Calcium in PDB 8wy5: Structure of Gabija Gaja in Complex with Dna

The binding sites of Calcium atom in the Structure of Gabija Gaja in Complex with Dna (pdb code 8wy5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Gabija Gaja in Complex with Dna, PDB code: 8wy5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of Gabija Gaja in Complex with Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Gabija Gaja in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:116.9 occ:1.00 OP1 E:DC11 2.5 45.2 1.0 OD2 A:ASP432 2.7 120.1 1.0 OE1 A:GLU379 3.5 77.3 1.0 CG A:ASP432 3.7 117.3 1.0 CB A:ASP432 3.8 115.4 1.0 P E:DC11 3.8 34.2 1.0 O3' E:DC10 4.0 54.1 1.0 O5' E:DC11 4.6 49.1 1.0 CD A:GLU379 4.6 79.6 1.0 OD1 A:ASP432 4.9 116.7 1.0 CB A:ASP511 4.9 136.5 1.0 C5' E:DC11 4.9 44.1 1.0 N A:LEU512 5.0 129.7 1.0

Calcium binding site 2 out of 4 in the Structure of Gabija Gaja in Complex with Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Gabija Gaja in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:116.7 occ:1.00 OD2 B:ASP432 2.5 122.1 1.0 OP1 F:DG11 2.5 50.8 1.0 OE2 B:GLU379 3.2 76.9 1.0 CG B:ASP432 3.4 120.2 1.0 CB B:ASP432 3.6 119.6 1.0 P F:DG11 3.8 48.3 1.0 O3' F:DC10 4.0 51.3 1.0 CD B:GLU379 4.3 80.5 1.0 NZ B:LYS541 4.5 128.7 1.0 OD1 B:ASP432 4.6 118.6 1.0 OE2 B:GLU383 4.7 92.7 1.0 OP2 F:DG11 4.7 39.6 1.0 OE1 B:GLU379 4.8 79.7 1.0 CB B:ASP511 4.8 135.3 1.0 O5' F:DG11 4.9 33.0 1.0 C5' F:DG11 5.0 40.0 1.0

Calcium binding site 3 out of 4 in the Structure of Gabija Gaja in Complex with Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Gabija Gaja in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1001 b:112.4 occ:1.00 OP1 G:DC11 2.5 36.1 1.0 OD2 C:ASP432 2.7 112.9 1.0 OD1 C:ASP511 2.7 132.6 1.0 CG C:ASP432 3.6 109.8 1.0 OE1 C:GLU379 3.6 69.9 1.0 CB C:ASP432 3.8 108.1 1.0 P G:DC11 3.8 21.8 1.0 CG C:ASP511 3.9 132.2 1.0 O3' G:DC10 4.1 39.9 1.0 NZ C:LYS541 4.2 129.1 1.0 OD2 C:ASP511 4.4 132.4 1.0 O5' G:DC11 4.6 35.2 1.0 OD1 C:ASP432 4.8 109.1 1.0 CD C:GLU379 4.8 75.8 1.0 N C:LEU512 4.9 125.7 1.0 C5' G:DC11 4.9 33.6 1.0 CE C:LYS541 4.9 129.5 1.0 OP2 G:DC11 5.0 19.1 1.0

Calcium binding site 4 out of 4 in the Structure of Gabija Gaja in Complex with Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Gabija Gaja in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1001 b:101.2 occ:1.00 OP1 H:DG11 2.5 41.6 1.0 OD2 D:ASP432 2.5 111.7 1.0 OE2 D:GLU379 2.7 68.2 1.0 CG D:ASP432 3.5 108.2 1.0 CB D:ASP432 3.6 107.0 1.0 P H:DG11 3.8 40.1 1.0 CD D:GLU379 3.9 72.1 1.0 O3' H:DC10 4.2 43.4 1.0 CB D:ASP511 4.4 121.5 1.0 OE1 D:GLU379 4.6 70.9 1.0 OD1 D:ASP432 4.6 106.6 1.0 OE2 D:GLU383 4.7 86.4 1.0 CA D:ASP511 4.7 121.7 1.0 OP2 H:DG11 4.8 29.8 1.0 O5' H:DG11 4.8 25.7 1.0 C5' H:DG11 4.8 34.5 1.0 N D:LEU512 4.9 116.9 1.0 CG D:GLU379 4.9 70.9 1.0

J.Li, Z.Wang, L.Wang. Nucleotide-Sensing Endonuclease with Dsdna To Be Published.