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Zinc in PDB 7qtb: S1 Nuclease From Aspergillus Oryzae in Complex with Cytidine-5'- Monophosphate

Enzymatic activity of S1 Nuclease From Aspergillus Oryzae in Complex with Cytidine-5'- Monophosphate

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

Protein crystallography data

The structure of S1 Nuclease From Aspergillus Oryzae in Complex with Cytidine-5'- Monophosphate, PDB code: 7qtb was solved by K.Adamkova, T.Koval, P.Kolenko, L.H.Oestergaard, J.Dohnalek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.36 / 1.04
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 43.075, 48.459, 65.547, 107.47, 90.08, 105.7
R / Rfree (%) 10.9 / 13.1

Other elements in 7qtb:

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

Calcium (Ca) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the S1 Nuclease From Aspergillus Oryzae in Complex with Cytidine-5'- Monophosphate (pdb code 7qtb). 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 in Complex with Cytidine-5'- Monophosphate, PDB code: 7qtb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7qtb

Go back to Zinc Binding Sites List in 7qtb
Zinc binding site 1 out of 6 in the S1 Nuclease From Aspergillus Oryzae in Complex with Cytidine-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 Cytidine-5'- Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:6.5
occ:1.00
 O3 A:PO4406 2.0 6.9 0.7
NE2 A:HIS26 2.0 6.4 1.0
O A:HOH507 2.1 6.6 0.3
OD1 A:ASP139 2.1 6.1 1.0
N A:TRP21 2.1 6.7 1.0
O A:TRP21 2.2 6.7 1.0
O A:HOH501 2.2 14.2 0.3
C A:TRP21 2.9 7.0 1.0
CA A:TRP21 2.9 6.9 1.0
CE1 A:HIS26 3.0 6.1 1.0
P A:PO4406 3.0 7.3 0.7
CD2 A:HIS26 3.0 6.4 1.0
O4 A:PO4406 3.1 7.5 0.7
CG A:ASP139 3.1 5.6 1.0
ZN A:ZN402 3.4 7.0 1.0
OD2 A:ASP139 3.5 6.5 1.0
CB A:TRP21 3.6 6.7 1.0
O1 A:PO4406 3.7 8.8 0.7
NE2 A:HIS135 3.9 6.7 1.0
CE1 A:HIS135 4.1 6.4 1.0
ND1 A:HIS26 4.1 6.3 1.0
CG A:HIS26 4.2 6.3 1.0
OD2 A:ASP65 4.2 9.5 1.0
N A:GLY22 4.2 7.3 1.0
O2 A:PO4406 4.2 10.4 0.7
O A:HOH503 4.2 10.6 0.3
CE1 A:HIS145 4.2 6.8 1.0
CG A:TRP21 4.3 6.2 1.0
NE2 A:HIS145 4.3 6.7 1.0
CD1 A:TRP21 4.4 6.9 1.0
CB A:ASP139 4.4 6.0 1.0
OD1 A:ASP172 4.6 6.8 1.0
ZN A:ZN403 4.7 7.3 1.0
CA A:ASP139 4.7 5.9 1.0
OD1 A:ASP65 4.9 8.7 1.0
O A:GLY22 4.9 6.8 1.0
CA A:GLY22 4.9 7.5 1.0
CG A:ASP65 4.9 8.1 1.0
CD2 A:HIS135 4.9 6.7 1.0
O A:HOH633 5.0 15.0 1.0
ND1 A:HIS145 5.0 7.2 1.0

Zinc binding site 2 out of 6 in 7qtb

Go back to Zinc Binding Sites List in 7qtb
Zinc binding site 2 out of 6 in the S1 Nuclease From Aspergillus Oryzae in Complex with Cytidine-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 Cytidine-5'- Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:7.0
occ:1.00
 O3 A:PO4406 2.0 6.9 0.7
O A:HOH507 2.0 6.6 0.3
ND1 A:HIS80 2.0 6.8 1.0
NE2 A:HIS135 2.0 6.7 1.0
OD2 A:ASP139 2.1 6.5 1.0
OD1 A:ASP65 2.8 8.7 1.0
CE1 A:HIS80 2.9 7.8 1.0
CD2 A:HIS135 3.0 6.7 1.0
CG A:ASP139 3.0 5.6 1.0
CE1 A:HIS135 3.1 6.4 1.0
P A:PO4406 3.1 7.3 0.7
O2 A:PO4406 3.1 10.4 0.7
CG A:HIS80 3.1 7.4 1.0
OD1 A:ASP139 3.3 6.1 1.0
ZN A:ZN401 3.4 6.5 1.0
CB A:HIS80 3.6 7.2 1.0
CG A:ASP65 3.6 8.1 1.0
O A:HOH501 3.7 14.2 0.3
OD2 A:ASP65 3.8 9.5 1.0
O1 A:PO4406 3.9 8.8 0.7
NE2 A:HIS26 4.0 6.4 1.0
NE2 A:HIS80 4.1 8.1 1.0
ND1 A:HIS135 4.2 6.9 1.0
CD2 A:HIS80 4.2 8.0 1.0
CG A:HIS135 4.2 6.8 1.0
O4 A:PO4406 4.3 7.5 0.7
NZ A:LYS68 4.3 17.7 1.0
O A:HOH503 4.4 10.6 0.3
CB A:ASP139 4.4 6.0 1.0
CE1 A:HIS145 4.4 6.8 1.0
CE1 A:HIS26 4.4 6.1 1.0
CA A:HIS80 4.6 6.5 1.0
O A:TRP21 4.9 6.7 1.0
CD2 A:HIS26 4.9 6.4 1.0
CB A:ASP65 5.0 8.7 1.0
ND1 A:HIS145 5.0 7.2 1.0

Zinc binding site 3 out of 6 in 7qtb

Go back to Zinc Binding Sites List in 7qtb
Zinc binding site 3 out of 6 in the S1 Nuclease From Aspergillus Oryzae in Complex with Cytidine-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 Cytidine-5'- Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:7.3
occ:1.00
 O4 A:PO4406 2.0 7.5 0.7
NE2 A:HIS145 2.0 6.7 1.0
OD2 A:ASP172 2.1 8.2 1.0
O A:HOH503 2.1 10.6 0.3
NE2 A:HIS168 2.1 7.5 1.0
O3' A:C5P407 2.2 10.3 0.7
OD1 A:ASP172 2.6 6.8 1.0
CG A:ASP172 2.7 6.9 1.0
O A:HOH501 2.8 14.2 0.3
CE1 A:HIS145 2.9 6.8 1.0
CD2 A:HIS168 3.1 7.5 1.0
CE1 A:HIS168 3.1 7.2 1.0
CD2 A:HIS145 3.1 6.3 1.0
P A:PO4406 3.3 7.3 0.7
C3' A:C5P407 3.5 11.1 0.7
O2 A:PO4406 3.6 10.4 0.7
C4' A:C5P407 3.9 12.4 0.7
ND1 A:HIS145 4.1 7.2 1.0
C1' A:C5P407 4.1 11.5 0.7
O A:HOH633 4.1 15.0 1.0
CB A:ASP172 4.1 7.1 1.0
O4' A:C5P407 4.1 11.3 0.7
N A:TRP21 4.2 6.7 1.0
O1 A:PO4406 4.2 8.8 0.7
ND1 A:HIS168 4.2 7.6 1.0
CG A:HIS145 4.2 6.2 1.0
CG A:HIS168 4.2 7.5 1.0
C2' A:C5P407 4.3 11.3 0.7
O3 A:PO4406 4.3 6.9 0.7
O2' A:C5P407 4.4 12.0 0.7
NE2 A:GLN142 4.4 6.5 1.0
O A:HOH716 4.4 15.9 1.0
O A:HOH507 4.6 6.6 0.3
ZN A:ZN401 4.7 6.5 1.0
CE1 A:PHE81 4.7 10.4 0.3
CA A:TRP21 4.9 6.9 1.0
O A:TRP21 4.9 6.7 1.0
C A:TRP21 5.0 7.0 1.0

Zinc binding site 4 out of 6 in 7qtb

Go back to Zinc Binding Sites List in 7qtb
Zinc binding site 4 out of 6 in the S1 Nuclease From Aspergillus Oryzae in Complex with Cytidine-5'- Monophosphate


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 in Complex with Cytidine-5'- Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:7.0
occ:1.00
 O3 B:PO4406 1.9 7.0 0.7
O B:HOH503 2.0 17.1 0.3
NE2 B:HIS26 2.0 6.6 1.0
OD1 B:ASP139 2.1 6.8 1.0
N B:TRP21 2.1 7.4 1.0
O B:HOH501 2.1 7.7 0.3
O B:TRP21 2.2 7.2 1.0
C B:TRP21 2.9 7.1 1.0
CA B:TRP21 2.9 6.7 1.0
P B:PO4406 3.0 6.9 0.7
CD2 B:HIS26 3.0 6.6 1.0
CE1 B:HIS26 3.0 6.3 1.0
O4 B:PO4406 3.0 6.8 0.7
CG B:ASP139 3.1 6.4 1.0
ZN B:ZN402 3.4 7.5 1.0
OD2 B:ASP139 3.5 7.1 1.0
CB B:TRP21 3.6 7.3 1.0
O1 B:PO4406 3.7 8.6 0.7
NE2 B:HIS135 4.0 7.5 1.0
CE1 B:HIS135 4.1 7.3 1.0
O B:HOH505 4.1 14.3 0.3
ND1 B:HIS26 4.1 6.7 1.0
OD2 B:ASP65 4.2 10.4 1.0
CG B:HIS26 4.2 7.0 1.0
O2 B:PO4406 4.2 9.4 0.7
N B:GLY22 4.2 7.6 1.0
CE1 B:HIS145 4.2 7.4 1.0
CG B:TRP21 4.3 7.5 1.0
NE2 B:HIS145 4.4 7.3 1.0
CD1 B:TRP21 4.4 7.2 1.0
CB B:ASP139 4.4 6.4 1.0
OD1 B:ASP172 4.6 7.2 1.0
CA B:ASP139 4.7 6.2 1.0
ZN B:ZN403 4.7 7.5 1.0
O B:GLY22 4.9 7.1 1.0
OD1 B:ASP65 4.9 9.7 1.0
CA B:GLY22 4.9 7.5 1.0
CD2 B:HIS135 4.9 7.2 1.0
CG B:ASP65 4.9 8.2 1.0

Zinc binding site 5 out of 6 in 7qtb

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Zinc binding site 5 out of 6 in the S1 Nuclease From Aspergillus Oryzae in Complex with Cytidine-5'- Monophosphate


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 in Complex with Cytidine-5'- Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:7.5
occ:1.00
 O B:HOH501 1.9 7.7 0.3
O3 B:PO4406 2.0 7.0 0.7
ND1 B:HIS80 2.0 7.1 1.0
NE2 B:HIS135 2.0 7.5 1.0
OD2 B:ASP139 2.0 7.1 1.0
OD1 B:ASP65 2.8 9.7 1.0
CE1 B:HIS80 2.9 8.3 1.0
CG B:ASP139 3.0 6.4 1.0
CD2 B:HIS135 3.0 7.2 1.0
O2 B:PO4406 3.1 9.4 0.7
CE1 B:HIS135 3.1 7.3 1.0
P B:PO4406 3.1 6.9 0.7
CG B:HIS80 3.1 7.0 1.0
OD1 B:ASP139 3.3 6.8 1.0
ZN B:ZN401 3.4 7.0 1.0
O B:HOH503 3.6 17.1 0.3
CB B:HIS80 3.6 7.3 1.0
CG B:ASP65 3.6 8.2 1.0
OD2 B:ASP65 3.8 10.4 1.0
O1 B:PO4406 3.9 8.6 0.7
NE2 B:HIS26 4.0 6.6 1.0
NE2 B:HIS80 4.1 8.6 1.0
CG B:HIS135 4.2 7.3 1.0
ND1 B:HIS135 4.2 7.5 1.0
CD2 B:HIS80 4.2 8.3 1.0
O4 B:PO4406 4.2 6.8 0.7
O B:HOH505 4.3 14.3 0.3
CB B:ASP139 4.3 6.4 1.0
NZ B:LYS68 4.4 18.1 1.0
CE1 B:HIS26 4.4 6.3 1.0
CE1 B:HIS145 4.4 7.4 1.0
CA B:HIS80 4.6 6.8 1.0
O B:TRP21 4.8 7.2 1.0
CD2 B:HIS26 4.9 6.6 1.0
ND1 B:HIS145 5.0 7.1 1.0

Zinc binding site 6 out of 6 in 7qtb

Go back to Zinc Binding Sites List in 7qtb
Zinc binding site 6 out of 6 in the S1 Nuclease From Aspergillus Oryzae in Complex with Cytidine-5'- Monophosphate


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 in Complex with Cytidine-5'- Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:7.5
occ:1.00
 NE2 B:HIS145 2.0 7.3 1.0
O4 B:PO4406 2.0 6.8 0.7
O B:HOH505 2.1 14.3 0.3
NE2 B:HIS168 2.1 7.3 1.0
OD2 B:ASP172 2.1 8.3 1.0
O3' B:C5P407 2.2 9.4 0.7
OD1 B:ASP172 2.6 7.2 1.0
CG B:ASP172 2.7 7.2 1.0
O B:HOH503 2.8 17.1 0.3
CE1 B:HIS145 2.9 7.4 1.0
CD2 B:HIS168 3.1 7.8 1.0
CE1 B:HIS168 3.1 7.2 1.0
CD2 B:HIS145 3.2 7.3 1.0
P B:PO4406 3.3 6.9 0.7
C3' B:C5P407 3.5 9.7 0.7
O2 B:PO4406 3.6 9.4 0.7
C4' B:C5P407 3.8 10.7 0.7
ND1 B:HIS145 4.1 7.1 1.0
C1' B:C5P407 4.1 10.1 0.7
N B:TRP21 4.1 7.4 1.0
O4' B:C5P407 4.2 10.3 0.7
CB B:ASP172 4.2 7.2 1.0
O B:HOH680 4.2 14.9 1.0
O1 B:PO4406 4.2 8.6 0.7
ND1 B:HIS168 4.2 7.5 1.0
CG B:HIS145 4.2 6.7 1.0
CG B:HIS168 4.2 7.5 1.0
C2' B:C5P407 4.3 9.6 0.7
O3 B:PO4406 4.3 7.0 0.7
O2' B:C5P407 4.4 10.8 0.7
NE2 B:GLN142 4.4 6.9 1.0
O B:HOH708 4.4 15.2 1.0
O B:HOH504 4.5 11.0 0.3
ZN B:ZN401 4.7 7.0 1.0
O B:HOH501 4.7 7.7 0.3
CA B:TRP21 4.9 6.7 1.0
O B:TRP21 5.0 7.2 1.0
O B:HOH890 5.0 33.8 1.0

Reference:

K.Adamkova, T.Koval', L.H.Ostergaard, J.Duskova, M.Maly, L.Svecova, T.Skalova, P.Kolenko, J.Dohnalek. Atomic Resolution Studies of S1 Nuclease Complexes Reveal Details of Rna Interaction with the Enzyme Despite Multiple Lattice-Translocation Defects. Acta Crystallogr D Struct V. 78 1194 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 36189740
DOI: 10.1107/S2059798322008397
Page generated: Wed Oct 30 10:03:24 2024

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