Sodium in PDB 1tw8: Hincii Bound to CA2+ and Cognate Dna Gtcgac

All present enzymatic activity of Hincii Bound to CA2+ and Cognate Dna Gtcgac:
3.1.21.4;

The structure of Hincii Bound to CA2+ and Cognate Dna Gtcgac, PDB code: 1tw8 was solved by C.Etzkorn, N.C.Horton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.945, 177.180, 254.890, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 28.6

The structure of Hincii Bound to CA2+ and Cognate Dna Gtcgac also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Sodium atom in the Hincii Bound to CA2+ and Cognate Dna Gtcgac (pdb code 1tw8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Hincii Bound to CA2+ and Cognate Dna Gtcgac, PDB code: 1tw8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Hincii Bound to CA2+ and Cognate Dna Gtcgac


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 CA2+ and Cognate Dna Gtcgac within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:38.8 occ:1.00 O A:ILE142 2.2 32.6 1.0 OD2 A:ASP127 2.4 24.9 1.0 OP2 F:DG8 2.4 8.5 1.0 O A:HOH1066 2.5 29.1 1.0 O A:HOH1060 2.5 27.3 1.0 NZ A:LYS129 2.7 32.3 1.0 O A:HOH1067 3.3 18.6 1.0 C A:ILE142 3.4 24.0 1.0 CG A:ASP127 3.6 23.6 1.0 P F:DG8 3.8 37.4 1.0 O5' F:DC7 3.9 24.0 1.0 C3' F:DC7 3.9 40.3 1.0 CA A:ILE143 4.0 32.8 1.0 CE A:LYS129 4.0 47.0 1.0 N A:ILE143 4.1 25.1 1.0 OD1 A:ASP127 4.3 12.9 1.0 O3' F:DC7 4.3 31.9 1.0 CB A:ILE143 4.3 33.1 1.0 OP1 F:DG8 4.4 25.3 1.0 CA A:ILE142 4.5 19.1 1.0 O A:THR112 4.5 20.7 1.0 C2' F:DC7 4.5 43.0 1.0 CG1 A:ILE143 4.5 28.4 1.0 OP2 F:DC7 4.6 20.4 1.0 O A:ASN141 4.7 29.0 1.0 P F:DC7 4.7 34.4 1.0 OE1 A:GLN207 4.7 24.0 1.0 CB A:ASP127 4.7 29.9 1.0 CE1 A:TYR168 4.7 24.7 1.0 O A:HOH1020 4.8 39.2 1.0 C5' F:DC7 4.8 31.7 1.0 OP1 F:DC7 4.9 28.5 1.0 O5' F:DG8 4.9 35.7 1.0 C4' F:DC7 5.0 31.0 1.0

Sodium binding site 2 out of 4 in the Hincii Bound to CA2+ and Cognate Dna Gtcgac


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 CA2+ and Cognate Dna Gtcgac within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:23.7 occ:1.00 O B:HOH998 2.2 11.7 1.0 OD1 B:ASP127 2.2 25.0 1.0 O B:ILE142 2.3 12.7 1.0 O B:HOH976 2.4 27.8 1.0 OP2 E:DG8 2.5 8.7 1.0 O B:HOH1054 3.2 14.4 1.0 NZ B:LYS129 3.3 21.0 1.0 CG B:ASP127 3.4 28.5 1.0 C B:ILE142 3.5 25.8 1.0 P E:DG8 3.8 33.4 1.0 C3' E:DC7 4.0 44.0 1.0 O5' E:DC7 4.0 23.6 1.0 CA B:ILE143 4.0 23.1 1.0 OD2 B:ASP127 4.1 19.5 1.0 N B:ILE143 4.2 19.6 1.0 O3' E:DC7 4.3 38.5 1.0 CB B:ILE143 4.3 27.4 1.0 O B:THR112 4.4 27.5 1.0 O B:ASN141 4.4 25.5 1.0 CB B:ASP127 4.4 17.9 1.0 OP1 E:DG8 4.5 30.3 1.0 CE B:LYS129 4.5 19.7 1.0 CG1 B:ILE143 4.5 25.0 1.0 O E:HOH244 4.6 35.2 1.0 CA B:ILE142 4.6 25.2 1.0 OP1 E:DC7 4.6 14.3 1.0 P E:DC7 4.7 27.5 1.0 C2' E:DC7 4.7 55.2 1.0 OP2 E:DC7 4.8 32.2 1.0 C5' E:DC7 4.8 36.3 1.0 CE1 B:TYR168 4.8 13.1 1.0 OE1 B:GLN207 4.8 19.3 1.0 O5' E:DG8 4.9 36.9 1.0

Sodium binding site 3 out of 4 in the Hincii Bound to CA2+ and Cognate Dna Gtcgac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hincii Bound to CA2+ and Cognate Dna Gtcgac within 5.0Å range: probe atom residue distance (Å) B Occ C:Na903 b:72.5 occ:1.00 O C:ILE142 2.1 52.7 1.0 O C:HOH967 2.9 37.5 1.0 C C:ILE142 2.9 54.7 1.0 OP2 H:DG8 3.1 34.5 1.0 OD2 C:ASP127 3.3 55.9 1.0 CA C:ILE143 3.3 58.1 1.0 N C:ILE143 3.4 57.9 1.0 CG2 C:ILE143 3.5 69.8 1.0 NZ C:LYS129 3.5 50.9 1.0 O5' H:DC7 3.7 55.0 1.0 C3' H:DC7 3.7 57.1 1.0 C2' H:DC7 3.8 65.3 1.0 CB C:ILE143 4.0 66.7 1.0 OE1 C:GLN207 4.0 73.5 1.0 O C:ASN141 4.1 34.9 1.0 CA C:ILE142 4.1 56.6 1.0 OP2 H:DC7 4.1 56.5 1.0 P H:DG8 4.3 62.0 1.0 CG C:ASP127 4.3 62.4 1.0 P H:DC7 4.4 61.6 1.0 C C:ASN141 4.5 43.9 1.0 O3' H:DC7 4.5 64.6 1.0 N C:ILE142 4.5 48.6 1.0 C C:ILE143 4.6 55.0 1.0 O C:HOH970 4.6 26.1 1.0 OD1 C:ASP127 4.6 53.3 1.0 C5' H:DC7 4.7 47.5 1.0 C4' H:DC7 4.8 51.4 1.0 OP1 H:DC7 4.9 58.2 1.0 OP1 H:DG8 4.9 64.8 1.0

Sodium binding site 4 out of 4 in the Hincii Bound to CA2+ and Cognate Dna Gtcgac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Hincii Bound to CA2+ and Cognate Dna Gtcgac within 5.0Å range: probe atom residue distance (Å) B Occ D:Na904 b:62.4 occ:1.00 OD1 D:ASP127 2.1 34.5 1.0 O D:ILE142 2.2 40.2 1.0 OP2 G:DG8 2.3 61.2 1.0 O D:HOH989 2.4 34.4 1.0 O G:HOH551 2.5 16.8 1.0 NZ D:LYS129 2.6 78.5 1.0 O D:HOH965 3.2 15.3 1.0 CG D:ASP127 3.3 42.1 1.0 C D:ILE142 3.4 44.4 1.0 P G:DG8 3.7 68.7 1.0 CE D:LYS129 3.7 68.3 1.0 C3' G:DC7 3.9 46.2 1.0 CG2 D:ILE143 4.0 62.6 1.0 OD2 D:ASP127 4.0 40.9 1.0 O3' G:DC7 4.2 57.2 1.0 CA D:ILE142 4.3 50.4 1.0 N D:ILE143 4.4 43.9 1.0 CB D:ASP127 4.4 45.6 1.0 O5' G:DC7 4.4 28.6 1.0 C2' G:DC7 4.5 56.5 1.0 CA D:ILE143 4.5 52.2 1.0 O D:ASN141 4.5 46.8 1.0 O D:THR112 4.5 44.6 1.0 OP1 G:DG8 4.6 71.7 1.0 CE2 D:TYR168 4.7 36.0 1.0 O5' G:DG8 4.7 67.4 1.0 CA D:CA804 4.9 43.4 1.0 CB D:ILE143 4.9 52.8 1.0 OE1 D:GLN207 4.9 43.0 1.0 CD D:LYS129 4.9 63.6 1.0 N D:ILE142 5.0 47.6 1.0

C.Etzkorn, N.C.Horton. CA2+ Binding in the Active Site of Hincii: Implications For the Catalytic Mechanism Biochemistry V. 43 13256 2004.
ISSN: ISSN 0006-2960
PubMed: 15491133