Calcium in PDB 4z1x: Crystal Structure of Laglidadg Homing Endonuclease I-Gzeii in Complex with Dna Target

The structure of Crystal Structure of Laglidadg Homing Endonuclease I-Gzeii in Complex with Dna Target, PDB code: 4z1x was solved by B.L.Stoddard, A.R.Lambert, N.Kulshina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.833, 61.186, 128.871, 90.00, 116.30, 90.00
R / Rfree (%)	17.3 / 24

The binding sites of Calcium atom in the Crystal Structure of Laglidadg Homing Endonuclease I-Gzeii in Complex with Dna Target (pdb code 4z1x). 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 Laglidadg Homing Endonuclease I-Gzeii in Complex with Dna Target, PDB code: 4z1x:
Jump to Calcium binding site number: 1; 2; 3; 4;

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


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 Laglidadg Homing Endonuclease I-Gzeii in Complex with Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:21.1 occ:1.00 OP1 E:DT15 2.3 23.8 1.0 O A:HOH503 2.3 10.7 1.0 OE2 A:GLU177 2.3 23.4 1.0 O A:HOH522 2.3 15.6 1.0 OP2 F:DG16 2.3 23.4 1.0 O A:ALA18 2.3 20.9 1.0 CD A:GLU177 3.1 24.7 1.0 OE1 A:GLU177 3.2 25.0 1.0 P F:DG16 3.3 24.4 1.0 O5' F:DG16 3.4 23.5 1.0 C A:ALA18 3.5 20.5 1.0 P E:DT15 3.7 23.5 1.0 OP1 F:DG16 4.0 26.0 1.0 CA A:ALA18 4.1 20.1 1.0 OE1 A:GLN199 4.2 17.4 1.0 OE1 A:GLU19 4.3 34.1 1.0 NZ A:LYS97 4.3 40.1 1.0 O3' E:DA14 4.3 24.9 1.0 C5' E:DT15 4.4 27.4 1.0 CG A:GLU177 4.4 25.1 1.0 O A:HOH501 4.4 17.8 1.0 O5' E:DT15 4.5 24.9 1.0 N A:GLU19 4.5 21.6 1.0 O3' F:DT15 4.6 26.8 1.0 C5' F:DG16 4.6 23.2 1.0 OP2 E:DT15 4.6 24.3 1.0 O A:ASP17 4.7 18.4 1.0 C4' E:DT15 4.7 28.4 1.0 NE2 A:GLN199 4.7 18.0 1.0 CA A:GLU19 4.8 23.4 1.0 CD A:GLN199 4.8 18.2 1.0 C4' F:DG16 4.8 22.9 1.0 CB A:ALA18 4.9 20.1 1.0

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


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 Laglidadg Homing Endonuclease I-Gzeii in Complex with Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:29.1 occ:1.00 OE2 A:GLU19 2.3 31.6 1.0 OP2 E:DT16 2.3 33.4 1.0 OP1 F:DT15 2.3 32.9 1.0 O E:HOH109 2.3 18.3 1.0 O A:HOH518 2.3 23.4 1.0 O A:GLY176 2.3 25.9 1.0 O A:HOH501 2.6 17.8 1.0 CD A:GLU19 3.2 31.7 1.0 OE1 A:GLU19 3.4 34.1 1.0 C A:GLY176 3.5 24.2 1.0 P E:DT16 3.6 32.8 1.0 P F:DT15 3.8 34.2 1.0 OP1 E:DT16 4.1 35.7 1.0 CA A:GLY176 4.2 23.8 1.0 C5' F:DT15 4.4 32.7 1.0 OE1 A:GLU177 4.4 25.0 1.0 O5' E:DT16 4.4 34.6 1.0 O3' F:DA14 4.5 33.8 1.0 C4' F:DT15 4.5 32.1 1.0 N A:GLU177 4.6 24.7 1.0 C5' E:DT16 4.6 36.1 1.0 CG A:GLU19 4.6 28.6 1.0 O5' F:DT15 4.6 33.5 1.0 O3' E:DT15 4.6 32.8 1.0 O3' F:DT15 4.7 26.8 1.0 OP2 F:DT15 4.7 35.3 1.0 CA A:GLU177 4.8 25.2 1.0 O A:SER175 5.0 22.2 1.0

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


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 Laglidadg Homing Endonuclease I-Gzeii in Complex with Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:30.1 occ:1.00 O B:HOH507 2.3 19.7 1.0 OE2 B:GLU177 2.3 31.8 1.0 OP1 C:DT15 2.3 29.1 1.0 O B:HOH509 2.3 21.2 1.0 O B:ALA18 2.3 26.2 1.0 OP1 D:DG16 2.4 34.4 1.0 P D:DG16 2.9 33.1 1.0 OP2 D:DG16 3.0 36.2 1.0 CD B:GLU177 3.1 32.4 1.0 O5' D:DG16 3.2 31.7 1.0 OE1 B:GLU177 3.3 31.6 1.0 C B:ALA18 3.5 26.6 1.0 O D:HOH101 3.7 32.2 1.0 P C:DT15 3.8 28.8 1.0 CA B:ALA18 4.2 26.1 1.0 O3' C:DA14 4.3 30.1 1.0 O D:HOH102 4.4 38.1 1.0 OE1 B:GLU19 4.4 44.9 1.0 NZ B:LYS97 4.4 44.8 1.0 C5' C:DT15 4.4 28.1 1.0 NE2 B:GLN199 4.4 30.8 1.0 O3' D:DT15 4.4 32.1 1.0 C4' C:DT15 4.5 27.2 1.0 CG B:GLU177 4.5 31.9 1.0 C5' D:DG16 4.6 30.2 1.0 N B:GLU19 4.6 27.2 1.0 O5' C:DT15 4.6 28.9 1.0 OE1 B:GLN199 4.8 31.4 1.0 CA B:GLU19 4.8 28.9 1.0 O B:ASP17 4.8 25.1 1.0 OP2 C:DT15 4.8 30.0 1.0 CD B:GLN199 4.9 30.9 1.0 C4' D:DG16 5.0 29.8 1.0

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


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 Laglidadg Homing Endonuclease I-Gzeii in Complex with Dna Target within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:32.3 occ:1.00 OP1 D:DT15 2.1 33.4 1.0 O C:HOH106 2.3 25.0 1.0 OE2 B:GLU19 2.4 41.2 1.0 OP1 C:DT16 2.4 25.6 1.0 O B:GLY176 2.4 29.8 1.0 CD B:GLU19 3.1 40.0 1.0 OE1 B:GLU19 3.2 44.9 1.0 C B:GLY176 3.5 26.9 1.0 P D:DT15 3.6 32.5 1.0 P C:DT16 3.8 25.5 1.0 O D:HOH101 4.0 32.2 1.0 CA B:GLY176 4.1 26.3 1.0 C5' D:DT15 4.3 32.0 1.0 OP2 C:DT16 4.4 26.2 1.0 O C:HOH101 4.4 36.3 1.0 O5' D:DT15 4.4 32.8 1.0 O3' D:DA14 4.4 31.2 1.0 OP2 D:DT15 4.5 32.4 1.0 CG B:GLU19 4.5 35.9 1.0 O5' C:DT16 4.6 26.7 1.0 N B:GLU177 4.6 27.7 1.0 C5' C:DT16 4.7 27.3 1.0 OE1 B:GLU177 4.7 31.6 1.0 C4' D:DT15 4.8 32.0 1.0 OP2 D:DG16 4.8 36.2 1.0 O B:SER175 4.8 24.7 1.0 O3' C:DT15 4.8 25.5 1.0 CA B:GLU177 4.9 29.1 1.0

B.L.Stoddard, A.R.Lambert, N.Kulshina. Crystal Structure of Laglidadg Homing Endonuclease I-Gzeii in Complex with Dna Target To Be Published.