:CYS63 2.4 22.9 1.0
SG A:CYS83 2.4 21.5 1.0
SG A:CYS88 2.4 19.5 1.0
CD2 A:HIS67 3.1 32.7 1.0
CB A:CYS88 3.2 17.6 1.0
CE1 A:HIS67 3.2 25.8 1.0
CB A:CYS63 3.3 27.0 1.0
CB A:CYS83 3.3 23.5 1.0
CA A:CYS88 4.2 20.7 1.0
CG A:HIS67 4.3 30.1 1.0
ND1 A:HIS67 4.3 24.0 1.0
CB A:ASN85 4.4 21.5 1.0
O A:HOH402 4.4 32.1 1.0
O A:CYS63 4.5 34.3 1.0
CA A:CYS63 4.6 32.1 1.0
CA A:CYS83 4.7 20.8 1.0
ND2 A:ASN85 4.7 22.5 1.0
C A:CYS63 4.8 34.4 1.0

Zinc binding site 2 out of 2 in 4gel

Go back to Zinc Binding Sites List in 4gel
Zinc binding site 2 out of 2 in the Crystal Structure of Zucchini


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:20.6
occ:1.00
NE2 B:HIS67 2.2 23.6 1.0
SG B:CYS63 2.4 20.2 1.0
SG B:CYS83 2.4 24.7 1.0
SG B:CYS88 2.4 18.3 1.0
CD2 B:HIS67 3.1 20.9 1.0
CB B:CYS88 3.2 22.6 1.0
CE1 B:HIS67 3.2 26.8 1.0
CB B:CYS63 3.3 23.7 1.0
CB B:CYS83 3.3 29.9 1.0
CA B:CYS88 4.2 18.8 1.0
CG B:HIS67 4.2 19.8 1.0
ND1 B:HIS67 4.3 26.1 1.0
CB B:ASN85 4.4 24.0 1.0
O B:HOH467 4.5 29.0 1.0
CA B:CYS63 4.6 21.8 1.0
ND2 B:ASN85 4.7 20.8 1.0
CA B:CYS83 4.7 33.2 1.0
O B:CYS63 4.7 19.2 1.0
C B:CYS63 4.9 20.8 1.0

Reference:

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
Page generated: Sat Oct 26 23:15:25 2024

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