Calcium 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:

Sodium

(Na)

3 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+, PDB code: 3e40:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Q138F Hincii Bound to Gttaac and Cocrystallized with 5 Mm CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca259 b:25.0 occ:1.00 OP1 F:DA8 2.4 20.2 1.0 OD1 A:ASP114 2.4 20.3 1.0 O A:VAL128 2.4 22.6 1.0 OP2 F:DA9 2.5 22.8 1.0 OD2 A:ASP127 2.5 21.7 1.0 O A:HOH432 2.6 28.2 1.0 O F:HOH31 3.0 26.1 1.0 CG A:ASP114 3.4 26.0 1.0 P F:DA8 3.5 19.6 1.0 C A:VAL128 3.6 23.4 1.0 CG A:ASP127 3.7 26.4 1.0 OD2 A:ASP114 3.7 22.2 1.0 P F:DA9 3.7 25.2 1.0 N A:VAL128 3.9 21.5 1.0 NZ A:LYS129 3.9 19.8 1.0 O5' F:DA8 3.9 17.9 1.0 C5' F:DA8 4.0 20.7 1.0 OP2 F:DA8 4.1 21.6 1.0 O A:HOH317 4.2 24.2 1.0 CA A:VAL128 4.2 21.2 1.0 OP1 F:DA9 4.2 26.3 1.0 CE A:LYS129 4.2 25.5 1.0 OD1 A:ASP127 4.3 29.4 1.0 C A:ASP127 4.5 22.2 1.0 O3' F:DA8 4.5 25.1 1.0 CB A:VAL128 4.6 23.7 1.0 N A:LYS129 4.6 23.6 1.0 NA A:NA261 4.7 39.3 1.0 CA A:ASP127 4.7 17.9 1.0 CB A:ASP114 4.8 21.4 1.0 CB A:ASP127 4.8 21.8 1.0 O3' F:DT7 4.8 15.8 1.0 O5' F:DA9 4.9 24.8 1.0 CD A:LYS129 4.9 20.3 1.0 CA A:LYS129 4.9 22.2 1.0 C4' F:DA8 5.0 23.6 1.0 C3' F:DA8 5.0 21.8 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 B:Ca259 b:26.9 occ:1.00 O B:VAL128 2.4 29.0 1.0 OD2 B:ASP114 2.5 27.1 1.0 OP1 E:DA8 2.5 26.0 1.0 O B:HOH342 2.5 27.2 1.0 OD1 B:ASP127 2.5 28.1 1.0 OP2 E:DA9 2.6 29.1 1.0 O E:HOH369 2.9 33.5 1.0 CG B:ASP114 3.4 30.9 1.0 C B:VAL128 3.5 26.6 1.0 OD1 B:ASP114 3.6 30.6 1.0 P E:DA8 3.6 23.1 1.0 CG B:ASP127 3.6 31.5 1.0 N B:VAL128 3.7 25.2 1.0 P E:DA9 3.8 26.0 1.0 NZ B:LYS129 3.9 31.7 1.0 OP2 E:DA8 4.0 24.5 1.0 C5' E:DA8 4.1 24.4 1.0 O5' E:DA8 4.1 24.6 1.0 CA B:VAL128 4.1 22.3 1.0 OP1 E:DA9 4.2 27.8 1.0 OD2 B:ASP127 4.2 30.5 1.0 O B:HOH333 4.3 27.6 1.0 CD B:LYS129 4.4 25.1 1.0 C B:ASP127 4.4 26.2 1.0 CB B:VAL128 4.6 29.8 1.0 N B:LYS129 4.6 27.3 1.0 CE B:LYS129 4.6 28.5 1.0 O3' E:DA8 4.6 26.0 1.0 CA B:ASP127 4.7 22.0 1.0 CB B:ASP127 4.7 25.2 1.0 CB B:ASP114 4.8 25.9 1.0 CA B:LYS129 4.8 28.4 1.0 O3' E:DT7 4.9 22.4 1.0 O5' E:DA9 4.9 28.7 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