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Calcium in PDB 1f0o: Pvuii Endonuclease/Cognate Dna Complex (Glutaraldehyde-Crosslinked Crystal) at pH 7.5 with Two Calcium Ions at Each Active Site

Enzymatic activity of Pvuii Endonuclease/Cognate Dna Complex (Glutaraldehyde-Crosslinked Crystal) at pH 7.5 with Two Calcium Ions at Each Active Site

All present enzymatic activity of Pvuii Endonuclease/Cognate Dna Complex (Glutaraldehyde-Crosslinked Crystal) at pH 7.5 with Two Calcium Ions at Each Active Site:
3.1.21.4;

Protein crystallography data

The structure of Pvuii Endonuclease/Cognate Dna Complex (Glutaraldehyde-Crosslinked Crystal) at pH 7.5 with Two Calcium Ions at Each Active Site, PDB code: 1f0o was solved by J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.043, 84.702, 45.993, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 27.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Pvuii Endonuclease/Cognate Dna Complex (Glutaraldehyde-Crosslinked Crystal) at pH 7.5 with Two Calcium Ions at Each Active Site (pdb code 1f0o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Pvuii Endonuclease/Cognate Dna Complex (Glutaraldehyde-Crosslinked Crystal) at pH 7.5 with Two Calcium Ions at Each Active Site, PDB code: 1f0o:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1f0o

Go back to Calcium Binding Sites List in 1f0o
Calcium binding site 1 out of 4 in the Pvuii Endonuclease/Cognate Dna Complex (Glutaraldehyde-Crosslinked Crystal) at pH 7.5 with Two Calcium Ions at Each Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pvuii Endonuclease/Cognate Dna Complex (Glutaraldehyde-Crosslinked Crystal) at pH 7.5 with Two Calcium Ions at Each Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:51.6
occ:1.00
 O A:LEU69 2.4 15.4 1.0
OP1 D:DC9 2.6 20.4 1.0
OE2 A:GLU68 2.7 32.4 1.0
O A:HOH847 2.8 20.3 1.0
OD2 A:ASP58 3.1 28.8 1.0
CE A:LYS70 3.1 25.1 1.0
P D:DC9 3.6 15.2 1.0
C A:LEU69 3.6 15.0 1.0
CD A:GLU68 3.8 28.3 1.0
CD A:LYS70 3.8 21.9 1.0
O5' D:DC9 3.9 14.5 1.0
C5' D:DC9 3.9 11.4 1.0
CG A:ASP58 4.0 29.2 1.0
OP2 D:DT10 4.0 22.9 1.0
O A:HOH839 4.1 28.8 1.0
OP2 D:DC9 4.1 15.5 1.0
CA A:CA784 4.2 76.5 1.0
N A:LEU69 4.3 12.8 1.0
OD1 A:ASP58 4.3 32.3 1.0
CG A:LYS70 4.3 18.6 1.0
NZ A:LYS70 4.3 28.7 1.0
CA A:LEU69 4.5 13.1 1.0
N A:LYS70 4.5 16.5 1.0
OE1 A:GLU68 4.5 27.4 1.0
CA A:LYS70 4.5 17.5 1.0
O3' D:DC9 4.6 22.0 1.0
CG A:GLU68 4.6 23.6 1.0
C3' D:DC9 4.8 19.6 1.0
P D:DT10 4.9 21.0 1.0
C4' D:DC9 4.9 14.6 1.0
O3' D:DG8 5.0 21.1 1.0

Calcium binding site 2 out of 4 in 1f0o

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Calcium binding site 2 out of 4 in the Pvuii Endonuclease/Cognate Dna Complex (Glutaraldehyde-Crosslinked Crystal) at pH 7.5 with Two Calcium Ions at Each Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pvuii Endonuclease/Cognate Dna Complex (Glutaraldehyde-Crosslinked Crystal) at pH 7.5 with Two Calcium Ions at Each Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca784

b:76.5
occ:1.00
 OP1 D:DC9 2.6 20.4 1.0
O A:GLY56 2.6 38.5 1.0
O D:HOH981 2.7 46.5 1.0
OE1 A:GLU68 3.0 27.4 1.0
OD1 A:ASP58 3.1 32.3 1.0
OE2 A:GLU68 3.2 32.4 1.0
P D:DC9 3.4 15.2 1.0
OD2 A:ASP58 3.4 28.8 1.0
O3' D:DG8 3.5 21.1 1.0
O A:HOH848 3.5 40.8 1.0
CD A:GLU68 3.5 28.3 1.0
CG A:ASP58 3.6 29.2 1.0
C A:GLY56 3.7 37.5 1.0
OP2 D:DC9 3.8 15.5 1.0
O A:HOH840 4.1 30.2 1.0
CA A:CA701 4.2 51.6 1.0
N A:GLY56 4.4 39.8 1.0
CA A:GLY56 4.5 38.8 1.0
C3' D:DG8 4.6 17.4 1.0
N A:ASN57 4.7 35.5 1.0
N A:ASP58 4.7 29.1 1.0
C A:ASN57 4.7 30.4 1.0
CA A:ASN57 4.8 32.2 1.0
O5' D:DC9 4.8 14.5 1.0
CB A:ASP58 4.9 27.1 1.0
C5' D:DG8 4.9 19.1 1.0
C A:GLU55 5.0 40.8 1.0
C4' D:DG8 5.0 19.3 1.0

Calcium binding site 3 out of 4 in 1f0o

Go back to Calcium Binding Sites List in 1f0o
Calcium binding site 3 out of 4 in the Pvuii Endonuclease/Cognate Dna Complex (Glutaraldehyde-Crosslinked Crystal) at pH 7.5 with Two Calcium Ions at Each Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pvuii Endonuclease/Cognate Dna Complex (Glutaraldehyde-Crosslinked Crystal) at pH 7.5 with Two Calcium Ions at Each Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca725

b:49.3
occ:1.00
 OP1 C:DC9 2.3 26.0 1.0
O B:GLY56 2.3 41.9 1.0
O C:HOH1028 2.5 27.1 1.0
OE1 B:GLU68 2.7 29.2 1.0
OD1 B:ASP58 2.8 32.6 1.0
OE2 B:GLU68 2.9 32.2 1.0
CD B:GLU68 3.2 30.1 1.0
OD2 B:ASP58 3.3 35.7 1.0
O B:GLU55 3.4 45.7 1.0
P C:DC9 3.4 21.8 1.0
CG B:ASP58 3.4 34.7 1.0
C B:GLY56 3.5 40.4 1.0
CA B:CA761 3.5 45.9 1.0
O3' C:DG8 3.8 27.8 1.0
OP2 C:DC9 3.9 26.0 1.0
CA B:GLY56 4.2 40.5 1.0
C B:GLU55 4.4 43.9 1.0
N B:ASN57 4.5 40.3 1.0
O B:HOH722 4.6 32.3 1.0
C B:ASN57 4.7 37.2 1.0
CA B:ASN57 4.7 38.7 1.0
N B:ASP58 4.7 36.0 1.0
CG B:GLU68 4.7 26.5 1.0
O5' C:DC9 4.7 21.6 1.0
O B:HOH994 4.8 38.6 1.0
N B:GLY56 4.8 42.9 1.0
CB B:ASP58 4.8 33.5 1.0
C3' C:DG8 5.0 29.2 1.0

Calcium binding site 4 out of 4 in 1f0o

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Calcium binding site 4 out of 4 in the Pvuii Endonuclease/Cognate Dna Complex (Glutaraldehyde-Crosslinked Crystal) at pH 7.5 with Two Calcium Ions at Each Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pvuii Endonuclease/Cognate Dna Complex (Glutaraldehyde-Crosslinked Crystal) at pH 7.5 with Two Calcium Ions at Each Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca761

b:45.9
occ:1.00
 O B:LEU69 2.3 21.2 1.0
OE2 B:GLU68 2.4 32.2 1.0
O B:HOH762 2.4 15.1 1.0
OD2 B:ASP58 2.6 35.7 1.0
OP1 C:DC9 2.6 26.0 1.0
O C:HOH898 2.8 16.0 1.0
CD B:GLU68 3.3 30.1 1.0
C B:LEU69 3.4 19.4 1.0
CG B:ASP58 3.5 34.7 1.0
CA B:CA725 3.5 49.3 1.0
N B:LEU69 3.7 20.5 1.0
P C:DC9 3.8 21.8 1.0
OD1 B:ASP58 3.8 32.6 1.0
NZ B:LYS70 3.9 30.2 1.0
OE1 B:GLU68 4.0 29.2 1.0
O5' C:DC9 4.0 21.6 1.0
CA B:LEU69 4.1 19.3 1.0
CD B:LYS70 4.1 21.4 1.0
C5' C:DC9 4.1 17.3 1.0
O B:HOH994 4.2 38.6 1.0
CE B:LYS70 4.3 24.7 1.0
CG B:GLU68 4.3 26.5 1.0
O C:HOH906 4.4 18.7 1.0
OP2 C:DC9 4.5 26.0 1.0
N B:LYS70 4.5 18.4 1.0
OP2 C:DT10 4.5 22.4 1.0
CB B:LEU69 4.6 17.0 1.0
C B:GLU68 4.7 23.1 1.0
CB B:ASP58 4.7 33.5 1.0
CA B:LYS70 4.8 17.2 1.0
O3' C:DG8 5.0 27.8 1.0
CA B:GLU68 5.0 25.7 1.0

Reference:

J.R.Horton, X.Cheng. Pvuii Endonuclease Contains Two Calcium Ions in Active Sites. J.Mol.Biol. V. 300 1049 2000.
ISSN: ISSN 0022-2836
PubMed: 10903853
DOI: 10.1006/JMBI.2000.3938
Page generated: Thu Jul 11 07:59:45 2024

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