Calcium in PDB 3dpg: Sgrai with Noncognate Dna Bound

All present enzymatic activity of Sgrai with Noncognate Dna Bound:
3.1.21.4;

The structure of Sgrai with Noncognate Dna Bound, PDB code: 3dpg was solved by P.W.Dunten, N.C.Horton, E.J.Little, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.26 / 1.91
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.726, 78.621, 86.834, 90.00, 109.76, 90.00
R / Rfree (%)	18.5 / 22.5

The binding sites of Calcium atom in the Sgrai with Noncognate Dna Bound (pdb code 3dpg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Sgrai with Noncognate Dna Bound, PDB code: 3dpg:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Sgrai with Noncognate Dna Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Sgrai with Noncognate Dna Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:18.3 occ:1.00 OP1 C:DC8 2.4 19.1 1.0 O A:HOH503 2.4 13.8 1.0 OD2 A:ASP188 2.5 15.9 1.0 O A:PHE241 2.5 18.1 1.0 O C:HOH18 2.5 13.0 1.0 O A:HOH502 2.5 13.1 1.0 OD1 A:ASP188 2.9 27.7 1.0 CG A:ASP188 3.0 17.3 1.0 P C:DC8 3.5 21.1 1.0 C A:PHE241 3.6 14.8 1.0 N A:PHE241 3.9 13.4 1.0 C5' C:DC8 3.9 18.1 1.0 O5' C:DC8 3.9 19.3 1.0 CA A:PHE241 4.2 13.9 1.0 OP2 C:DC8 4.2 18.9 1.0 O A:HOH680 4.4 31.7 1.0 O A:HOH656 4.4 34.3 1.0 O C:HOH20 4.4 16.7 1.0 CB A:ASP188 4.5 16.8 1.0 CB A:PHE241 4.5 14.2 1.0 O C:HOH19 4.5 33.8 1.0 OE1 A:GLU103 4.6 35.3 1.0 OP2 C:DC9 4.6 19.0 1.0 CG A:LYS242 4.6 18.0 1.0 O A:HOH573 4.7 25.0 1.0 N A:LYS242 4.7 17.7 1.0 O3' C:DA7 4.7 21.1 1.0 C A:ALA240 4.8 17.8 1.0

Calcium binding site 2 out of 4 in the Sgrai with Noncognate Dna Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Sgrai with Noncognate Dna Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:48.3 occ:1.00 O A:LEU150 2.5 21.5 1.0 OD1 A:ASN149 2.5 20.2 1.0 OE2 A:GLU103 2.5 34.7 1.0 O A:HOH506 2.6 52.4 1.0 O A:HOH504 2.8 26.1 1.0 O A:HOH505 3.0 39.7 1.0 CD A:GLU103 3.3 27.3 1.0 CG A:ASN149 3.6 29.0 1.0 C A:LEU150 3.6 21.3 1.0 OE1 A:GLU103 3.7 35.3 1.0 ND2 A:ASN149 4.0 24.6 1.0 O A:ASP188 4.1 21.3 1.0 O C:HOH19 4.1 33.8 1.0 N A:LEU150 4.2 19.7 1.0 CA A:PRO151 4.4 25.0 1.0 N A:PRO151 4.5 25.1 1.0 CG A:GLU103 4.5 22.0 1.0 O A:HOH542 4.5 26.9 1.0 CA A:LEU150 4.6 21.3 1.0 C A:ASN149 4.6 24.1 1.0 O A:HOH611 4.8 34.6 1.0 C A:PRO151 4.8 26.6 1.0 CB A:ASN149 4.9 18.4 1.0 C A:ASP188 5.0 15.3 1.0

Calcium binding site 3 out of 4 in the Sgrai with Noncognate Dna Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Sgrai with Noncognate Dna Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca500 b:20.0 occ:1.00 OD2 B:ASP188 2.4 19.2 1.0 OP1 D:DC8 2.4 22.4 1.0 O B:PHE241 2.5 16.4 1.0 O D:HOH18 2.5 14.7 1.0 O B:HOH502 2.5 17.6 1.0 O B:HOH503 2.5 22.5 1.0 OD1 B:ASP188 2.9 25.4 1.0 CG B:ASP188 3.0 22.6 1.0 P D:DC8 3.6 21.6 1.0 C B:PHE241 3.6 16.0 1.0 N B:PHE241 3.8 14.7 1.0 O5' D:DC8 3.9 23.2 1.0 C5' D:DC8 4.1 22.8 1.0 CA B:PHE241 4.2 19.0 1.0 OP2 D:DC8 4.2 28.2 1.0 O D:HOH27 4.2 30.5 1.0 O B:HOH647 4.3 33.7 1.0 OE1 B:GLU103 4.4 24.9 1.0 O D:HOH20 4.5 18.7 1.0 CB B:PHE241 4.5 13.8 1.0 CB B:ASP188 4.5 14.0 1.0 O B:HOH511 4.5 22.8 1.0 CG B:LYS242 4.6 17.2 1.0 O B:HOH662 4.6 39.8 1.0 OP2 D:DC9 4.6 17.4 1.0 N B:LYS242 4.7 13.5 1.0 C B:ALA240 4.7 16.1 1.0 O3' D:DA7 4.8 21.4 1.0 CA B:LYS242 5.0 12.9 1.0

Calcium binding site 4 out of 4 in the Sgrai with Noncognate Dna Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Sgrai with Noncognate Dna Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:39.8 occ:1.00 O B:LEU150 2.3 23.1 1.0 OE2 B:GLU103 2.4 31.5 1.0 O B:HOH504 2.5 31.5 1.0 O B:HOH505 2.5 33.2 1.0 OD1 B:ASN149 2.5 21.1 1.0 O B:ASP188 2.7 25.5 1.0 C B:LEU150 3.4 27.6 1.0 CD B:GLU103 3.5 30.8 1.0 O B:HOH566 3.5 31.2 1.0 N B:LEU150 3.5 26.3 1.0 C B:ASP188 3.5 20.4 1.0 CG B:ASN149 3.7 27.4 1.0 CA B:ASP188 3.7 17.6 1.0 CA B:LEU150 4.0 19.7 1.0 OE1 B:GLU103 4.0 24.9 1.0 O D:HOH27 4.0 30.5 1.0 CB B:ASP188 4.1 14.0 1.0 C B:ASN149 4.1 21.9 1.0 O B:HOH530 4.1 27.3 1.0 OD1 B:ASP188 4.3 25.4 1.0 O B:HOH620 4.5 31.0 1.0 ND2 B:ASN149 4.5 23.1 1.0 O B:HOH623 4.5 40.8 1.0 CA B:ASN149 4.6 20.3 1.0 N B:PRO151 4.6 24.0 1.0 CG B:GLU103 4.6 20.3 1.0 CB B:LEU150 4.6 25.0 1.0 CG B:ASP188 4.6 22.6 1.0 CB B:ASN149 4.8 17.5 1.0 CA B:PRO151 4.8 18.3 1.0 N B:LEU189 4.8 19.5 1.0 O B:ASN149 4.8 22.7 1.0

P.W.Dunten, E.J.Little, M.T.Gregory, V.M.Manohar, M.Dalton, D.Hough, J.Bitinaite, N.C.Horton. The Structure of Sgrai Bound to Dna; Recognition of An 8 Base Pair Target. Nucleic Acids Res. V. 36 5405 2008.
ISSN: ISSN 0305-1048
PubMed: 18701646
DOI: 10.1093/NAR/GKN510