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Zinc in PDB 5fbf: S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate

Enzymatic activity of S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate

All present enzymatic activity of S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate:
3.1.30.1;

Protein crystallography data

The structure of S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate, PDB code: 5fbf 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) 44.25 / 1.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.742, 62.388, 62.762, 90.00, 90.00, 90.00
R / Rfree (%) 11.1 / 13.5

Other elements in 5fbf:

The structure of S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate (pdb code 5fbf). 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 Two Molecules of 2'-Deoxycytidine-5'-Monophosphate, PDB code: 5fbf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5fbf

Go back to Zinc Binding Sites List in 5fbf
Zinc binding site 1 out of 3 in the S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate


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 Two Molecules of 2'-Deoxycytidine-5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:4.2
occ:1.00
 O1P A:DCM602 1.9 5.7 1.0
NE2 A:HIS26 2.1 4.2 1.0
OD1 A:ASP139 2.1 4.7 1.0
N A:TRP21 2.1 4.4 1.0
O A:TRP21 2.2 4.7 1.0
C A:TRP21 2.9 4.4 1.0
CA A:TRP21 3.0 4.6 1.0
CE1 A:HIS26 3.0 4.0 1.0
CD2 A:HIS26 3.0 4.0 1.0
CG A:ASP139 3.1 4.1 1.0
P A:DCM602 3.3 4.7 1.0
OD2 A:ASP139 3.6 4.5 1.0
ZN A:ZN402 3.7 4.2 1.0
CB A:TRP21 3.8 5.0 1.0
O2P A:DCM602 3.8 4.9 1.0
OD2 A:ASP65 3.8 6.5 1.0
NE2 A:HIS135 4.1 4.0 1.0
ND1 A:HIS26 4.1 4.3 1.0
O A:HOH1059 4.1 10.8 1.0
CE1 A:HIS135 4.2 4.3 1.0
CG A:HIS26 4.2 4.0 1.0
O5' A:DCM602 4.2 5.9 1.0
N A:GLY22 4.2 5.1 1.0
O3P A:DCM602 4.3 5.2 1.0
CE1 A:HIS145 4.3 5.0 1.0
NE2 A:HIS145 4.3 4.5 1.0
ZN A:ZN403 4.4 4.5 1.0
OD1 A:ASP172 4.5 4.9 1.0
CB A:ASP139 4.5 3.8 1.0
CG A:TRP21 4.5 5.1 1.0
OD2 A:ASP172 4.6 5.7 1.0
CA A:ASP139 4.7 3.7 1.0
CD1 A:TRP21 4.7 5.7 1.0
C5' A:DCM602 4.7 7.0 1.0
CG A:ASP172 4.7 4.4 1.0
CG A:ASP65 4.8 5.0 1.0
O A:GLY22 4.9 4.9 1.0
OD1 A:ASP65 4.9 5.1 1.0
CA A:GLY22 5.0 5.5 1.0

Zinc binding site 2 out of 3 in 5fbf

Go back to Zinc Binding Sites List in 5fbf
Zinc binding site 2 out of 3 in the S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate


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 Two Molecules of 2'-Deoxycytidine-5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:4.2
occ:1.00
 O2P A:DCM602 2.0 4.9 1.0
ND1 A:HIS80 2.1 4.5 1.0
NE2 A:HIS135 2.1 4.0 1.0
OD2 A:ASP139 2.1 4.5 1.0
OD1 A:ASP65 2.3 5.1 1.0
CE1 A:HIS80 2.9 4.3 1.0
CD2 A:HIS135 3.0 4.2 1.0
CG A:ASP65 3.1 5.0 1.0
CG A:ASP139 3.1 4.1 1.0
P A:DCM602 3.1 4.7 1.0
CE1 A:HIS135 3.1 4.3 1.0
CG A:HIS80 3.2 4.2 1.0
OD2 A:ASP65 3.2 6.5 1.0
O1P A:DCM602 3.4 5.7 1.0
OD1 A:ASP139 3.5 4.7 1.0
CB A:HIS80 3.6 4.4 1.0
O5' A:DCM602 3.7 5.9 1.0
ZN A:ZN401 3.7 4.2 1.0
NZ A:LYS68 3.8 4.8 1.0
NE2 A:HIS80 4.1 4.4 1.0
CG A:HIS135 4.2 4.2 1.0
ND1 A:HIS135 4.2 4.3 1.0
CD2 A:HIS80 4.3 4.9 1.0
NE2 A:HIS26 4.3 4.2 1.0
O3P A:DCM602 4.4 5.2 1.0
CB A:ASP139 4.4 3.8 1.0
CE1 A:HIS145 4.5 5.0 1.0
CB A:ASP65 4.5 5.4 1.0
CE1 A:HIS26 4.7 4.0 1.0
CA A:HIS80 4.7 4.1 1.0
CA A:ASP65 4.9 5.2 1.0
CE A:LYS68 4.9 5.2 1.0

Zinc binding site 3 out of 3 in 5fbf

Go back to Zinc Binding Sites List in 5fbf
Zinc binding site 3 out of 3 in the S1 Nuclease From Aspergillus Oryzae in Complex with Two Molecules of 2'-Deoxycytidine-5'-Monophosphate


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 Two Molecules of 2'-Deoxycytidine-5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:4.5
occ:1.00
 O3P A:DCM602 2.0 5.2 1.0
NE2 A:HIS168 2.0 4.5 1.0
OD2 A:ASP172 2.0 5.7 1.0
NE2 A:HIS145 2.1 4.5 1.0
CG A:ASP172 2.7 4.4 1.0
OD1 A:ASP172 2.7 4.9 1.0
CE1 A:HIS145 2.9 5.0 1.0
CE1 A:HIS168 3.0 4.8 1.0
O1P A:DCM602 3.0 5.7 1.0
P A:DCM602 3.0 4.7 1.0
CD2 A:HIS168 3.0 4.9 1.0
CD2 A:HIS145 3.1 4.5 1.0
O4' A:DCM601 3.8 6.9 0.3
C1' A:DCM601 4.0 5.8 0.3
C1' A:DCM601 4.0 5.3 0.4
C1' A:DCM601 4.0 5.8 0.3
O4' A:DCM601 4.1 6.0 0.3
O4' A:DCM601 4.1 5.1 0.4
ND1 A:HIS145 4.1 4.5 1.0
O2P A:DCM602 4.1 4.9 1.0
O5' A:DCM602 4.1 5.9 1.0
ND1 A:HIS168 4.1 4.9 1.0
C4' A:DCM601 4.1 6.7 0.3
N A:TRP21 4.1 4.4 1.0
C5' A:DCM602 4.2 7.0 1.0
CG A:HIS168 4.2 4.8 1.0
CB A:ASP172 4.2 4.3 1.0
CG A:HIS145 4.2 4.1 1.0
NE2 A:GLN142 4.3 4.8 1.0
ZN A:ZN401 4.4 4.2 1.0
C4' A:DCM601 4.4 6.4 0.4
O A:HOH1083 4.4 16.2 1.0
C4' A:DCM601 4.4 7.1 0.3
C2' A:DCM601 4.6 6.2 0.4
C2' A:DCM601 4.6 6.8 0.3
O2 A:DCM601 4.6 5.7 1.0
C2' A:DCM601 4.7 6.8 0.3
O5' A:DCM601 4.7 9.3 0.3
O A:TRP21 4.8 4.7 1.0
CA A:TRP21 4.9 4.6 1.0
OD1 A:ASP139 4.9 4.7 1.0
C A:TRP21 5.0 4.4 1.0
C3' A:DCM601 5.0 6.5 0.4

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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