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Zinc in PDB 1yt3: Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing

Enzymatic activity of Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing

All present enzymatic activity of Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing:
3.1.26.3;

Protein crystallography data

The structure of Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing, PDB code: 1yt3 was solved by Y.Zuo, Y.Wang, A.Malhotra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.95 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.000, 80.100, 103.700, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 21.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing (pdb code 1yt3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing, PDB code: 1yt3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1yt3

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Zinc binding site 1 out of 6 in the Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing


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 Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:15.6
occ:0.70
 ZN A:ZN1001 0.0 15.6 0.7
ZN A:ZN1001 1.4 14.6 0.3
OD2 A:ASP155 1.9 22.7 1.0
OD2 A:ASP28 1.9 16.0 0.7
O A:HOH1184 1.9 25.2 1.0
OE2 A:GLU30 2.1 18.5 1.0
CG A:ASP155 2.9 18.4 1.0
OD2 A:ASP28 2.9 19.4 0.3
CG A:ASP28 3.0 16.4 0.7
CD A:GLU30 3.1 18.9 1.0
CG A:ASP28 3.2 16.5 0.3
OD1 A:ASP28 3.3 16.5 0.3
OD1 A:ASP28 3.3 16.0 0.7
CB A:ASP155 3.4 17.1 1.0
OE1 A:GLU30 3.5 17.6 1.0
O A:HOH1185 3.7 30.6 1.0
NE2 A:GLN45 3.8 14.8 1.0
O A:THR29 3.8 14.3 1.0
O A:HOH1178 3.8 23.0 1.0
OD1 A:ASP155 4.0 20.5 1.0
CE2 A:TYR151 4.2 28.1 1.0
CB A:ASP28 4.3 14.8 1.0
O A:HOH1177 4.3 30.8 1.0
OH A:TYR151 4.4 30.4 1.0
CG A:GLU30 4.4 16.9 1.0
O A:HOH1188 4.6 20.2 1.0
CZ A:TYR151 4.6 28.7 1.0
C A:THR29 4.7 12.4 1.0
CA A:ASP155 4.9 15.3 1.0
N A:THR29 4.9 12.7 1.0
CD A:GLN45 5.0 12.7 1.0

Zinc binding site 2 out of 6 in 1yt3

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Zinc binding site 2 out of 6 in the Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing


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 Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:14.6
occ:0.30
 ZN A:ZN1001 0.0 14.6 0.3
ZN A:ZN1001 1.4 15.6 0.7
OE2 A:GLU30 1.7 18.5 1.0
OD2 A:ASP155 2.0 22.7 1.0
CD A:GLU30 2.6 18.9 1.0
O A:HOH1184 2.7 25.2 1.0
OE1 A:GLU30 2.8 17.6 1.0
CE2 A:TYR151 2.8 28.1 1.0
O A:HOH1185 3.0 30.6 1.0
OD2 A:ASP28 3.2 16.0 0.7
CG A:ASP155 3.2 18.4 1.0
OH A:TYR151 3.4 30.4 1.0
CZ A:TYR151 3.5 28.7 1.0
CD2 A:TYR151 3.7 25.8 1.0
CG A:GLU30 4.0 16.9 1.0
CB A:ASP155 4.0 17.1 1.0
OD1 A:ASP155 4.1 20.5 1.0
NE2 A:GLN45 4.2 14.8 1.0
O A:HOH1177 4.3 30.8 1.0
OD2 A:ASP28 4.3 19.4 0.3
CG A:ASP28 4.3 16.4 0.7
O A:THR29 4.3 14.3 1.0
CG A:ASP28 4.6 16.5 0.3
CA A:ALA152 4.6 15.3 1.0
OD1 A:ASP28 4.6 16.5 0.3
CE1 A:TYR151 4.7 29.4 1.0
OD1 A:ASP28 4.7 16.0 0.7
O A:HOH1178 4.7 23.0 1.0
O A:TYR151 4.8 17.9 1.0
CG A:TYR151 4.9 25.1 1.0

Zinc binding site 3 out of 6 in 1yt3

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Zinc binding site 3 out of 6 in the Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:31.6
occ:0.50
 O A:HOH1181 1.7 22.6 1.0
O A:HOH1188 2.1 20.2 1.0
OD2 A:ASP85 2.2 19.9 1.0
OD1 A:ASP28 2.6 16.0 0.7
OD1 A:ASP85 2.6 19.7 1.0
OD1 A:ASP28 2.6 16.5 0.3
CG A:ASP85 2.7 19.1 1.0
O A:HOH1180 2.9 36.2 1.0
O A:HOH1189 3.6 30.7 1.0
CG A:ASP28 3.6 16.5 0.3
CG A:ASP28 3.8 16.4 0.7
O A:HOH1184 3.8 25.2 1.0
O A:ALA81 4.1 15.1 1.0
OD2 A:ASP28 4.1 19.4 0.3
O A:HOH1182 4.1 12.5 1.0
O A:HIS80 4.2 14.9 1.0
CB A:ASP85 4.2 14.7 1.0
N A:THR29 4.3 12.7 1.0
O A:THR29 4.4 14.3 1.0
O A:HOH1179 4.6 25.4 1.0
CA A:ASP28 4.6 12.9 1.0
OG1 A:THR29 4.6 14.9 1.0
OD2 A:ASP28 4.6 16.0 0.7
O A:HOH1178 4.6 23.0 1.0
CB A:ASP28 4.7 14.8 1.0
CA A:GLY82 4.9 16.6 1.0
C A:ALA81 4.9 13.8 1.0
C A:ASP28 5.0 11.5 1.0

Zinc binding site 4 out of 6 in 1yt3

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Zinc binding site 4 out of 6 in the Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:88.3
occ:1.00
 O A:HOH1410 2.0 23.2 1.0
O A:HOH1412 2.3 44.3 1.0
O A:HOH1411 3.1 37.8 1.0
O A:HOH1409 3.8 16.6 1.0
OG A:SER14 3.9 17.4 0.5
O A:SER14 4.1 15.1 1.0
CA A:LEU15 4.1 14.9 1.0
O A:HOH1415 4.3 27.5 1.0
C A:SER14 4.3 16.0 1.0
N A:LEU15 4.3 15.5 1.0
OE1 A:GLN4 4.3 27.2 1.0
CB A:ALA18 4.6 17.6 1.0
CD2 A:HIS51 4.7 21.3 1.0
CB A:SER14 4.8 17.3 1.0
NE2 A:GLN4 4.8 31.1 1.0
CD1 A:LEU15 4.9 15.7 1.0
CB A:LEU15 4.9 15.8 1.0

Zinc binding site 5 out of 6 in 1yt3

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Zinc binding site 5 out of 6 in the Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1004

b:86.7
occ:1.00
 O A:HOH1011 2.0 22.5 1.0
O A:HOH1013 2.3 31.5 1.0
O A:HOH1488 2.3 40.9 1.0
O A:HOH1012 2.4 42.5 1.0
NZ A:LYS227 3.7 17.8 1.0
NE1 A:TRP223 3.9 15.3 1.0
CE A:LYS227 4.1 16.0 1.0
OG1 A:THR274 4.4 18.0 1.0
O A:HOH1010 4.4 34.1 1.0
CD1 A:TRP223 4.4 13.8 1.0
O A:HOH1014 4.8 19.3 1.0
CG2 A:THR274 4.8 16.3 1.0

Zinc binding site 6 out of 6 in 1yt3

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Zinc binding site 6 out of 6 in the Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1005

b:63.0
occ:0.50
 OE1 A:GLU17 2.0 30.6 0.5
CD A:GLU17 2.5 29.1 0.5
OE2 A:GLU17 2.7 31.4 0.5
O A:HOH1416 3.0 35.4 1.0
CG A:GLU17 3.7 26.8 0.5
OG A:SER14 3.9 20.3 0.6
CA A:SER14 4.1 16.3 1.0
N A:SER14 4.1 17.1 1.0
C A:ALA13 4.2 17.2 1.0
O A:ALA13 4.3 17.8 1.0
CB A:ALA13 4.4 17.8 1.0
CB A:SER14 4.6 17.3 1.0
CB A:GLU17 4.8 24.6 1.0
CA A:ALA13 5.0 17.6 1.0

Reference:

Y.Zuo, Y.Wang, A.Malhotra. Crystal Structure of Escherichia Coli Rnase D, An Exoribonuclease Involved in Structured Rna Processing Structure V. 13 973 2005.
ISSN: ISSN 0969-2126
PubMed: 16004870
DOI: 10.1016/J.STR.2005.04.015
Page generated: Wed Oct 16 21:04:26 2024

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