Calcium in PDB 3eh8: Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium

The structure of Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium, PDB code: 3eh8 was solved by R.Takeuchi, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.14 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	107.555, 192.603, 161.800, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.3

The binding sites of Calcium atom in the Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium (pdb code 3eh8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium, PDB code: 3eh8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:2.0 occ:1.00 OP1 C:DA16 2.3 66.3 1.0 O A:ALA147 2.4 40.4 1.0 O B:HOH33 2.4 40.6 1.0 OP2 B:DT19 2.5 57.7 1.0 OD1 A:ASP16 2.6 46.7 1.0 OD2 A:ASP16 2.6 42.9 1.0 CG A:ASP16 3.0 44.4 1.0 O A:HOH324 3.0 45.6 1.0 O A:HOH314 3.4 24.2 1.0 C A:ALA147 3.4 40.5 1.0 P C:DA16 3.8 66.6 1.0 CA A:ALA147 3.8 40.2 1.0 P B:DT19 3.8 58.8 1.0 C5' C:DA16 4.3 61.5 1.0 O3' C:DA15 4.5 67.3 1.0 O A:GLU146 4.5 41.3 1.0 CB A:ASP16 4.5 43.1 1.0 OP1 B:DT19 4.5 61.0 1.0 C4' C:DA16 4.5 60.5 1.0 O5' B:DT19 4.5 58.4 1.0 CB A:ALA147 4.6 39.8 1.0 O5' C:DA16 4.6 64.4 1.0 N A:GLU148 4.6 40.5 1.0 C5' B:DT19 4.7 60.0 1.0 OE2 A:GLU148 4.7 45.0 1.0 OP2 C:DA16 4.8 66.2 1.0 CD2 A:LEU36 4.9 45.7 1.0 O3' B:DC18 5.0 58.6 1.0 O3' C:DA16 5.0 60.4 1.0 N A:ALA147 5.0 40.2 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:2.0 occ:1.00 OP2 C:DC17 2.1 61.9 1.0 OP1 B:DC18 2.2 54.4 1.0 O A:HOH313 2.3 36.7 1.0 O A:GLY15 2.3 41.9 1.0 O A:HOH315 2.4 28.1 1.0 OE1 A:GLU148 2.4 43.2 1.0 CD A:GLU148 3.2 43.9 1.0 P C:DC17 3.3 61.3 1.0 OE2 A:GLU148 3.4 45.0 1.0 C A:GLY15 3.5 42.4 1.0 P B:DC18 3.7 53.5 1.0 O5' C:DC17 3.8 62.1 1.0 OP1 C:DC17 3.9 62.2 1.0 C5' C:DC17 3.9 59.3 1.0 O A:HOH314 3.9 24.2 1.0 CA A:GLY15 4.1 41.9 1.0 C4' B:DC18 4.3 59.1 1.0 O3' B:DT17 4.3 57.1 1.0 C5' B:DC18 4.3 57.6 1.0 OE1 A:GLN171 4.4 45.9 1.0 O A:GLU14 4.5 41.4 1.0 O5' B:DC18 4.5 55.8 1.0 O3' C:DA16 4.5 60.4 1.0 N A:ASP16 4.6 42.9 1.0 NE2 A:GLN171 4.6 46.5 1.0 OP2 B:DC18 4.6 53.9 1.0 CG A:GLU148 4.6 41.3 1.0 C4' C:DC17 4.8 58.2 1.0 O3' B:DC18 4.9 58.6 1.0 CD A:GLN171 4.9 46.2 1.0 CA A:ASP16 4.9 43.4 1.0 O A:HOH323 4.9 37.8 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:6.9 occ:1.00 OP1 F:DA16 2.3 61.8 1.0 O D:ALA147 2.3 58.1 1.0 OP2 E:DT19 2.4 55.2 1.0 O F:HOH34 2.4 44.8 1.0 OD1 D:ASP16 2.7 61.6 1.0 OD2 D:ASP16 2.8 61.8 1.0 CG D:ASP16 3.1 60.8 1.0 C D:ALA147 3.4 58.2 1.0 O E:HOH34 3.5 30.7 1.0 P E:DT19 3.6 54.8 1.0 P F:DA16 3.7 63.1 1.0 CA D:ALA147 4.0 58.2 1.0 O3' F:DA15 4.2 64.7 1.0 O5' E:DT19 4.2 55.6 1.0 OP1 E:DT19 4.2 53.8 1.0 C5' F:DA16 4.3 59.5 1.0 OE2 D:GLU148 4.4 62.8 1.0 C4' F:DA16 4.4 58.2 1.0 C5' E:DT19 4.4 57.0 1.0 O5' F:DA16 4.6 62.7 1.0 N D:GLU148 4.6 58.0 1.0 CB D:ASP16 4.6 59.6 1.0 O D:GLU146 4.7 58.4 1.0 OP2 F:DA16 4.7 63.6 1.0 CB D:ALA147 4.7 57.9 1.0 O3' E:DC18 4.9 54.3 1.0 CA D:GLU148 5.0 57.8 1.0 CD2 D:LEU36 5.0 61.3 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca304 b:2.0 occ:1.00 OE1 D:GLU148 2.1 59.3 1.0 O D:HOH322 2.2 43.4 1.0 OP1 E:DC18 2.2 54.5 1.0 O D:HOH316 2.3 28.3 1.0 O D:GLY15 2.4 59.8 1.0 OP2 F:DC17 2.4 60.3 1.0 CD D:GLU148 3.2 61.2 1.0 C D:GLY15 3.4 59.6 1.0 P F:DC17 3.4 59.6 1.0 OE2 D:GLU148 3.6 62.8 1.0 OE1 D:GLN171 3.6 62.8 1.0 P E:DC18 3.7 55.4 1.0 OP1 F:DC17 3.9 59.9 1.0 O E:HOH34 3.9 30.7 1.0 CA D:GLY15 3.9 59.2 1.0 O5' F:DC17 3.9 59.5 1.0 C5' F:DC17 4.0 57.5 1.0 C5' E:DC18 4.2 55.0 1.0 O3' E:DT17 4.3 58.0 1.0 C4' E:DC18 4.3 56.8 1.0 O5' E:DC18 4.4 55.9 1.0 CG D:GLU148 4.5 58.0 1.0 O D:GLU14 4.5 60.4 1.0 N D:ASP16 4.6 59.3 1.0 CD D:GLN171 4.7 60.7 1.0 OP2 E:DC18 4.7 54.2 1.0 O3' F:DA16 4.8 56.6 1.0 C4' F:DC17 4.9 56.3 1.0 CA D:ASP16 5.0 59.7 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca305 b:3.9 occ:1.00 OP1 I:DA16 2.3 60.7 1.0 O G:ALA147 2.5 60.5 1.0 OP2 H:DT19 2.5 50.2 1.0 OD2 G:ASP16 2.6 56.5 1.0 O I:HOH33 2.6 44.0 1.0 OD1 G:ASP16 2.8 56.2 1.0 CG G:ASP16 3.0 57.0 1.0 C G:ALA147 3.6 60.0 1.0 P I:DA16 3.8 60.2 1.0 P H:DT19 3.8 50.3 1.0 O G:HOH311 3.8 31.9 1.0 CA G:ALA147 4.0 59.6 1.0 C5' I:DA16 4.1 58.7 1.0 O3' I:DA15 4.2 63.3 1.0 C4' I:DA16 4.3 57.5 1.0 OP1 H:DT19 4.3 52.7 1.0 O5' H:DT19 4.5 48.7 1.0 O5' I:DA16 4.5 60.1 1.0 C5' H:DT19 4.5 47.6 1.0 CB G:ASP16 4.6 56.5 1.0 OE2 G:GLU148 4.6 66.3 1.0 O G:GLU146 4.6 59.7 1.0 N G:GLU148 4.7 60.0 1.0 CB G:ALA147 4.8 59.5 1.0 OP2 I:DA16 4.8 60.9 1.0 NZ G:LYS227 4.9 63.1 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Y2 I-Anii Variant (F13Y/S111Y)/Dna Complex with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca306 b:2.0 occ:1.00 O G:HOH312 1.9 29.9 1.0 OE1 G:GLU148 2.0 62.9 1.0 OP1 H:DC18 2.1 47.0 1.0 O I:HOH34 2.1 37.0 1.0 OP2 I:DC17 2.2 53.6 1.0 O G:GLY15 2.6 56.4 1.0 CD G:GLU148 3.0 65.0 1.0 OE2 G:GLU148 3.4 66.3 1.0 O G:HOH311 3.4 31.9 1.0 P H:DC18 3.5 48.0 1.0 P I:DC17 3.5 56.4 1.0 OE1 G:GLN171 3.5 66.4 1.0 C G:GLY15 3.7 57.2 1.0 C4' H:DC18 4.0 51.5 1.0 C5' H:DC18 4.0 50.1 1.0 O3' H:DT17 4.1 51.2 1.0 CA G:GLY15 4.2 57.3 1.0 O5' I:DC17 4.2 57.7 1.0 OP1 I:DC17 4.3 57.5 1.0 O5' H:DC18 4.3 49.2 1.0 CG G:GLU148 4.4 62.0 1.0 C5' I:DC17 4.5 57.9 1.0 OP2 H:DC18 4.5 48.1 1.0 O G:GLU14 4.6 57.9 1.0 CD G:GLN171 4.6 63.4 1.0 O3' I:DA16 4.6 55.7 1.0 C3' H:DC18 4.8 51.9 1.0 O3' H:DC18 4.8 50.0 1.0 N G:ASP16 4.8 57.1 1.0 NE2 G:GLN171 5.0 62.9 1.0

R.Takeuchi, M.Certo, M.G.Caprara, A.M.Scharenberg, B.L.Stoddard. Optimization of in Vivo Activity of A Bifunctional Homing Endonuclease and Maturase Reverses Evolutionary Degradation. Nucleic Acids Res. V. 37 877 2009.
ISSN: ISSN 0305-1048
PubMed: 19103658
DOI: 10.1093/NAR/GKN1007