Zinc in PDB 5fbg: S1 Nuclease From Aspergillus Oryzae, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine.
Enzymatic activity of S1 Nuclease From Aspergillus Oryzae, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine.
All present enzymatic activity of S1 Nuclease From Aspergillus Oryzae, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine.:
3.1.30.1;
Protein crystallography data
The structure of S1 Nuclease From Aspergillus Oryzae, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine., PDB code: 5fbg
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)
|
37.47 /
1.97
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.760,
106.760,
127.910,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
15.8 /
18.7
|
Zinc Binding Sites:
The binding sites of Zinc atom in the S1 Nuclease From Aspergillus Oryzae, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine.
(pdb code 5fbg). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
S1 Nuclease From Aspergillus Oryzae, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine., PDB code: 5fbg:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 5fbg
Go back to
Zinc Binding Sites List in 5fbg
Zinc binding site 1 out
of 6 in the S1 Nuclease From Aspergillus Oryzae, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine.
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, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:15.5
occ:1.00
|
O1
|
A:PO4601
|
1.8
|
19.2
|
1.0
|
NE2
|
A:HIS26
|
2.0
|
15.6
|
1.0
|
OD1
|
A:ASP139
|
2.1
|
13.5
|
1.0
|
N
|
A:TRP21
|
2.1
|
14.9
|
1.0
|
O
|
A:TRP21
|
2.2
|
14.3
|
1.0
|
C
|
A:TRP21
|
2.9
|
15.8
|
1.0
|
CA
|
A:TRP21
|
3.0
|
15.0
|
1.0
|
CE1
|
A:HIS26
|
3.0
|
15.6
|
1.0
|
CD2
|
A:HIS26
|
3.0
|
16.8
|
1.0
|
P
|
A:PO4601
|
3.1
|
17.1
|
1.0
|
CG
|
A:ASP139
|
3.2
|
12.4
|
1.0
|
O3
|
A:PO4601
|
3.4
|
26.9
|
1.0
|
ZN
|
A:ZN402
|
3.6
|
14.4
|
1.0
|
OD2
|
A:ASP139
|
3.7
|
12.0
|
1.0
|
CB
|
A:TRP21
|
3.7
|
15.1
|
1.0
|
CE1
|
A:HIS135
|
3.9
|
15.2
|
1.0
|
NE2
|
A:HIS135
|
3.9
|
14.1
|
1.0
|
O2
|
A:PO4601
|
4.0
|
15.7
|
1.0
|
ND1
|
A:HIS26
|
4.1
|
16.3
|
1.0
|
CG
|
A:HIS26
|
4.1
|
15.8
|
1.0
|
N
|
A:GLY22
|
4.2
|
14.9
|
1.0
|
ND2
|
A:ASN65
|
4.2
|
12.5
|
1.0
|
O4
|
A:PO4601
|
4.3
|
18.1
|
1.0
|
ZN
|
A:ZN403
|
4.3
|
18.5
|
1.0
|
NE2
|
A:HIS145
|
4.3
|
14.7
|
1.0
|
CE1
|
A:HIS145
|
4.3
|
14.3
|
1.0
|
CG
|
A:TRP21
|
4.4
|
16.4
|
1.0
|
CB
|
A:ASP139
|
4.5
|
13.6
|
1.0
|
OD1
|
A:ASP172
|
4.5
|
19.5
|
1.0
|
CD1
|
A:TRP21
|
4.6
|
15.7
|
1.0
|
OD2
|
A:ASP172
|
4.6
|
20.2
|
1.0
|
CA
|
A:ASP139
|
4.7
|
14.2
|
1.0
|
CG
|
A:ASP172
|
4.7
|
18.2
|
1.0
|
ND1
|
A:HIS135
|
4.9
|
14.1
|
1.0
|
O
|
A:GLY22
|
4.9
|
15.7
|
1.0
|
CA
|
A:GLY22
|
5.0
|
17.2
|
1.0
|
CD2
|
A:HIS135
|
5.0
|
13.6
|
1.0
|
|
Zinc binding site 2 out
of 6 in 5fbg
Go back to
Zinc Binding Sites List in 5fbg
Zinc binding site 2 out
of 6 in the S1 Nuclease From Aspergillus Oryzae, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine.
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, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:14.4
occ:1.00
|
ND1
|
A:HIS80
|
2.1
|
14.5
|
1.0
|
O2
|
A:PO4601
|
2.1
|
15.7
|
1.0
|
NE2
|
A:HIS135
|
2.1
|
14.1
|
1.0
|
OD2
|
A:ASP139
|
2.1
|
12.0
|
1.0
|
O1
|
A:PO4601
|
2.5
|
19.2
|
1.0
|
OD1
|
A:ASN65
|
2.6
|
11.9
|
1.0
|
P
|
A:PO4601
|
2.8
|
17.1
|
1.0
|
CE1
|
A:HIS80
|
2.9
|
15.8
|
1.0
|
CD2
|
A:HIS135
|
3.1
|
13.6
|
1.0
|
CG
|
A:ASP139
|
3.1
|
12.4
|
1.0
|
CE1
|
A:HIS135
|
3.1
|
15.2
|
1.0
|
CG
|
A:HIS80
|
3.2
|
14.8
|
1.0
|
OD1
|
A:ASP139
|
3.4
|
13.5
|
1.0
|
CG
|
A:ASN65
|
3.5
|
12.7
|
1.0
|
CB
|
A:HIS80
|
3.6
|
13.0
|
1.0
|
ZN
|
A:ZN401
|
3.6
|
15.5
|
1.0
|
ND2
|
A:ASN65
|
3.7
|
12.5
|
1.0
|
O4
|
A:PO4601
|
3.8
|
18.1
|
1.0
|
NZ
|
A:LYS68
|
3.9
|
13.2
|
1.0
|
O3
|
A:PO4601
|
4.1
|
26.9
|
1.0
|
NE2
|
A:HIS80
|
4.1
|
15.1
|
1.0
|
ND1
|
A:HIS135
|
4.2
|
14.1
|
1.0
|
CG
|
A:HIS135
|
4.2
|
12.9
|
1.0
|
CD2
|
A:HIS80
|
4.2
|
14.3
|
1.0
|
NE2
|
A:HIS26
|
4.4
|
15.6
|
1.0
|
CE1
|
A:HIS145
|
4.4
|
14.3
|
1.0
|
CB
|
A:ASP139
|
4.4
|
13.6
|
1.0
|
CA
|
A:HIS80
|
4.6
|
13.9
|
1.0
|
CE1
|
A:HIS26
|
4.7
|
15.6
|
1.0
|
CB
|
A:ASN65
|
4.9
|
12.9
|
1.0
|
O
|
A:HIS80
|
5.0
|
13.8
|
1.0
|
|
Zinc binding site 3 out
of 6 in 5fbg
Go back to
Zinc Binding Sites List in 5fbg
Zinc binding site 3 out
of 6 in the S1 Nuclease From Aspergillus Oryzae, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine.
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, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn403
b:18.5
occ:1.00
|
O3
|
A:PO4601
|
1.9
|
26.9
|
1.0
|
OD2
|
A:ASP172
|
2.1
|
20.2
|
1.0
|
NE2
|
A:HIS168
|
2.1
|
19.7
|
1.0
|
NE2
|
A:HIS145
|
2.1
|
14.7
|
1.0
|
OD1
|
A:ASP172
|
2.6
|
19.5
|
1.0
|
CG
|
A:ASP172
|
2.7
|
18.2
|
1.0
|
CE1
|
A:HIS145
|
3.0
|
14.3
|
1.0
|
CE1
|
A:HIS168
|
3.0
|
20.2
|
1.0
|
CD2
|
A:HIS168
|
3.1
|
19.5
|
1.0
|
CD2
|
A:HIS145
|
3.2
|
14.6
|
1.0
|
P
|
A:PO4601
|
3.3
|
17.1
|
1.0
|
O4'
|
A:DCZ701
|
3.7
|
27.4
|
1.0
|
N
|
A:TRP21
|
3.8
|
14.9
|
1.0
|
C1'
|
A:DCZ701
|
3.9
|
26.5
|
1.0
|
O1
|
A:PO4601
|
4.0
|
19.2
|
1.0
|
O
|
A:HOH1175
|
4.1
|
36.1
|
1.0
|
CB
|
A:ASP172
|
4.1
|
17.5
|
1.0
|
O4
|
A:PO4601
|
4.1
|
18.1
|
1.0
|
C4'
|
A:DCZ701
|
4.1
|
31.0
|
1.0
|
ND1
|
A:HIS145
|
4.1
|
15.3
|
1.0
|
O2
|
A:PO4601
|
4.1
|
15.7
|
1.0
|
ND1
|
A:HIS168
|
4.2
|
21.5
|
1.0
|
CG
|
A:HIS168
|
4.2
|
20.5
|
1.0
|
CG
|
A:HIS145
|
4.3
|
14.8
|
1.0
|
ZN
|
A:ZN401
|
4.3
|
15.5
|
1.0
|
NE2
|
A:GLN142
|
4.3
|
16.4
|
1.0
|
C2'
|
A:DCZ701
|
4.5
|
27.4
|
1.0
|
O2
|
A:DCZ701
|
4.6
|
20.0
|
1.0
|
CA
|
A:TRP21
|
4.7
|
15.0
|
1.0
|
O
|
A:HOH1234
|
4.7
|
36.5
|
1.0
|
O
|
A:TRP21
|
4.7
|
14.3
|
1.0
|
OD1
|
A:ASP139
|
4.7
|
13.5
|
1.0
|
C
|
A:TRP21
|
4.8
|
15.8
|
1.0
|
O5'
|
A:DCZ701
|
4.9
|
29.6
|
1.0
|
C3'
|
A:DCZ701
|
5.0
|
29.6
|
1.0
|
|
Zinc binding site 4 out
of 6 in 5fbg
Go back to
Zinc Binding Sites List in 5fbg
Zinc binding site 4 out
of 6 in the S1 Nuclease From Aspergillus Oryzae, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of S1 Nuclease From Aspergillus Oryzae, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:13.8
occ:1.00
|
O3
|
B:PO4601
|
2.0
|
14.2
|
1.0
|
NE2
|
B:HIS26
|
2.0
|
13.7
|
1.0
|
OD1
|
B:ASP139
|
2.0
|
10.5
|
1.0
|
N
|
B:TRP21
|
2.1
|
14.2
|
1.0
|
O
|
B:TRP21
|
2.2
|
12.9
|
1.0
|
O2
|
B:PO4601
|
2.9
|
13.5
|
1.0
|
C
|
B:TRP21
|
2.9
|
13.7
|
1.0
|
CA
|
B:TRP21
|
2.9
|
13.0
|
1.0
|
P
|
B:PO4601
|
3.0
|
15.8
|
1.0
|
CE1
|
B:HIS26
|
3.0
|
13.9
|
1.0
|
CD2
|
B:HIS26
|
3.0
|
14.4
|
1.0
|
CG
|
B:ASP139
|
3.1
|
12.3
|
1.0
|
ZN
|
B:ZN402
|
3.5
|
14.7
|
1.0
|
CB
|
B:TRP21
|
3.7
|
12.7
|
1.0
|
OD2
|
B:ASP139
|
3.7
|
12.4
|
1.0
|
CE1
|
B:HIS135
|
3.9
|
16.2
|
1.0
|
NE2
|
B:HIS135
|
4.0
|
15.9
|
1.0
|
O1
|
B:PO4601
|
4.0
|
14.1
|
1.0
|
O4
|
B:PO4601
|
4.1
|
15.4
|
1.0
|
ND1
|
B:HIS26
|
4.1
|
13.1
|
1.0
|
CG
|
B:HIS26
|
4.1
|
13.3
|
1.0
|
N
|
B:GLY22
|
4.2
|
15.2
|
1.0
|
ND2
|
B:ASN65
|
4.3
|
17.1
|
1.0
|
CE1
|
B:HIS145
|
4.3
|
11.9
|
1.0
|
NE2
|
B:HIS145
|
4.4
|
11.4
|
1.0
|
CG
|
B:TRP21
|
4.4
|
13.5
|
1.0
|
CB
|
B:ASP139
|
4.4
|
11.9
|
1.0
|
ZN
|
B:ZN403
|
4.5
|
15.1
|
1.0
|
OD1
|
B:ASP172
|
4.5
|
14.8
|
1.0
|
CD1
|
B:TRP21
|
4.5
|
14.3
|
1.0
|
CA
|
B:ASP139
|
4.7
|
12.5
|
1.0
|
OD2
|
B:ASP172
|
4.8
|
16.1
|
1.0
|
CG
|
B:ASP172
|
4.8
|
15.8
|
1.0
|
O
|
B:GLY22
|
4.9
|
14.9
|
1.0
|
O
|
B:HOH1137
|
4.9
|
28.7
|
1.0
|
ND1
|
B:HIS135
|
4.9
|
14.3
|
1.0
|
CA
|
B:GLY22
|
5.0
|
15.0
|
1.0
|
|
Zinc binding site 5 out
of 6 in 5fbg
Go back to
Zinc Binding Sites List in 5fbg
Zinc binding site 5 out
of 6 in the S1 Nuclease From Aspergillus Oryzae, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of S1 Nuclease From Aspergillus Oryzae, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:14.7
occ:1.00
|
NE2
|
B:HIS135
|
2.1
|
15.9
|
1.0
|
OD2
|
B:ASP139
|
2.1
|
12.4
|
1.0
|
O3
|
B:PO4601
|
2.1
|
14.2
|
1.0
|
ND1
|
B:HIS80
|
2.1
|
17.0
|
1.0
|
O1
|
B:PO4601
|
2.2
|
14.1
|
1.0
|
P
|
B:PO4601
|
2.7
|
15.8
|
1.0
|
OD1
|
B:ASN65
|
2.8
|
16.6
|
1.0
|
CE1
|
B:HIS80
|
3.0
|
17.1
|
1.0
|
CG
|
B:ASP139
|
3.0
|
12.3
|
1.0
|
CD2
|
B:HIS135
|
3.1
|
14.8
|
1.0
|
CE1
|
B:HIS135
|
3.1
|
16.2
|
1.0
|
CG
|
B:HIS80
|
3.2
|
16.4
|
1.0
|
OD1
|
B:ASP139
|
3.3
|
10.5
|
1.0
|
ZN
|
B:ZN401
|
3.5
|
13.8
|
1.0
|
CB
|
B:HIS80
|
3.6
|
15.0
|
1.0
|
CG
|
B:ASN65
|
3.7
|
17.2
|
1.0
|
O4
|
B:PO4601
|
3.8
|
15.4
|
1.0
|
ND2
|
B:ASN65
|
3.9
|
17.1
|
1.0
|
O2
|
B:PO4601
|
3.9
|
13.5
|
1.0
|
NZ
|
B:LYS68
|
4.1
|
16.5
|
1.0
|
NE2
|
B:HIS80
|
4.1
|
17.7
|
1.0
|
ND1
|
B:HIS135
|
4.2
|
14.3
|
1.0
|
NE2
|
B:HIS26
|
4.2
|
13.7
|
1.0
|
CG
|
B:HIS135
|
4.2
|
14.1
|
1.0
|
CD2
|
B:HIS80
|
4.3
|
17.8
|
1.0
|
CE1
|
B:HIS145
|
4.3
|
11.9
|
1.0
|
CB
|
B:ASP139
|
4.4
|
11.9
|
1.0
|
CE1
|
B:HIS26
|
4.5
|
13.9
|
1.0
|
CA
|
B:HIS80
|
4.6
|
15.4
|
1.0
|
O
|
B:HOH1027
|
4.7
|
24.8
|
1.0
|
|
Zinc binding site 6 out
of 6 in 5fbg
Go back to
Zinc Binding Sites List in 5fbg
Zinc binding site 6 out
of 6 in the S1 Nuclease From Aspergillus Oryzae, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of S1 Nuclease From Aspergillus Oryzae, Mutant D65N, in Complex with Phosphate, 2'-Deoxycytidine and 2'-Deoxyguanosine. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn403
b:15.1
occ:1.00
|
O2
|
B:PO4601
|
2.0
|
13.5
|
1.0
|
OD2
|
B:ASP172
|
2.1
|
16.1
|
1.0
|
NE2
|
B:HIS168
|
2.1
|
11.1
|
1.0
|
NE2
|
B:HIS145
|
2.2
|
11.4
|
1.0
|
O
|
B:HOH1034
|
2.2
|
18.3
|
1.0
|
OD1
|
B:ASP172
|
2.7
|
14.8
|
1.0
|
CG
|
B:ASP172
|
2.7
|
15.8
|
1.0
|
CE1
|
B:HIS145
|
3.0
|
11.9
|
1.0
|
CE1
|
B:HIS168
|
3.1
|
11.0
|
1.0
|
CD2
|
B:HIS168
|
3.1
|
11.3
|
1.0
|
CD2
|
B:HIS145
|
3.2
|
12.1
|
1.0
|
P
|
B:PO4601
|
3.4
|
15.8
|
1.0
|
N
|
B:TRP21
|
3.9
|
14.2
|
1.0
|
O1
|
B:PO4601
|
4.0
|
14.1
|
1.0
|
O4
|
B:PO4601
|
4.0
|
15.4
|
1.0
|
O
|
B:HOH1137
|
4.1
|
28.7
|
1.0
|
CB
|
B:ASP172
|
4.2
|
14.5
|
1.0
|
ND1
|
B:HIS145
|
4.2
|
11.4
|
1.0
|
ND1
|
B:HIS168
|
4.2
|
11.7
|
1.0
|
CG
|
B:HIS168
|
4.3
|
11.6
|
1.0
|
O
|
B:HOH1095
|
4.3
|
21.9
|
1.0
|
CG
|
B:HIS145
|
4.3
|
12.1
|
1.0
|
N7
|
B:GNG701
|
4.3
|
32.0
|
1.0
|
NE2
|
B:GLN142
|
4.4
|
13.4
|
1.0
|
O
|
B:HOH1027
|
4.4
|
24.8
|
1.0
|
O3
|
B:PO4601
|
4.4
|
14.2
|
1.0
|
ZN
|
B:ZN401
|
4.5
|
13.8
|
1.0
|
O6
|
B:GNG701
|
4.6
|
30.0
|
1.0
|
O
|
B:HOH1243
|
4.8
|
22.9
|
1.0
|
CA
|
B:TRP21
|
4.8
|
13.0
|
1.0
|
O
|
B:TRP21
|
4.9
|
12.9
|
1.0
|
OD1
|
B:ASP139
|
4.9
|
10.5
|
1.0
|
C
|
B:TRP21
|
4.9
|
13.7
|
1.0
|
O
|
B:HOH1091
|
5.0
|
22.1
|
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
|