Zinc in PDB 5fbd: S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine
Enzymatic activity of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine
All present enzymatic activity of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine:
3.1.30.1;
Protein crystallography data
The structure of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine, PDB code: 5fbd
was solved by
T.Koval,
L.H.Oestergaard,
J.Dohnalek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.08 /
1.75
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
43.040,
62.426,
84.118,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.2 /
21.2
|
Zinc Binding Sites:
The binding sites of Zinc atom in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine
(pdb code 5fbd). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the
S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine, PDB code: 5fbd:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 5fbd
Go back to
Zinc Binding Sites List in 5fbd
Zinc binding site 1 out
of 3 in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:6.3
occ:1.00
|
O1
|
A:PO4601
|
2.0
|
10.9
|
1.0
|
N
|
A:TRP21
|
2.1
|
7.0
|
1.0
|
NE2
|
A:HIS26
|
2.1
|
5.2
|
1.0
|
OD1
|
A:ASP139
|
2.1
|
5.2
|
1.0
|
O
|
A:TRP21
|
2.2
|
6.6
|
1.0
|
C
|
A:TRP21
|
2.9
|
6.7
|
1.0
|
CA
|
A:TRP21
|
3.0
|
6.8
|
1.0
|
CE1
|
A:HIS26
|
3.0
|
5.6
|
1.0
|
CD2
|
A:HIS26
|
3.1
|
5.6
|
1.0
|
CG
|
A:ASP139
|
3.2
|
4.8
|
1.0
|
P
|
A:PO4601
|
3.3
|
10.4
|
1.0
|
OD2
|
A:ASP139
|
3.5
|
4.9
|
1.0
|
O
|
A:HOH1002
|
3.6
|
4.2
|
0.5
|
ZN
|
A:ZN402
|
3.7
|
5.7
|
1.0
|
O2
|
A:PO4601
|
3.7
|
8.7
|
1.0
|
CB
|
A:TRP21
|
3.8
|
6.7
|
1.0
|
OD2
|
A:ASP65
|
3.9
|
6.1
|
1.0
|
NE2
|
A:HIS135
|
4.1
|
4.5
|
1.0
|
ND1
|
A:HIS26
|
4.1
|
5.8
|
1.0
|
O4
|
A:PO4601
|
4.2
|
10.1
|
1.0
|
NE2
|
A:HIS145
|
4.2
|
6.7
|
1.0
|
CG
|
A:HIS26
|
4.2
|
5.8
|
1.0
|
O3
|
A:PO4601
|
4.2
|
9.6
|
1.0
|
N
|
A:GLY22
|
4.2
|
6.7
|
1.0
|
CE1
|
A:HIS145
|
4.2
|
6.5
|
1.0
|
CE1
|
A:HIS135
|
4.3
|
4.5
|
1.0
|
ZN
|
A:ZN403
|
4.3
|
8.8
|
1.0
|
OD2
|
A:ASP172
|
4.4
|
9.4
|
1.0
|
OD1
|
A:ASP172
|
4.4
|
9.0
|
1.0
|
CB
|
A:ASP139
|
4.5
|
4.9
|
1.0
|
CG
|
A:TRP21
|
4.5
|
6.8
|
1.0
|
CD1
|
A:TRP21
|
4.6
|
6.4
|
1.0
|
CG
|
A:ASP172
|
4.6
|
8.8
|
1.0
|
CA
|
A:ASP139
|
4.6
|
4.9
|
1.0
|
O
|
A:HOH1134
|
4.8
|
18.6
|
1.0
|
CG
|
A:ASP65
|
4.8
|
6.3
|
1.0
|
OD1
|
A:ASP65
|
4.9
|
5.8
|
1.0
|
O
|
A:GLY22
|
4.9
|
6.2
|
1.0
|
O
|
A:HOH1122
|
5.0
|
17.5
|
1.0
|
CA
|
A:GLY22
|
5.0
|
6.5
|
1.0
|
|
Zinc binding site 2 out
of 3 in 5fbd
Go back to
Zinc Binding Sites List in 5fbd
Zinc binding site 2 out
of 3 in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:5.7
occ:1.00
|
ND1
|
A:HIS80
|
2.0
|
3.9
|
1.0
|
O2
|
A:PO4601
|
2.0
|
8.7
|
1.0
|
OD2
|
A:ASP139
|
2.0
|
4.9
|
1.0
|
NE2
|
A:HIS135
|
2.2
|
4.5
|
1.0
|
OD1
|
A:ASP65
|
2.3
|
5.8
|
1.0
|
CE1
|
A:HIS80
|
2.8
|
3.9
|
1.0
|
CD2
|
A:HIS135
|
3.1
|
4.7
|
1.0
|
CG
|
A:ASP139
|
3.1
|
4.8
|
1.0
|
CG
|
A:HIS80
|
3.1
|
4.1
|
1.0
|
P
|
A:PO4601
|
3.2
|
10.4
|
1.0
|
CE1
|
A:HIS135
|
3.2
|
4.5
|
1.0
|
CG
|
A:ASP65
|
3.2
|
6.3
|
1.0
|
OD2
|
A:ASP65
|
3.4
|
6.1
|
1.0
|
OD1
|
A:ASP139
|
3.5
|
5.2
|
1.0
|
O1
|
A:PO4601
|
3.5
|
10.9
|
1.0
|
CB
|
A:HIS80
|
3.6
|
4.5
|
1.0
|
ZN
|
A:ZN401
|
3.7
|
6.3
|
1.0
|
O4
|
A:PO4601
|
3.8
|
10.1
|
1.0
|
NZ
|
A:LYS68
|
3.8
|
6.4
|
1.0
|
NE2
|
A:HIS80
|
4.0
|
3.8
|
1.0
|
CD2
|
A:HIS80
|
4.2
|
3.9
|
1.0
|
CG
|
A:HIS135
|
4.2
|
4.5
|
1.0
|
NE2
|
A:HIS26
|
4.2
|
5.2
|
1.0
|
ND1
|
A:HIS135
|
4.3
|
4.7
|
1.0
|
O3
|
A:PO4601
|
4.4
|
9.6
|
1.0
|
CE1
|
A:HIS145
|
4.4
|
6.5
|
1.0
|
CB
|
A:ASP139
|
4.4
|
4.9
|
1.0
|
CE1
|
A:HIS26
|
4.5
|
5.6
|
1.0
|
CB
|
A:ASP65
|
4.6
|
6.3
|
1.0
|
CA
|
A:HIS80
|
4.6
|
4.7
|
1.0
|
O
|
A:HOH1002
|
4.8
|
4.2
|
0.5
|
CA
|
A:ASP65
|
5.0
|
6.3
|
1.0
|
|
Zinc binding site 3 out
of 3 in 5fbd
Go back to
Zinc Binding Sites List in 5fbd
Zinc binding site 3 out
of 3 in the S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of S1 Nuclease From Aspergillus Oryzae in Complex with Phosphate and 2'- Deoxycytidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn403
b:8.8
occ:1.00
|
O3
|
A:PO4601
|
1.9
|
9.6
|
1.0
|
OD2
|
A:ASP172
|
2.0
|
9.4
|
1.0
|
NE2
|
A:HIS145
|
2.1
|
6.7
|
1.0
|
NE2
|
A:HIS168
|
2.1
|
9.0
|
1.0
|
CG
|
A:ASP172
|
2.7
|
8.8
|
1.0
|
OD1
|
A:ASP172
|
2.8
|
9.0
|
1.0
|
O1
|
A:PO4601
|
2.9
|
10.9
|
1.0
|
CE1
|
A:HIS145
|
2.9
|
6.5
|
1.0
|
CE1
|
A:HIS168
|
3.0
|
9.2
|
1.0
|
P
|
A:PO4601
|
3.0
|
10.4
|
1.0
|
CD2
|
A:HIS168
|
3.1
|
9.5
|
1.0
|
CD2
|
A:HIS145
|
3.1
|
6.5
|
1.0
|
C1'
|
A:DCZ701
|
3.9
|
14.3
|
1.0
|
O4'
|
A:DCZ701
|
3.9
|
14.6
|
1.0
|
O4
|
A:PO4601
|
4.1
|
10.1
|
1.0
|
ND1
|
A:HIS145
|
4.1
|
6.4
|
1.0
|
O2
|
A:PO4601
|
4.1
|
8.7
|
1.0
|
N
|
A:TRP21
|
4.1
|
7.0
|
1.0
|
CB
|
A:ASP172
|
4.1
|
9.3
|
1.0
|
ND1
|
A:HIS168
|
4.1
|
9.0
|
1.0
|
CG
|
A:HIS145
|
4.2
|
6.2
|
1.0
|
CG
|
A:HIS168
|
4.2
|
8.8
|
1.0
|
C4'
|
A:DCZ701
|
4.2
|
15.8
|
1.0
|
O
|
A:HOH1134
|
4.3
|
18.6
|
1.0
|
ZN
|
A:ZN401
|
4.3
|
6.3
|
1.0
|
C2'
|
A:DCZ701
|
4.5
|
13.7
|
1.0
|
O2
|
A:DCZ701
|
4.5
|
12.9
|
1.0
|
NE2
|
A:GLN142
|
4.6
|
6.7
|
1.0
|
O
|
A:HOH1274
|
4.6
|
24.9
|
1.0
|
O
|
A:HOH1307
|
4.7
|
21.5
|
1.0
|
OD1
|
A:ASP139
|
4.8
|
5.2
|
1.0
|
O
|
A:TRP21
|
4.8
|
6.6
|
1.0
|
C3'
|
A:DCZ701
|
5.0
|
14.6
|
1.0
|
CA
|
A:TRP21
|
5.0
|
6.8
|
1.0
|
|
Reference:
T.Koval,
L.H.Stergaard,
J.Lehmbeck,
A.Nrgaard,
P.Lipovova,
J.Duskova,
T.Skalova,
M.Trundova,
P.Kolenko,
K.Fejfarova,
J.Stransky,
L.Svecova,
J.Hasek,
J.Dohnalek.
Structural and Catalytic Properties of S1 Nuclease From Aspergillus Oryzae Responsible For Substrate Recognition, Cleavage, Non-Specificity, and Inhibition. Plos One V. 11 68832 2016.
ISSN: ESSN 1932-6203
PubMed: 28036383
DOI: 10.1371/JOURNAL.PONE.0168832
Page generated: Sun Oct 27 15:59:41 2024
|