Sodium in PDB 3e40: Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+

All present enzymatic activity of Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+:
3.1.21.4;

The structure of Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+, PDB code: 3e40 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)	44.59 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.330, 91.630, 66.150, 90.00, 104.77, 90.00
R / Rfree (%)	16.9 / 23.2

The structure of Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+ also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+ (pdb code 3e40). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+, PDB code: 3e40:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+


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 Gttaac and Cocrystallized with 5 Mm CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na260 b:24.0 occ:1.00 O A:ILE142 2.4 16.2 1.0 OD1 A:ASP127 2.5 29.4 1.0 OP2 F:DA8 2.5 21.6 1.0 O A:HOH378 2.8 21.7 1.0 O A:HOH308 2.8 17.6 1.0 C A:ILE142 3.5 21.0 1.0 P F:DA8 3.5 19.6 1.0 O A:HOH345 3.6 26.8 1.0 CG A:ASP127 3.7 26.4 1.0 O3' F:DT7 3.7 15.8 1.0 NZ A:LYS129 3.7 19.8 1.0 O F:HOH43 3.8 27.7 1.0 O A:HOH317 4.0 24.2 1.0 O5' F:DT7 4.0 15.8 1.0 OP1 F:DA8 4.0 20.2 1.0 C3' F:DT7 4.1 19.9 1.0 CA A:ILE143 4.2 18.6 1.0 OD2 A:ASP127 4.2 21.7 1.0 N A:ILE143 4.2 17.6 1.0 CE A:LYS129 4.3 25.5 1.0 C5' F:DT7 4.4 12.5 1.0 O A:THR112 4.5 22.2 1.0 CA A:ILE142 4.5 13.4 1.0 OP1 F:DT7 4.5 14.5 1.0 O A:ASN141 4.6 17.0 1.0 CB A:ILE143 4.6 17.5 1.0 P F:DT7 4.7 16.2 1.0 OP2 F:DT7 4.8 18.7 1.0 C4' F:DT7 4.8 18.5 1.0 CB A:ASP127 4.8 21.8 1.0 OE1 A:GLN207 4.8 14.5 1.0 O5' F:DA8 4.9 17.9 1.0 CE1 A:TYR168 5.0 24.4 1.0 CG1 A:ILE143 5.0 16.1 1.0

Sodium binding site 2 out of 3 in the Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+


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 Gttaac and Cocrystallized with 5 Mm CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na261 b:39.3 occ:1.00 O A:HOH263 2.0 44.9 1.0 O A:HOH407 2.7 35.4 1.0 O A:HOH317 2.8 24.2 1.0 OD2 A:ASP114 2.9 22.2 1.0 OP1 F:DA8 3.0 20.2 1.0 O3' F:DT7 3.2 15.8 1.0 O A:ASP111 3.5 19.0 1.0 CG A:ASP114 3.8 26.0 1.0 P F:DA8 3.8 19.6 1.0 O A:ALA113 3.9 22.1 1.0 C A:ALA113 4.1 21.4 1.0 O A:HOH432 4.3 28.2 1.0 N A:ASP114 4.3 21.3 1.0 OD1 A:ASP114 4.3 20.3 1.0 C3' F:DT7 4.3 19.9 1.0 C4' F:DT7 4.4 18.5 1.0 CA A:ASP114 4.4 18.8 1.0 O A:GLN109 4.5 22.6 1.0 C A:ASP111 4.5 22.3 1.0 C5' F:DA8 4.5 20.7 1.0 O A:THR112 4.6 22.2 1.0 O5' F:DA8 4.6 17.9 1.0 CA A:CA259 4.7 25.0 1.0 CB A:ASP114 4.7 21.4 1.0 C A:THR112 4.8 22.3 1.0 N A:ALA113 4.9 22.4 1.0 CA A:ALA113 4.9 20.7 1.0 C2' F:DT7 5.0 18.0 1.0

Sodium binding site 3 out of 3 in the Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na260 b:29.4 occ:1.00 O E:HOH468 2.5 20.7 1.0 O B:ILE142 2.6 19.2 1.0 OP2 E:DA8 2.6 24.5 1.0 OD2 B:ASP127 2.7 30.5 1.0 O B:HOH330 2.7 17.5 1.0 O B:HOH335 3.5 26.0 1.0 P E:DA8 3.5 23.1 1.0 C B:ILE142 3.6 22.8 1.0 O3' E:DT7 3.6 22.4 1.0 O5' E:DT7 3.8 25.5 1.0 CG B:ASP127 3.8 31.5 1.0 O B:HOH333 3.9 27.6 1.0 C3' E:DT7 4.0 24.6 1.0 OP1 E:DA8 4.1 26.0 1.0 CA B:ILE143 4.1 20.8 1.0 NZ B:LYS129 4.1 31.7 1.0 C5' E:DT7 4.2 20.4 1.0 O B:THR112 4.3 22.7 1.0 N B:ILE143 4.3 17.8 1.0 OP1 E:DT7 4.3 19.1 1.0 OD1 B:ASP127 4.4 28.1 1.0 P E:DT7 4.5 19.9 1.0 CB B:ILE143 4.6 19.4 1.0 CA B:ILE142 4.6 17.2 1.0 OP2 E:DT7 4.6 20.6 1.0 C4' E:DT7 4.6 22.1 1.0 OE1 B:GLN207 4.8 18.3 1.0 O B:ASN141 4.8 22.6 1.0 O5' E:DA8 4.9 24.6 1.0 O B:HOH317 4.9 33.5 1.0 CG1 B:ILE143 4.9 20.1 1.0 CB B:ASP127 5.0 25.2 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