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Calcium 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:

Zinc (Zn) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 5 binding sites of Calcium where determined in the S1 Nuclease From Aspergillus Oryzae in Complex with Cytidine-5'- Monophosphate, PDB code: 7qtb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 7qtb

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Calcium binding site 1 out of 5 in the S1 Nuclease From Aspergillus Oryzae in Complex with Cytidine-5'- Monophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca410

b:12.8
occ:0.40
 O A:HOH527 2.2 30.9 1.0
O A:HOH711 2.3 17.4 1.0
OD1 A:ASN148 2.3 11.8 1.0
OD2 A:ASP83 2.3 15.5 0.7
OD2 A:ASP83 2.4 9.3 0.3
O A:HOH700 2.4 22.9 1.0
O A:HOH900 2.5 25.6 1.0
O A:HOH528 2.5 36.7 1.0
CG A:ASP83 3.1 13.6 0.7
CG A:ASP83 3.4 7.8 0.3
CG A:ASN148 3.5 9.9 1.0
CB A:ASP83 3.7 8.6 0.3
CB A:ASP83 3.7 12.1 0.7
O A:HOH526 3.7 38.1 1.0
OD1 A:ASP83 4.0 14.8 0.7
N4 A:C5P407 4.0 16.1 0.7
ND2 A:ASN148 4.2 13.4 1.0
O A:HOH502 4.5 15.9 0.3
OD1 A:ASP83 4.6 8.7 0.3
CB A:ASN148 4.6 9.1 1.0
O A:ASN148 4.6 10.6 1.0
CA A:ASN148 4.8 8.5 1.0
O A:HOH626 4.9 13.8 1.0

Calcium binding site 2 out of 5 in 7qtb

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Calcium binding site 2 out of 5 in the S1 Nuclease From Aspergillus Oryzae in Complex with Cytidine-5'- Monophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca411

b:22.0
occ:0.25
 O1 A:BTB409 2.1 18.4 0.5
O A:HOH552 2.1 27.4 1.0
O A:HOH548 2.2 19.7 1.0
O A:PHE36 2.2 10.5 1.0
C7 A:BTB409 2.7 17.9 0.5
O A:HOH762 2.8 21.5 1.0
O A:HOH609 3.0 14.3 1.0
C8 A:BTB409 3.2 18.8 0.5
C A:PHE36 3.4 7.8 1.0
O8 A:BTB409 3.4 19.7 0.5
C1 A:BTB409 3.5 17.5 0.5
N A:BTB409 3.8 17.0 0.5
C2 A:BTB409 4.0 16.7 0.5
CA A:PHE36 4.1 7.6 1.0
OD2 A:ASP280 4.1 9.8 1.0
C3 A:BTB409 4.2 16.7 0.5
CB A:PHE36 4.2 7.5 1.0
N A:VAL37 4.5 7.5 1.0
C A:VAL37 4.5 8.1 1.0
O A:HOH616 4.5 13.3 1.0
O A:HOH736 4.6 12.2 1.0
CA A:VAL37 4.6 7.8 1.0
N A:ALA38 4.7 7.8 1.0
O A:HOH909 4.7 20.7 1.0
CD1 A:PHE36 4.8 7.9 1.0
O A:HOH898 4.8 30.8 1.0
O A:VAL37 4.9 8.7 1.0

Calcium binding site 3 out of 5 in 7qtb

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Calcium binding site 3 out of 5 in the S1 Nuclease From Aspergillus Oryzae in Complex with Cytidine-5'- Monophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
B:Ca410

b:17.6
occ:0.40
 O6 B:BTB409 2.3 33.5 0.8
O B:HOH565 2.3 32.9 1.0
O B:HOH515 2.3 21.2 0.5
O8 B:BTB409 2.4 30.0 0.8
O1 B:BTB409 2.4 27.6 0.8
O B:ASN122 2.5 31.3 1.0
O3 B:BTB409 2.6 30.9 0.8
N B:BTB409 2.7 29.1 0.8
C6 B:BTB409 3.2 35.0 0.8
C2 B:BTB409 3.3 30.1 0.8
C1 B:BTB409 3.4 26.5 0.8
C8 B:BTB409 3.4 36.1 0.8
C5 B:BTB409 3.5 33.9 0.8
C3 B:BTB409 3.5 31.2 0.8
C7 B:BTB409 3.5 35.1 0.8
C B:ASN122 3.5 26.4 1.0
CA B:ASN122 4.0 22.2 1.0
CB B:ASN122 4.0 24.1 1.0
O B:HOH522 4.3 27.9 1.0
N B:GLY123 4.7 21.6 1.0
C4 B:BTB409 4.8 32.0 0.8
O B:HOH843 4.9 35.6 1.0
CG B:ASN122 5.0 26.4 1.0
OD1 B:ASN122 5.0 30.1 1.0

Calcium binding site 4 out of 5 in 7qtb

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Calcium binding site 4 out of 5 in the S1 Nuclease From Aspergillus Oryzae in Complex with Cytidine-5'- Monophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca411

b:12.4
occ:0.50
 O B:HOH667 2.3 17.2 1.0
OD1 B:ASN148 2.3 11.6 1.0
O B:HOH516 2.3 27.1 1.0
OD2 B:ASP83 2.3 15.0 0.7
OD2 B:ASP83 2.4 11.2 0.3
O B:HOH720 2.4 19.2 1.0
O B:HOH507 2.5 21.8 0.7
CG B:ASP83 3.0 9.8 0.3
CG B:ASP83 3.4 11.6 0.7
CG B:ASN148 3.5 10.1 1.0
CB B:ASP83 3.7 9.7 0.3
CB B:ASP83 3.7 10.8 0.7
OD1 B:ASP83 3.7 8.6 0.3
O B:HOH546 3.9 31.3 1.0
N4 B:C5P407 4.0 15.1 0.7
ND2 B:ASN148 4.2 12.3 1.0
OD1 B:ASP83 4.5 10.9 0.7
O B:ASN148 4.6 10.6 1.0
CB B:ASN148 4.6 8.7 1.0
CA B:ASN148 4.7 8.2 1.0

Calcium binding site 5 out of 5 in 7qtb

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca412

b:15.5
occ:0.25
 O B:HOH775 2.2 27.7 1.0
O B:HOH911 2.2 29.1 1.0
O B:PHE36 2.2 11.4 1.0
O B:HOH584 2.2 20.7 1.0
O B:HOH829 2.5 37.8 1.0
O B:HOH869 2.8 21.5 1.0
O B:HOH610 3.0 14.9 1.0
O B:HOH945 3.1 26.0 0.5
C B:PHE36 3.4 8.8 1.0
CA B:PHE36 4.1 8.7 1.0
OD2 B:ASP280 4.1 10.4 1.0
CB B:PHE36 4.3 8.2 1.0
N B:VAL37 4.4 8.4 1.0
C B:VAL37 4.5 8.8 1.0
O B:HOH754 4.6 11.9 1.0
O B:HOH620 4.6 13.1 1.0
CA B:VAL37 4.6 8.5 1.0
N B:ALA38 4.6 8.7 1.0
O B:HOH912 4.8 19.2 1.0
O B:VAL37 4.8 9.6 1.0
O B:HOH932 4.9 37.6 1.0
CD1 B:PHE36 4.9 9.2 1.0
O B:HOH908 4.9 31.7 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: Thu Jul 10 00:37:13 2025

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