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Zinc in PDB 1y44: Crystal Structure of Rnase Z

Enzymatic activity of Crystal Structure of Rnase Z

All present enzymatic activity of Crystal Structure of Rnase Z:
3.1.26.11;

Protein crystallography data

The structure of Crystal Structure of Rnase Z, PDB code: 1y44 was solved by I.L.De La Sierra-Gallay, O.Pellegrini, C.Condon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.78 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 42.980, 188.330, 177.910, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 24.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rnase Z (pdb code 1y44). 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 Rnase Z, PDB code: 1y44:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1y44

Go back to Zinc Binding Sites List in 1y44
Zinc binding site 1 out of 2 in the Crystal Structure of Rnase Z


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 Rnase Z within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:38.4
occ:1.00
O A:HOH1007 2.0 33.8 1.0
OD2 A:ASP211 2.2 29.4 1.0
ND1 A:HIS65 2.2 31.6 1.0
NE2 A:HIS140 2.3 39.2 1.0
O2 A:PO4945 2.3 61.9 1.0
NE2 A:HIS63 2.4 32.2 1.0
CE1 A:HIS140 3.0 38.7 1.0
CE1 A:HIS65 3.2 34.5 1.0
CG A:ASP211 3.2 28.2 1.0
CD2 A:HIS63 3.2 30.4 1.0
CG A:HIS65 3.3 33.9 1.0
ZN A:ZN401 3.3 40.3 1.0
P A:PO4945 3.3 65.9 1.0
CD2 A:HIS140 3.3 36.7 1.0
CE1 A:HIS63 3.4 33.6 1.0
CB A:ASP211 3.5 26.8 1.0
CB A:HIS65 3.6 32.7 1.0
O4 A:PO4945 3.6 63.7 1.0
O3 A:PO4945 3.7 63.0 1.0
ND1 A:HIS140 4.2 37.4 1.0
NE2 A:HIS68 4.3 29.4 1.0
OD1 A:ASP211 4.3 27.0 1.0
NE2 A:HIS65 4.3 33.8 1.0
CG A:HIS140 4.3 37.2 1.0
CG A:HIS63 4.3 30.4 1.0
CD2 A:HIS65 4.4 33.5 1.0
ND1 A:HIS63 4.4 31.5 1.0
CD2 A:HIS68 4.4 28.9 1.0
CE1 A:HIS247 4.5 37.5 1.0
OD1 A:ASP67 4.5 26.0 1.0
O1 A:PO4945 4.6 65.2 1.0

Zinc binding site 2 out of 2 in 1y44

Go back to Zinc Binding Sites List in 1y44
Zinc binding site 2 out of 2 in the Crystal Structure of Rnase Z


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 Rnase Z within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:40.3
occ:1.00
OD2 A:ASP211 2.2 29.4 1.0
NE2 A:HIS68 2.3 29.4 1.0
NE2 A:HIS269 2.3 35.3 1.0
O A:HOH1007 2.3 33.8 1.0
OD2 A:ASP67 2.5 27.0 1.0
O3 A:PO4945 2.5 63.0 1.0
CG A:ASP211 3.0 28.2 1.0
CD2 A:HIS68 3.1 28.9 1.0
OD1 A:ASP211 3.2 27.0 1.0
CE1 A:HIS269 3.2 34.6 1.0
CD2 A:HIS269 3.2 34.8 1.0
CG A:ASP67 3.3 27.1 1.0
ZN A:ZN400 3.3 38.4 1.0
CE1 A:HIS68 3.4 30.8 1.0
OD1 A:ASP67 3.4 26.0 1.0
P A:PO4945 3.6 65.9 1.0
O2 A:PO4945 3.7 61.9 1.0
O A:HOH949 4.1 30.6 1.0
NE2 A:HIS63 4.1 32.2 1.0
O4 A:PO4945 4.2 63.7 1.0
CE1 A:HIS63 4.2 33.6 1.0
CG A:HIS68 4.3 29.1 1.0
ND1 A:HIS269 4.3 35.3 1.0
CG A:HIS269 4.4 34.4 1.0
ND1 A:HIS68 4.4 30.9 1.0
CB A:ASP211 4.5 26.8 1.0
CE1 A:HIS247 4.5 37.5 1.0
N A:GLY11 4.5 33.0 1.0
CB A:ASP67 4.7 24.5 1.0
O1 A:PO4945 4.8 65.2 1.0
OG1 A:THR20 4.9 30.1 1.0

Reference:

I.L.De La Sierra-Gallay, O.Pellegrini, C.Condon. Structural Basis For Substrate Binding, Cleavage and Allostery in the Trna Maturase Rnase Z. Nature V. 433 657 2005.
ISSN: ISSN 0028-0836
PubMed: 15654328
DOI: 10.1038/NATURE03284
Page generated: Wed Dec 16 03:13:39 2020

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