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
Go back to
Zinc Binding Sites List in 1yt3
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
Go back to
Zinc Binding Sites List in 1yt3
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
Go back to
Zinc Binding Sites List in 1yt3
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
Go back to
Zinc Binding Sites List in 1yt3
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
Go back to
Zinc Binding Sites List in 1yt3
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
Go back to
Zinc Binding Sites List in 1yt3
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
|