Calcium in PDB 4efj: Crystal Structure of I-Gzeii Laglidadg Homing Endonuclease in Complex with Dna Target Site

The structure of Crystal Structure of I-Gzeii Laglidadg Homing Endonuclease in Complex with Dna Target Site, PDB code: 4efj was solved by N.Kulshina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.51 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.827, 61.178, 128.877, 90.00, 116.30, 90.00
R / Rfree (%)	18.3 / 27.8

The binding sites of Calcium atom in the Crystal Structure of I-Gzeii Laglidadg Homing Endonuclease in Complex with Dna Target Site (pdb code 4efj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of I-Gzeii Laglidadg Homing Endonuclease in Complex with Dna Target Site, PDB code: 4efj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of I-Gzeii Laglidadg Homing Endonuclease in Complex with Dna Target Site


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 I-Gzeii Laglidadg Homing Endonuclease in Complex with Dna Target Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca101 b:41.4 occ:1.00 OP1 C:DT16 2.1 30.9 1.0 OP1 D:DT15 2.2 36.8 1.0 O B:GLY176 2.4 31.2 1.0 OE2 B:GLU19 2.4 52.8 1.0 P C:DT16 3.4 28.7 1.0 C B:GLY176 3.5 30.6 1.0 CD B:GLU19 3.5 52.6 1.0 P D:DT15 3.6 33.9 1.0 O5' C:DT16 3.6 31.1 1.0 O C:HOH201 3.8 32.8 1.0 OE1 B:GLU19 3.9 56.4 1.0 OP2 C:DT16 4.1 27.4 1.0 CA B:GLY176 4.2 32.0 1.0 OP2 D:DT15 4.4 30.9 1.0 O3' D:DA14 4.4 32.0 1.0 C5' D:DT15 4.5 33.4 1.0 O5' D:DT15 4.6 34.7 1.0 N B:GLU177 4.6 31.0 1.0 O3' C:DT15 4.6 26.6 1.0 C4' D:DT15 4.7 33.6 1.0 CA B:GLU177 4.8 33.5 1.0 O B:SER175 4.8 34.7 1.0 CG B:GLU19 4.9 45.4 1.0 OE1 B:GLU177 4.9 40.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of I-Gzeii Laglidadg Homing Endonuclease in Complex with Dna Target Site


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 I-Gzeii Laglidadg Homing Endonuclease in Complex with Dna Target Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:27.8 occ:1.00 OE2 A:GLU177 2.2 36.1 1.0 OP2 F:DG16 2.2 32.5 1.0 O A:ALA18 2.3 27.6 1.0 OP1 E:DT15 2.3 26.2 1.0 CD A:GLU177 3.1 34.0 1.0 P F:DG16 3.2 31.9 1.0 O5' F:DG16 3.3 33.9 1.0 C A:ALA18 3.4 28.2 1.0 OE1 A:GLU177 3.4 32.6 1.0 P E:DT15 3.8 24.0 1.0 OP1 F:DG16 4.0 33.4 1.0 CA A:ALA18 4.1 27.6 1.0 OE1 A:GLU19 4.2 54.1 1.0 O3' E:DA14 4.3 25.9 1.0 NE2 A:GLN199 4.3 17.2 1.0 NZ A:LYS97 4.4 32.3 1.0 CG A:GLU177 4.4 35.1 1.0 O A:ASP17 4.5 26.5 1.0 N A:GLU19 4.5 32.0 1.0 O3' F:DT15 4.5 31.9 1.0 C5' F:DG16 4.5 32.0 1.0 C5' E:DT15 4.6 27.5 1.0 O5' E:DT15 4.7 26.3 1.0 OP2 E:DT15 4.7 22.5 1.0 CA A:GLU19 4.7 33.2 1.0 C4' F:DG16 4.8 30.3 1.0 C4' E:DT15 4.8 27.9 1.0 CB A:ALA18 5.0 25.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of I-Gzeii Laglidadg Homing Endonuclease in Complex with Dna Target Site


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 I-Gzeii Laglidadg Homing Endonuclease in Complex with Dna Target Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:31.5 occ:1.00 OP2 E:DT16 2.2 42.0 1.0 OP1 F:DT15 2.3 37.2 1.0 OE2 A:GLU19 2.3 39.9 1.0 O A:GLY176 2.4 31.1 1.0 O E:HOH104 2.7 18.7 1.0 CD A:GLU19 3.5 43.5 1.0 C A:GLY176 3.5 30.6 1.0 NZ A:LYS256 3.5 48.0 1.0 P E:DT16 3.6 36.5 1.0 P F:DT15 3.7 38.5 1.0 CA A:GLY176 4.1 29.2 1.0 OE1 A:GLU19 4.2 54.1 1.0 O5' E:DT16 4.2 37.7 1.0 OP1 E:DT16 4.3 40.9 1.0 O3' F:DA14 4.4 34.9 1.0 OP2 F:DT15 4.5 34.4 1.0 N A:GLU177 4.6 31.7 1.0 CE A:LYS256 4.6 43.0 1.0 C5' E:DT16 4.6 40.9 1.0 CG A:GLU19 4.6 38.6 1.0 O A:SER175 4.7 26.9 1.0 OE1 A:GLU177 4.7 32.6 1.0 C4' F:DT15 4.7 36.9 1.0 O3' E:DT15 4.8 33.3 1.0 O5' F:DT15 4.8 38.7 1.0 C5' F:DT15 4.8 36.6 1.0 CA A:GLU177 4.9 34.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of I-Gzeii Laglidadg Homing Endonuclease in Complex with Dna Target Site


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 I-Gzeii Laglidadg Homing Endonuclease in Complex with Dna Target Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:37.0 occ:1.00 OE2 B:GLU177 2.1 43.8 1.0 OP1 D:DG16 2.3 44.5 1.0 OP1 C:DT15 2.3 27.4 1.0 O B:ALA18 2.4 31.9 1.0 CD B:GLU177 3.0 41.9 1.0 OE1 B:GLU177 3.2 40.4 1.0 P D:DG16 3.4 40.7 1.0 C B:ALA18 3.5 30.9 1.0 P C:DT15 3.7 29.1 1.0 OP2 D:DG16 3.8 46.8 1.0 O5' D:DG16 4.0 40.4 1.0 CA B:ALA18 4.0 29.8 1.0 NZ B:LYS97 4.2 45.4 1.0 CG B:GLU177 4.4 39.7 1.0 NE2 B:GLN199 4.4 31.4 1.0 O3' C:DA14 4.4 30.1 1.0 O C:HOH201 4.4 32.8 1.0 C5' D:DG16 4.4 36.9 1.0 OP2 C:DT15 4.5 27.5 1.0 N B:GLU19 4.6 33.5 1.0 O B:ASP17 4.6 31.8 1.0 C5' C:DT15 4.6 30.4 1.0 C4' C:DT15 4.7 29.4 1.0 O5' C:DT15 4.7 31.2 1.0 OE1 B:GLU19 4.8 56.4 1.0 O3' D:DT15 4.8 35.7 1.0 OE1 B:GLN199 4.8 34.6 1.0 CB B:ALA18 4.8 28.4 1.0 CA B:GLU19 4.9 37.0 1.0 CD B:GLN199 5.0 32.5 1.0

N.Kulshina, N.Kulshina. N/A N/A.