Cadmium in PDB 1ipp: Homing Endonuclease/Dna Complex

The structure of Homing Endonuclease/Dna Complex, PDB code: 1ipp was solved by K.E.Flick, M.S.Jurica, R.J.Monnat Jr., B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.900, 113.900, 88.500, 90.00, 90.00, 120.00
R / Rfree (%)	21.2 / 31.6

The structure of Homing Endonuclease/Dna Complex also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Cadmium atom in the Homing Endonuclease/Dna Complex (pdb code 1ipp). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Homing Endonuclease/Dna Complex, PDB code: 1ipp:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Homing Endonuclease/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:35.8 occ:1.00 ND1 A:HIS134 2.4 22.9 1.0 SG A:CYS125 2.7 30.7 1.0 SG A:CYS138 2.7 31.4 1.0 SG A:CYS132 2.7 34.2 1.0 O A:HOH457 3.0 74.7 1.0 CE1 A:HIS134 3.3 22.9 1.0 CB A:CYS132 3.4 29.4 1.0 CB A:CYS138 3.4 30.1 1.0 CG A:HIS134 3.4 29.1 1.0 CB A:CYS125 3.6 24.9 1.0 CB A:HIS134 3.8 28.9 1.0 O A:HOH327 3.8 44.6 1.0 CA A:CYS132 4.0 27.9 1.0 N A:CYS138 4.1 29.1 1.0 CA A:CYS138 4.3 28.5 1.0 N A:HIS134 4.3 28.6 1.0 NH2 A:ARG122 4.4 29.4 1.0 NE2 A:HIS134 4.5 20.8 1.0 CD2 A:HIS134 4.5 27.7 1.0 N A:VAL133 4.6 27.0 1.0 C A:CYS132 4.6 27.1 1.0 CA A:HIS134 4.7 26.7 1.0 NE A:ARG122 4.9 29.3 1.0 CZ A:ARG122 4.9 25.9 1.0

Cadmium binding site 2 out of 4 in the Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Homing Endonuclease/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:35.5 occ:1.00 ND1 A:HIS110 2.3 26.1 1.0 SG A:CYS105 2.6 32.0 1.0 SG A:CYS100 2.6 33.8 1.0 SG A:CYS41 2.6 31.9 1.0 CB A:CYS100 3.2 30.1 1.0 CB A:CYS105 3.3 30.1 1.0 CE1 A:HIS110 3.3 26.2 1.0 CG A:HIS110 3.3 25.8 1.0 CB A:CYS41 3.4 27.6 1.0 CB A:HIS110 3.6 24.4 1.0 CA A:CYS41 3.8 26.0 1.0 CB A:ASN102 4.3 28.9 1.0 NE2 A:HIS110 4.4 23.2 1.0 CD2 A:HIS110 4.4 24.3 1.0 N A:CYS41 4.5 25.4 1.0 O A:HIS40 4.5 24.0 1.0 ND2 A:ASN102 4.6 23.9 1.0 CA A:CYS100 4.7 27.7 1.0 CB A:ASN107 4.7 21.0 1.0 CA A:CYS105 4.8 32.4 1.0 C A:HIS40 4.8 24.5 1.0 C A:CYS41 4.9 27.1 1.0 O A:ASN102 4.9 32.3 1.0 CG A:ASN102 5.0 24.6 1.0 N A:TYR42 5.0 27.0 1.0

Cadmium binding site 3 out of 4 in the Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Homing Endonuclease/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd303 b:37.2 occ:1.00 ND1 B:HIS134 2.4 28.0 1.0 SG B:CYS138 2.6 27.6 1.0 SG B:CYS125 2.6 31.5 1.0 SG B:CYS132 2.7 32.8 1.0 CE1 B:HIS134 3.3 22.1 1.0 CB B:CYS138 3.3 27.7 1.0 CG B:HIS134 3.4 24.8 1.0 CB B:CYS132 3.4 33.1 1.0 CB B:CYS125 3.5 28.0 1.0 O B:HOH334 3.7 37.4 1.0 CB B:HIS134 3.7 26.3 1.0 N B:CYS138 4.1 28.3 1.0 CA B:CYS132 4.1 29.6 1.0 CA B:CYS138 4.3 28.4 1.0 NH2 B:ARG122 4.3 30.9 1.0 NE2 B:HIS134 4.4 18.8 1.0 CD2 B:HIS134 4.5 21.0 1.0 N B:HIS134 4.5 27.3 1.0 O B:HOH352 4.7 34.3 1.0 O A:HOH453 4.7 85.8 1.0 N B:VAL133 4.8 26.1 1.0 C B:CYS132 4.8 28.9 1.0 CA B:HIS134 4.8 25.9 1.0 CA B:CYS125 4.9 24.9 1.0 CZ B:ARG122 4.9 30.6 1.0 NE B:ARG122 5.0 35.6 1.0 O B:HOH340 5.0 33.2 1.0

Cadmium binding site 4 out of 4 in the Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Homing Endonuclease/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd304 b:31.9 occ:1.00 ND1 B:HIS110 2.4 26.6 1.0 SG B:CYS100 2.6 28.7 1.0 SG B:CYS105 2.6 30.5 1.0 SG B:CYS41 2.7 32.5 1.0 CB B:CYS100 3.2 29.5 1.0 CB B:CYS105 3.3 30.0 1.0 CG B:HIS110 3.3 25.2 1.0 CE1 B:HIS110 3.3 22.4 1.0 CB B:CYS41 3.4 31.4 1.0 CB B:HIS110 3.6 25.9 1.0 CA B:CYS41 3.8 27.5 1.0 ND2 B:ASN102 4.3 24.2 1.0 CB B:ASN102 4.3 26.4 1.0 O B:HOH370 4.4 76.3 1.0 NE2 B:HIS110 4.5 24.0 1.0 CD2 B:HIS110 4.5 26.2 1.0 N B:CYS41 4.5 25.5 1.0 O B:HIS40 4.7 22.5 1.0 CA B:CYS100 4.7 26.7 1.0 CA B:CYS105 4.8 31.6 1.0 CB B:ASN107 4.8 27.2 1.0 CG B:ASN102 4.8 20.9 1.0 C B:HIS40 4.9 25.9 1.0 C B:CYS41 5.0 26.6 1.0

K.E.Flick, M.S.Jurica, R.J.Monnat Jr., B.L.Stoddard. Dna Binding and Cleavage By the Nuclear Intron-Encoded Homing Endonuclease I-Ppoi. Nature V. 394 96 1998.
ISSN: ISSN 0028-0836
PubMed: 9665136
DOI: 10.1038/27952