Atomistry » Zinc » PDB 5f8j-5fi9 » 5fbf
Atomistry »
  Zinc »
    PDB 5f8j-5fi9 »
      5fbf »

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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy