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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

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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

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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

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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

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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

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