Zinc in PDB 1cyq: Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex

The structure of Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex, PDB code: 1cyq was solved by E.A.Galburt, B.Chevalier, M.S.Jurica, K.E.Flick, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.93
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.866, 113.866, 89.040, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 23.5

The structure of Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex (pdb code 1cyq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex, PDB code: 1cyq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:15.6 occ:1.00 ND1 A:HIS134 2.2 11.2 1.0 SG A:CYS125 2.3 15.2 1.0 SG A:CYS138 2.4 13.4 1.0 SG A:CYS132 2.4 13.8 1.0 CE1 A:HIS134 3.0 13.5 1.0 CB A:CYS132 3.2 13.3 1.0 CG A:HIS134 3.3 13.1 1.0 CB A:CYS138 3.3 14.0 1.0 CB A:CYS125 3.3 12.7 1.0 O A:HOH657 3.7 14.8 1.0 CB A:HIS134 3.7 10.7 1.0 CA A:CYS132 4.0 14.7 1.0 N A:CYS138 4.0 13.0 1.0 NE2 A:HIS134 4.2 11.3 1.0 CA A:CYS138 4.2 13.7 1.0 N A:HIS134 4.3 12.7 1.0 CD2 A:HIS134 4.3 12.1 1.0 NH2 A:ARG122 4.3 12.4 1.0 N A:VAL133 4.5 13.4 1.0 C A:CYS132 4.6 15.2 1.0 CA A:HIS134 4.7 13.0 1.0 CA A:CYS125 4.7 13.5 1.0 CG A:ARG122 5.0 9.3 1.0

Zinc binding site 2 out of 4 in the Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:16.4 occ:1.00 ND1 A:HIS110 2.1 6.8 1.0 SG A:CYS100 2.3 12.8 1.0 SG A:CYS105 2.4 10.8 1.0 SG A:CYS41 2.4 11.7 1.0 CE1 A:HIS110 3.0 8.7 1.0 CB A:CYS100 3.0 13.2 1.0 CB A:CYS105 3.1 10.0 1.0 CG A:HIS110 3.2 7.5 1.0 CB A:CYS41 3.2 9.3 1.0 CB A:HIS110 3.6 9.2 1.0 CA A:CYS41 3.7 11.7 1.0 NE2 A:HIS110 4.2 9.5 1.0 CD2 A:HIS110 4.3 7.2 1.0 N A:CYS41 4.4 11.8 1.0 CB A:ASN102 4.5 13.7 1.0 CA A:CYS100 4.5 11.8 1.0 CA A:CYS105 4.6 13.2 1.0 CB A:ASN107 4.6 9.8 1.0 ND2 A:ASN102 4.7 13.8 1.0 O A:HIS40 4.8 11.6 1.0 C A:CYS41 4.9 11.8 1.0 C A:HIS40 4.9 11.2 1.0 N A:TYR42 5.0 11.7 1.0

Zinc binding site 3 out of 4 in the Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:16.7 occ:1.00 ND1 B:HIS334 2.3 11.8 1.0 SG B:CYS338 2.3 12.1 1.0 SG B:CYS325 2.3 11.7 1.0 SG B:CYS332 2.4 12.2 1.0 CE1 B:HIS334 3.2 11.8 1.0 CB B:CYS338 3.2 12.3 1.0 CB B:CYS332 3.3 12.4 1.0 CG B:HIS334 3.3 11.3 1.0 CB B:CYS325 3.4 9.2 1.0 CB B:HIS334 3.6 11.4 1.0 O B:HOH658 3.8 18.2 1.0 N B:CYS338 4.0 12.0 1.0 CA B:CYS332 4.0 12.8 1.0 CA B:CYS338 4.2 11.1 1.0 N B:HIS334 4.3 12.0 1.0 NE2 B:HIS334 4.3 11.4 1.0 NH2 B:ARG322 4.4 8.4 1.0 CD2 B:HIS334 4.4 10.3 1.0 CA B:HIS334 4.6 12.3 1.0 N B:VAL333 4.6 11.8 1.0 C B:CYS332 4.6 13.8 1.0 CA B:CYS325 4.8 10.2 1.0

Zinc binding site 4 out of 4 in the Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Intron Encoded Homing Endonuclease I-Ppoi (H98A)/Dna Homing Site Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:14.6 occ:1.00 ND1 B:HIS310 2.2 11.8 1.0 SG B:CYS305 2.3 11.3 1.0 SG B:CYS300 2.3 12.0 1.0 SG B:CYS241 2.4 13.1 1.0 CB B:CYS305 3.0 12.6 1.0 CB B:CYS300 3.1 13.6 1.0 CE1 B:HIS310 3.2 10.5 1.0 CG B:HIS310 3.2 13.9 1.0 CB B:CYS241 3.3 11.3 1.0 CB B:HIS310 3.5 12.5 1.0 CA B:CYS241 3.7 12.3 1.0 NE2 B:HIS310 4.3 12.0 1.0 CD2 B:HIS310 4.4 15.5 1.0 CB B:ASN302 4.4 12.6 1.0 CA B:CYS305 4.5 13.2 1.0 ND2 B:ASN302 4.5 10.9 1.0 N B:CYS241 4.5 12.7 1.0 CA B:CYS300 4.6 12.4 1.0 CB B:ASN307 4.6 12.8 1.0 C B:CYS241 4.9 11.7 1.0 O B:HIS240 4.9 12.7 1.0 O B:ASN302 4.9 13.7 1.0 CG B:ASN302 5.0 11.1 1.0 N B:TYR242 5.0 13.6 1.0

E.A.Galburt, B.Chevalier, W.Tang, M.S.Jurica, K.E.Flick, R.J.Monnat Jr., B.L.Stoddard. A Novel Endonuclease Mechanism Directly Visualized For I-Ppoi. Nat.Struct.Biol. V. 6 1096 1999.
ISSN: ISSN 1072-8368
PubMed: 10581547
DOI: 10.1038/70027