Sodium in PDB 3e42: Q138F Hincii Bound to Gtcgac and CA2+ (Cocrystallized)

All present enzymatic activity of Q138F Hincii Bound to Gtcgac and CA2+ (Cocrystallized):
3.1.21.4;

The structure of Q138F Hincii Bound to Gtcgac and CA2+ (Cocrystallized), PDB code: 3e42 was solved by N.C.Horton, A.C.Babic, E.J.Little, V.M.Manohar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.46 / 2.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.030, 90.140, 66.440, 90.00, 104.40, 90.00
R / Rfree (%)	18.8 / 28.3

The structure of Q138F Hincii Bound to Gtcgac and CA2+ (Cocrystallized) also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Q138F Hincii Bound to Gtcgac and CA2+ (Cocrystallized) (pdb code 3e42). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Q138F Hincii Bound to Gtcgac and CA2+ (Cocrystallized), PDB code: 3e42:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Q138F Hincii Bound to Gtcgac and CA2+ (Cocrystallized)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Q138F Hincii Bound to Gtcgac and CA2+ (Cocrystallized) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na259 b:44.9 occ:1.00 O A:ILE142 2.9 34.8 1.0 O A:HOH273 3.0 34.2 1.0 OD2 A:ASP127 3.0 43.8 1.0 OP2 F:DG8 3.0 37.3 1.0 O A:THR112 3.7 33.4 1.0 O3' F:DC7 3.8 37.7 1.0 O5' F:DC7 3.8 26.9 1.0 P F:DG8 3.9 33.5 1.0 C5' F:DC7 3.9 28.5 1.0 C A:ILE142 3.9 33.1 1.0 CG A:ASP127 4.0 44.1 1.0 CA A:ILE143 4.0 30.2 1.0 O F:HOH60 4.1 34.7 1.0 OP1 F:DC7 4.1 27.3 1.0 CB A:ILE143 4.2 34.8 1.0 C3' F:DC7 4.2 32.1 1.0 NZ A:LYS129 4.2 37.2 1.0 CG1 A:ILE143 4.3 33.6 1.0 P F:DC7 4.4 30.9 1.0 N A:ILE143 4.5 30.9 1.0 OP1 F:DG8 4.5 39.5 1.0 C4' F:DC7 4.6 31.2 1.0 OP2 F:DC7 4.7 28.3 1.0 OD1 A:ASP127 4.7 42.9 1.0 CB A:ASP127 4.8 41.3 1.0 C A:THR112 4.9 33.0 1.0

Sodium binding site 2 out of 2 in the Q138F Hincii Bound to Gtcgac and CA2+ (Cocrystallized)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Q138F Hincii Bound to Gtcgac and CA2+ (Cocrystallized) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na259 b:51.4 occ:1.00 O B:ILE142 3.0 41.5 1.0 OP2 E:DG8 3.1 42.3 1.0 O B:HOH280 3.2 40.2 1.0 OD2 B:ASP127 3.4 52.5 1.0 OP1 E:DC7 3.5 38.1 1.0 O5' E:DC7 3.5 40.2 1.0 O B:THR112 3.7 42.0 1.0 CA B:ILE143 3.8 37.9 1.0 C5' E:DC7 3.9 36.3 1.0 P E:DC7 3.9 45.6 1.0 C B:ILE142 3.9 38.7 1.0 CB B:ILE143 4.0 36.1 1.0 CG1 B:ILE143 4.0 38.1 1.0 P E:DG8 4.1 39.8 1.0 OP2 E:DC7 4.3 43.0 1.0 N B:ILE143 4.3 36.8 1.0 O3' E:DC7 4.4 38.3 1.0 OP1 E:DG8 4.5 53.9 1.0 CG B:ASP127 4.5 56.5 1.0 C3' E:DC7 4.5 38.5 1.0 C B:THR112 4.7 42.9 1.0 C4' E:DC7 4.7 37.1 1.0 NZ B:LYS129 4.8 51.1 1.0 CD1 B:ILE143 4.9 33.7 1.0 OE1 B:GLN207 4.9 35.8 1.0 CA B:THR112 5.0 42.3 1.0

A.C.Babic, E.J.Little, V.M.Manohar, J.Bitinaite, N.C.Horton. Dna Distortion and Specificity in A Sequence-Specific Endonuclease. J.Mol.Biol. V. 383 186 2008.
ISSN: ISSN 0022-2836
PubMed: 18762194
DOI: 10.1016/J.JMB.2008.08.032