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Calcium in PDB 7ss5: Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna

Calcium Binding Sites:

The binding sites of Calcium atom in the Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna (pdb code 7ss5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna, PDB code: 7ss5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7ss5

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Calcium binding site 1 out of 6 in the Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:18.8
occ:1.00
 OP2 C:DC12 2.4 15.6 1.0
O A:HOH527 2.4 17.9 1.0
O C:HOH133 2.4 14.0 1.0
O A:PHE241 2.5 15.8 1.0
OD2 A:ASP188 2.6 20.9 1.0
O C:HOH103 3.0 14.4 1.0
CG A:ASP188 3.3 20.9 1.0
OD1 A:ASP188 3.3 20.9 1.0
P C:DC12 3.5 15.6 1.0
C A:PHE241 3.6 15.8 1.0
OE1 A:GLU103 3.6 18.2 1.0
OP1 C:DC12 3.7 15.6 1.0
C5' C:DC12 3.9 15.6 1.0
O5' C:DC12 4.1 15.6 1.0
N A:PHE241 4.1 15.8 1.0
CA A:PHE241 4.2 15.8 1.0
CB A:PHE241 4.2 15.8 1.0
CA A:CA402 4.2 33.4 1.0
CD A:GLU103 4.3 18.2 1.0
O A:HOH518 4.5 16.1 1.0
CG A:GLU103 4.5 18.2 1.0
O A:HOH504 4.6 17.8 1.0
N A:LYS242 4.7 16.0 1.0
OP2 C:DC13 4.7 10.6 1.0
O3' C:DC12 4.7 15.6 1.0
CB A:ASP188 4.7 20.9 1.0
O3' C:DA11 4.8 21.8 1.0
OP1 C:DC13 4.9 10.6 1.0
CB A:GLU103 4.9 18.2 1.0
P C:DC13 5.0 10.6 1.0
O A:HOH624 5.0 23.9 1.0
CA A:LYS242 5.0 16.0 1.0
C4' C:DC12 5.0 15.6 1.0

Calcium binding site 2 out of 6 in 7ss5

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Calcium binding site 2 out of 6 in the Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:33.4
occ:1.00
 OP1 C:DC12 2.5 15.6 1.0
O A:HOH504 2.5 17.8 1.0
OD1 A:ASP188 2.6 20.9 1.0
OE1 A:GLU103 2.6 18.2 1.0
CD A:GLU103 3.4 18.2 1.0
OE2 A:GLU103 3.4 18.2 1.0
CA A:CA403 3.6 30.0 1.0
O A:HOH518 3.6 16.1 1.0
CG A:ASP188 3.7 20.9 1.0
P C:DC12 3.8 15.6 1.0
CA A:CA401 4.2 18.8 1.0
O A:HOH617 4.4 27.2 1.0
OP2 C:DC12 4.4 15.6 1.0
OD2 A:ASP188 4.5 20.9 1.0
CB A:ASP188 4.6 20.9 1.0
CA A:ASP188 4.6 20.9 1.0
C5' C:DC12 4.7 15.6 1.0
O A:HOH703 4.7 22.7 1.0
CG A:GLU103 4.7 18.2 1.0
O5' C:DC12 4.8 15.6 1.0
C4' C:DA11 4.9 21.8 1.0
O3' C:DA11 4.9 21.8 1.0

Calcium binding site 3 out of 6 in 7ss5

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Calcium binding site 3 out of 6 in the Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:30.0
occ:1.00
 O A:LEU150 2.3 22.1 1.0
OE2 A:GLU103 2.4 18.2 1.0
OD1 A:ASN149 2.8 22.9 1.0
O A:HOH617 3.0 27.2 1.0
O A:ASP188 3.2 20.9 1.0
C A:LEU150 3.5 22.1 1.0
CD A:GLU103 3.5 18.2 1.0
CA A:CA402 3.6 33.4 1.0
CG A:ASN149 3.6 22.9 1.0
N A:LEU150 3.6 22.1 1.0
CA A:ASP188 3.9 20.9 1.0
C A:ASP188 3.9 20.9 1.0
ND2 A:ASN149 4.0 22.9 1.0
OE1 A:GLU103 4.1 18.2 1.0
CA A:LEU150 4.1 22.1 1.0
OD1 A:ASP188 4.2 20.9 1.0
C A:ASN149 4.3 22.9 1.0
CB A:ASP188 4.5 20.9 1.0
O A:PRO151 4.5 21.9 1.0
N A:PRO151 4.6 21.9 1.0
CB A:LEU150 4.6 22.1 1.0
O A:PRO187 4.7 22.1 1.0
CA A:ASN149 4.7 22.9 1.0
C A:PRO151 4.7 21.9 1.0
CG A:GLU103 4.7 18.2 1.0
CG A:ASP188 4.8 20.9 1.0
CB A:ASN149 4.8 22.9 1.0
CA A:PRO151 4.8 21.9 1.0
O A:HOH504 4.9 17.8 1.0
O A:HOH703 5.0 22.7 1.0
O A:ASN149 5.0 22.9 1.0

Calcium binding site 4 out of 6 in 7ss5

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Calcium binding site 4 out of 6 in the Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:18.8
occ:1.00
 OP2 D:DC12 2.4 15.6 1.0
O B:HOH527 2.4 17.9 1.0
O D:HOH133 2.4 14.0 1.0
O B:PHE241 2.5 15.8 1.0
OD2 B:ASP188 2.6 20.9 1.0
O D:HOH103 3.0 14.4 1.0
CG B:ASP188 3.3 20.9 1.0
OD1 B:ASP188 3.3 20.9 1.0
P D:DC12 3.5 15.6 1.0
C B:PHE241 3.6 15.8 1.0
OE1 B:GLU103 3.6 18.2 1.0
OP1 D:DC12 3.7 15.6 1.0
C5' D:DC12 3.9 15.6 1.0
O5' D:DC12 4.1 15.6 1.0
N B:PHE241 4.1 15.8 1.0
CA B:PHE241 4.2 15.8 1.0
CB B:PHE241 4.2 15.8 1.0
CA B:CA402 4.2 33.4 1.0
CD B:GLU103 4.3 18.2 1.0
O B:HOH518 4.5 16.1 1.0
CG B:GLU103 4.5 18.2 1.0
O B:HOH504 4.6 17.8 1.0
N B:LYS242 4.7 16.0 1.0
OP2 D:DC13 4.7 10.6 1.0
O3' D:DC12 4.7 15.6 1.0
CB B:ASP188 4.7 20.9 1.0
O3' D:DA11 4.8 21.8 1.0
OP1 D:DC13 4.9 10.6 1.0
CB B:GLU103 4.9 18.2 1.0
P D:DC13 5.0 10.6 1.0
O B:HOH625 5.0 23.9 1.0
CA B:LYS242 5.0 16.0 1.0
C4' D:DC12 5.0 15.6 1.0

Calcium binding site 5 out of 6 in 7ss5

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Calcium binding site 5 out of 6 in the Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:33.4
occ:1.00
 OP1 D:DC12 2.5 15.6 1.0
O B:HOH504 2.5 17.8 1.0
OD1 B:ASP188 2.6 20.9 1.0
OE1 B:GLU103 2.6 18.2 1.0
CD B:GLU103 3.4 18.2 1.0
OE2 B:GLU103 3.4 18.2 1.0
CA B:CA403 3.6 30.0 1.0
O B:HOH518 3.6 16.1 1.0
CG B:ASP188 3.7 20.9 1.0
P D:DC12 3.8 15.6 1.0
CA B:CA401 4.2 18.8 1.0
O B:HOH617 4.4 27.2 1.0
OP2 D:DC12 4.4 15.6 1.0
OD2 B:ASP188 4.5 20.9 1.0
CB B:ASP188 4.6 20.9 1.0
CA B:ASP188 4.6 20.9 1.0
C5' D:DC12 4.7 15.6 1.0
O B:HOH702 4.7 22.7 1.0
CG B:GLU103 4.7 18.2 1.0
O5' D:DC12 4.8 15.6 1.0
C4' D:DA11 4.9 21.8 1.0
O3' D:DA11 4.9 21.8 1.0

Calcium binding site 6 out of 6 in 7ss5

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Calcium binding site 6 out of 6 in the Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:30.0
occ:1.00
 O B:LEU150 2.3 22.1 1.0
OE2 B:GLU103 2.4 18.2 1.0
OD1 B:ASN149 2.8 22.9 1.0
O B:HOH617 3.0 27.2 1.0
O B:ASP188 3.2 20.9 1.0
C B:LEU150 3.5 22.1 1.0
CD B:GLU103 3.5 18.2 1.0
CA B:CA402 3.6 33.4 1.0
CG B:ASN149 3.6 22.9 1.0
N B:LEU150 3.6 22.1 1.0
CA B:ASP188 3.9 20.9 1.0
C B:ASP188 3.9 20.9 1.0
ND2 B:ASN149 4.0 22.9 1.0
OE1 B:GLU103 4.1 18.2 1.0
CA B:LEU150 4.1 22.1 1.0
OD1 B:ASP188 4.2 20.9 1.0
C B:ASN149 4.3 22.9 1.0
CB B:ASP188 4.5 20.9 1.0
O B:PRO151 4.5 21.9 1.0
N B:PRO151 4.6 21.9 1.0
CB B:LEU150 4.6 22.1 1.0
O B:PRO187 4.7 22.1 1.0
CA B:ASN149 4.7 22.9 1.0
C B:PRO151 4.7 21.9 1.0
CG B:GLU103 4.7 18.2 1.0
CG B:ASP188 4.8 20.9 1.0
CB B:ASN149 4.8 22.9 1.0
CA B:PRO151 4.8 21.9 1.0
O B:HOH504 4.9 17.8 1.0
O B:HOH702 5.0 22.7 1.0
O B:ASN149 5.0 22.9 1.0

Reference:

Z.Shan, D.Lyumkis, N.C.Horton. Activated Sgrai Endonuclease Dna-Bound Dimer with CA2+ and Intact Primary Site Dna To Be Published.
Page generated: Thu Jul 10 01:06:35 2025

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