Calcium in PDB 5v0q: Original Engineered Variant of I-Onui Meganuclease Targeting the Hiv Integrase Gene; Harbors 49 Point Mutations Relative to Wild-Type I- Onui

The structure of Original Engineered Variant of I-Onui Meganuclease Targeting the Hiv Integrase Gene; Harbors 49 Point Mutations Relative to Wild-Type I- Onui, PDB code: 5v0q was solved by R.Werther, A.R.Lambert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.21 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.693, 74.419, 164.861, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23

The binding sites of Calcium atom in the Original Engineered Variant of I-Onui Meganuclease Targeting the Hiv Integrase Gene; Harbors 49 Point Mutations Relative to Wild-Type I- Onui (pdb code 5v0q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Original Engineered Variant of I-Onui Meganuclease Targeting the Hiv Integrase Gene; Harbors 49 Point Mutations Relative to Wild-Type I- Onui, PDB code: 5v0q:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Original Engineered Variant of I-Onui Meganuclease Targeting the Hiv Integrase Gene; Harbors 49 Point Mutations Relative to Wild-Type I- Onui


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Original Engineered Variant of I-Onui Meganuclease Targeting the Hiv Integrase Gene; Harbors 49 Point Mutations Relative to Wild-Type I- Onui within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:39.7 occ:1.00 OE2 A:GLU22 2.3 44.5 1.0 O B:HOH112 2.4 39.0 1.0 OP1 C:DT15 2.4 38.3 1.0 OP2 B:DA15 2.5 37.1 1.0 O A:GLY177 2.5 37.4 1.0 O A:HOH508 2.5 41.4 1.0 CD A:GLU22 3.4 51.2 1.0 C A:GLY177 3.4 38.7 1.0 CA A:GLY177 3.7 35.9 1.0 O A:HOH529 3.7 41.5 1.0 OE1 A:GLU22 3.8 65.3 1.0 P B:DA15 3.8 34.5 1.0 P C:DT15 3.8 36.4 1.0 O A:HOH501 4.0 30.0 1.0 C5' B:DA15 4.2 37.2 1.0 O3' C:DA14 4.3 39.6 1.0 O5' B:DA15 4.4 33.0 1.0 O A:SER176 4.4 36.1 1.0 OP1 B:DA15 4.5 38.8 1.0 C5' C:DT15 4.6 35.3 1.0 CG A:GLU22 4.7 52.0 1.0 N A:GLU178 4.7 34.1 1.0 OE2 A:GLU178 4.7 50.8 1.0 OP2 C:DT15 4.8 41.7 1.0 C4' C:DT15 4.8 36.4 1.0 O5' C:DT15 4.8 40.1 1.0 N A:GLY177 4.9 34.8 1.0 CE A:LYS262 4.9 41.5 1.0 C4' B:DA15 4.9 35.3 1.0 O3' B:DC14 5.0 43.0 1.0

Calcium binding site 2 out of 2 in the Original Engineered Variant of I-Onui Meganuclease Targeting the Hiv Integrase Gene; Harbors 49 Point Mutations Relative to Wild-Type I- Onui


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Original Engineered Variant of I-Onui Meganuclease Targeting the Hiv Integrase Gene; Harbors 49 Point Mutations Relative to Wild-Type I- Onui within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:37.1 occ:1.00 OP1 B:DC14 2.2 33.6 1.0 O A:ALA21 2.3 36.0 1.0 OP2 C:DA16 2.4 31.1 1.0 O B:HOH111 2.5 42.5 1.0 O A:HOH509 2.6 33.8 1.0 OE1 A:GLU178 2.7 45.6 1.0 C A:ALA21 3.5 38.7 1.0 CD A:GLU178 3.5 48.7 1.0 P C:DA16 3.5 35.3 1.0 P B:DC14 3.7 35.2 1.0 O5' C:DA16 3.7 33.7 1.0 OE2 A:GLU178 3.7 50.8 1.0 O A:HOH501 3.9 30.0 1.0 CA A:ALA21 4.1 39.0 1.0 NE2 A:GLN204 4.2 38.0 1.0 O3' B:DT13 4.2 37.0 1.0 OE1 A:GLN204 4.2 34.2 1.0 OP1 C:DA16 4.3 41.8 1.0 OP2 B:DC14 4.5 41.4 1.0 N A:GLU22 4.5 35.1 1.0 O A:ASP20 4.6 39.4 1.0 CD A:GLN204 4.6 37.0 1.0 C5' B:DC14 4.6 33.8 1.0 O5' B:DC14 4.7 35.6 1.0 CG A:GLU178 4.7 38.9 1.0 O3' C:DT15 4.7 39.5 1.0 C4' B:DC14 4.8 38.1 1.0 NZ A:LYS103 4.8 40.4 1.0 C5' C:DA16 4.8 36.8 1.0 CA A:GLU22 4.8 34.4 1.0 CG A:GLU22 4.8 52.0 1.0 C4' C:DA16 4.9 38.8 1.0 CB A:ALA21 4.9 36.1 1.0

N.Niyonzima, A.R.Lambert, R.Werther, H.De Silva Feelixge, P.Roychoudhury, A.L.Greninger, D.Stone, B.L.Stoddard, K.R.Jerome. Tuning Dna Binding Affinity and Cleavage Specificity of An Engineered Gene-Targeting Nuclease Via Surface Display, Flow Cytometry and Cellular Analyses. Protein Eng. Des. Sel. V. 30 503 2017.
ISSN: ESSN 1741-0134
PubMed: 28873986
DOI: 10.1093/PROTEIN/GZX037