Sodium in PDB 1kc6: Hincii Bound to Cognate Dna

All present enzymatic activity of Hincii Bound to Cognate Dna:
3.1.21.4;

The structure of Hincii Bound to Cognate Dna, PDB code: 1kc6 was solved by N.C.Horton, L.F.Dorner, J.J.Perona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.60
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.120, 177.670, 256.360, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 28.5

The binding sites of Sodium atom in the Hincii Bound to Cognate Dna (pdb code 1kc6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hincii Bound to Cognate Dna, PDB code: 1kc6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hincii Bound to Cognate Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hincii Bound to Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:19.4 occ:1.00 O A:HOH757 2.4 1.1 1.0 O A:ILE142 2.6 16.2 1.0 OP2 F:DG8 2.7 13.0 1.0 O A:HOH756 2.8 17.3 1.0 OD2 A:ASP127 2.8 22.8 1.0 O A:HOH782 3.2 15.0 1.0 O5' F:DC7 3.5 17.6 1.0 C A:ILE142 3.6 16.5 1.0 NZ A:LYS129 3.8 20.7 1.0 CA A:ILE143 3.9 15.6 1.0 CG A:ASP127 4.0 19.6 1.0 OP1 F:DC7 4.0 11.1 1.0 P F:DG8 4.0 14.7 1.0 C3' F:DC7 4.1 16.8 1.0 O F:HOH15 4.1 18.8 1.0 P F:DC7 4.1 15.5 1.0 N A:ILE143 4.2 16.9 1.0 CB A:ILE143 4.2 17.2 1.0 O A:THR112 4.3 13.3 1.0 C5' F:DC7 4.3 16.8 1.0 OP2 F:DC7 4.4 14.7 1.0 O3' F:DC7 4.4 17.2 1.0 CG1 A:ILE143 4.4 15.6 1.0 OE1 A:GLN207 4.6 16.0 1.0 CE A:LYS129 4.7 16.6 1.0 OD1 A:ASP127 4.7 19.7 1.0 CA A:ILE142 4.8 15.3 1.0 OP1 F:DG8 4.8 14.8 1.0 C4' F:DC7 4.8 16.6 1.0 OH A:TYR168 4.9 9.5 1.0 CE1 A:TYR168 4.9 11.4 1.0 CB A:ASP127 5.0 16.2 1.0

Sodium binding site 2 out of 2 in the Hincii Bound to Cognate Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hincii Bound to Cognate Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Na702 b:15.3 occ:1.00 OP2 E:DG8 2.4 13.6 1.0 O E:HOH435 2.5 12.1 1.0 O B:ILE142 2.5 11.9 1.0 O B:HOH375 2.6 42.4 1.0 OD1 B:ASP127 2.8 22.5 1.0 C B:ILE142 3.5 12.8 1.0 O5' E:DC7 3.7 11.2 1.0 NZ B:LYS129 3.7 14.9 1.0 P E:DG8 3.8 18.5 1.0 O E:HOH411 3.8 13.7 1.0 CG B:ASP127 3.9 19.1 1.0 C3' E:DC7 4.0 13.2 1.0 CA B:ILE143 4.1 16.2 1.0 CG2 B:ILE143 4.2 22.8 1.0 N B:ILE143 4.2 14.0 1.0 O3' E:DC7 4.2 13.3 1.0 C5' E:DC7 4.3 12.5 1.0 P E:DC7 4.4 12.1 1.0 OD2 B:ASP127 4.4 21.1 1.0 OP1 E:DC7 4.4 5.3 1.0 O B:HOH374 4.5 28.9 1.0 OP2 E:DC7 4.5 10.2 1.0 CA B:ILE142 4.6 11.1 1.0 O B:THR112 4.6 13.9 1.0 CE B:LYS129 4.6 12.7 1.0 O B:ASN141 4.6 8.3 1.0 OP1 E:DG8 4.6 13.5 1.0 OE1 B:GLN207 4.7 13.9 1.0 C4' E:DC7 4.8 14.6 1.0 CB B:ILE143 4.8 19.6 1.0 O5' E:DG8 4.8 15.0 1.0

N.C.Horton, L.F.Dorner, J.J.Perona. Sequence Selectivity and Degeneracy of A Restriction Endonuclease Mediated By Dna Intercalation. Nat.Struct.Biol. V. 9 42 2002.
ISSN: ISSN 1072-8368
PubMed: 11742344
DOI: 10.1038/NSB741