Atomistry » Calcium » PDB 1ex0-1fae » 1f0o
Atomistry »
  Calcium »
    PDB 1ex0-1fae »
      1f0o »

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

Go back to Calcium Binding Sites List in 1f0o
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

Go back to Calcium Binding Sites List in 1f0o
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: Sat Dec 12 02:54:54 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy