Calcium in PDB 3n7b: Sgrai Bound to Secondary Site Dna and Ca(II)

All present enzymatic activity of Sgrai Bound to Secondary Site Dna and Ca(II):
3.1.21.4;

The structure of Sgrai Bound to Secondary Site Dna and Ca(II), PDB code: 3n7b was solved by N.C.Horton, E.J.Little, P.W.Dunten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.32 / 2.65
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	108.682, 133.662, 64.748, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 24.8

The binding sites of Calcium atom in the Sgrai Bound to Secondary Site Dna and Ca(II) (pdb code 3n7b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Sgrai Bound to Secondary Site Dna and Ca(II), PDB code: 3n7b:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Sgrai Bound to Secondary Site Dna and Ca(II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Sgrai Bound to Secondary Site Dna and Ca(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:36.3 occ:1.00 OD2 A:ASP188 2.3 27.4 1.0 O A:PHE241 2.5 22.9 1.0 O D:HOH380 2.5 26.9 1.0 O A:HOH429 2.5 22.8 1.0 OP1 D:DC8 2.6 25.2 0.5 OP1 C:DC8 2.6 25.2 0.5 O C:HOH383 2.6 30.4 1.0 CG A:ASP188 3.0 24.6 1.0 OD1 A:ASP188 3.1 28.8 1.0 C A:PHE241 3.6 22.0 1.0 P D:DC8 3.7 22.9 0.5 P C:DC8 3.7 22.8 0.5 N A:PHE241 3.8 21.6 1.0 O5' C:DC8 3.9 21.9 0.5 O5' D:DC8 3.9 21.9 0.5 C5' C:DC8 4.0 20.6 0.5 C5' D:DC8 4.0 20.6 0.5 CA A:PHE241 4.2 21.5 1.0 CB A:ASP188 4.4 22.4 1.0 OE1 A:GLU103 4.4 38.6 1.0 CB A:PHE241 4.5 21.4 1.0 OP2 D:DC8 4.5 23.6 0.5 OP2 C:DC8 4.5 23.5 0.5 O D:HOH122 4.7 17.8 1.0 CG A:LYS242 4.7 22.4 1.0 C A:ALA240 4.7 21.8 1.0 N A:LYS242 4.7 22.3 1.0 O3' D:DC7 4.8 24.3 0.5 O A:HOH391 4.9 30.3 1.0 NZ A:LYS242 4.9 20.9 1.0 O3' C:DA7 4.9 23.9 0.5 OP2 C:DC9 4.9 19.2 0.5 OP2 D:DC9 4.9 19.2 0.5 CA A:ALA240 4.9 21.7 1.0 O A:HOH340 5.0 9.9 1.0

Calcium binding site 2 out of 3 in the Sgrai Bound to Secondary Site Dna and Ca(II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Sgrai Bound to Secondary Site Dna and Ca(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:65.4 occ:1.00 O A:HOH511 2.3 47.4 1.0 OD2 B:ASP90 2.3 35.7 1.0 O A:HOH395 2.5 42.0 1.0 O A:HOH510 2.9 29.0 1.0 O B:HOH424 2.9 35.8 1.0 CG B:ASP90 3.0 34.0 1.0 OD2 A:ASP90 3.2 29.0 1.0 OD1 B:ASP90 3.3 32.8 1.0 OD1 A:ASP90 3.5 28.0 1.0 CG A:ASP90 3.5 29.4 1.0 N A:SER91 3.6 27.2 1.0 CB A:SER91 3.6 26.3 1.0 CB B:ASP90 4.2 33.8 1.0 CA A:SER91 4.2 26.7 1.0 N B:SER91 4.3 31.9 1.0 CA B:ASP90 4.5 33.6 1.0 OG A:SER91 4.5 29.3 1.0 CA A:ASP90 4.6 28.4 1.0 C A:ASP90 4.6 27.5 1.0 CB A:ASP90 4.6 28.6 1.0 OG B:SER91 4.8 33.4 1.0 CB B:SER91 4.8 30.9 1.0 C B:ASP90 4.9 33.0 1.0

Calcium binding site 3 out of 3 in the Sgrai Bound to Secondary Site Dna and Ca(II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Sgrai Bound to Secondary Site Dna and Ca(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca500 b:53.6 occ:1.00 OD2 B:ASP188 2.2 37.2 1.0 O C:HOH337 2.4 45.1 1.0 O B:PHE241 2.4 29.9 1.0 OP1 D:DC8 2.6 24.1 0.5 OP1 C:DC8 2.7 24.1 0.5 O B:HOH458 2.7 23.3 1.0 CG B:ASP188 2.9 34.5 1.0 OD1 B:ASP188 3.0 36.7 1.0 O B:HOH413 3.5 33.3 1.0 C B:PHE241 3.5 29.1 1.0 P D:DC8 3.6 26.8 0.5 O B:HOH476 3.6 41.2 1.0 P C:DC8 3.6 26.8 0.5 N B:PHE241 3.9 26.9 1.0 O5' C:DC8 4.0 25.2 0.5 O5' D:DC8 4.0 25.2 0.5 OP2 C:DC8 4.1 23.6 0.5 OP2 D:DC8 4.1 23.7 0.5 C5' C:DC8 4.2 23.8 0.5 CA B:PHE241 4.2 28.6 1.0 C5' D:DC8 4.2 23.8 0.5 OE1 B:GLU103 4.3 38.3 1.0 CB B:ASP188 4.4 33.9 1.0 N B:LYS242 4.5 28.8 1.0 C B:ALA240 4.6 25.9 1.0 O B:HOH358 4.7 20.7 1.0 CB B:PHE241 4.7 29.4 1.0 CA B:ALA240 4.7 25.8 1.0 OP2 C:DC9 4.7 21.6 0.5 OP2 D:DC9 4.7 21.6 0.5 CD B:LYS242 4.7 26.9 1.0 CB B:ALA240 4.8 25.4 1.0 CG B:LYS242 4.9 28.1 1.0 CA B:LYS242 4.9 28.1 1.0 O3' D:DC7 5.0 28.2 0.5

E.J.Little, P.W.Dunten, J.Bitinaite, N.C.Horton. New Clues in the Allosteric Activation of Dna Cleavage By Sgrai: Structures of Sgrai Bound to Cleaved Primary-Site Dna and Uncleaved Secondary-Site Dna. Acta Crystallogr.,Sect.D V. 67 67 2011.
ISSN: ISSN 0907-4449
PubMed: 21206063
DOI: 10.1107/S0907444910047785