Zinc in PDB 1cz0: Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion

The structure of Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion, PDB code: 1cz0 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 / 2.10
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 (%)	19.1 / 21.6

The structure of Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion (pdb code 1cz0). 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/Dna Complex Lacking Catalytic Metal Ion, PDB code: 1cz0:
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/Dna Complex Lacking Catalytic Metal Ion


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/Dna Complex Lacking Catalytic Metal Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:20.7 occ:1.00 ND1 A:HIS134 2.2 14.2 1.0 SG A:CYS125 2.3 21.4 1.0 SG A:CYS138 2.4 20.9 1.0 SG A:CYS132 2.4 18.4 1.0 CE1 A:HIS134 3.0 16.1 1.0 CB A:CYS132 3.2 20.9 1.0 CG A:HIS134 3.3 15.7 1.0 CB A:CYS125 3.4 14.8 1.0 CB A:CYS138 3.4 20.3 1.0 O A:HOH633 3.7 18.3 1.0 CB A:HIS134 3.8 14.1 1.0 CA A:CYS132 4.1 21.2 1.0 N A:CYS138 4.1 21.2 1.0 NE2 A:HIS134 4.2 17.0 1.0 CA A:CYS138 4.3 20.6 1.0 CD2 A:HIS134 4.4 16.7 1.0 NH2 A:ARG122 4.4 11.6 1.0 N A:HIS134 4.4 16.9 1.0 N A:VAL133 4.6 19.1 1.0 C A:CYS132 4.6 19.6 1.0 CA A:HIS134 4.8 16.1 1.0 CA A:CYS125 4.8 16.6 1.0

Zinc binding site 2 out of 4 in the Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion


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/Dna Complex Lacking Catalytic Metal Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:16.6 occ:1.00 ND1 A:HIS110 2.2 9.6 1.0 SG A:CYS41 2.3 14.8 1.0 SG A:CYS105 2.4 16.3 1.0 SG A:CYS100 2.4 17.5 1.0 CE1 A:HIS110 3.1 9.9 1.0 CB A:CYS105 3.1 13.7 1.0 CB A:CYS100 3.1 18.0 1.0 CG A:HIS110 3.3 11.2 1.0 CB A:CYS41 3.3 13.7 1.0 CB A:HIS110 3.7 11.9 1.0 CA A:CYS41 3.7 13.8 1.0 NE2 A:HIS110 4.2 8.3 1.0 CD2 A:HIS110 4.3 8.8 1.0 CB A:ASN102 4.5 18.5 1.0 N A:CYS41 4.5 14.3 1.0 CA A:CYS105 4.6 14.5 1.0 CB A:ASN107 4.6 9.9 1.0 CA A:CYS100 4.6 17.7 1.0 ND2 A:ASN102 4.7 19.5 1.0 O A:HIS40 4.8 13.1 1.0 C A:CYS41 4.9 13.8 1.0 C A:HIS40 4.9 12.9 1.0 N A:TYR42 5.0 13.1 1.0 O A:ASN102 5.0 19.7 1.0

Zinc binding site 3 out of 4 in the Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion


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/Dna Complex Lacking Catalytic Metal Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:20.3 occ:1.00 ND1 B:HIS334 2.3 13.5 1.0 SG B:CYS325 2.3 15.5 1.0 SG B:CYS338 2.3 15.8 1.0 SG B:CYS332 2.4 16.1 1.0 CE1 B:HIS334 3.1 13.3 1.0 CB B:CYS338 3.2 16.9 1.0 CB B:CYS332 3.3 17.3 1.0 CB B:CYS325 3.3 15.1 1.0 CG B:HIS334 3.4 14.8 1.0 CB B:HIS334 3.8 15.1 1.0 O B:HOH624 3.9 16.5 1.0 N B:CYS338 4.0 16.2 1.0 CA B:CYS332 4.0 18.9 1.0 CA B:CYS338 4.2 14.9 1.0 NE2 B:HIS334 4.3 13.8 1.0 NH2 B:ARG322 4.3 15.2 1.0 N B:HIS334 4.4 16.4 1.0 CD2 B:HIS334 4.4 13.7 1.0 N B:VAL333 4.6 17.9 1.0 C B:CYS332 4.6 19.9 1.0 CA B:HIS334 4.7 16.4 1.0 CA B:CYS325 4.8 15.5 1.0

Zinc binding site 4 out of 4 in the Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion


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/Dna Complex Lacking Catalytic Metal Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:18.1 occ:1.00 ND1 B:HIS310 2.3 15.2 1.0 SG B:CYS241 2.3 17.3 1.0 SG B:CYS300 2.3 15.5 1.0 SG B:CYS305 2.4 17.6 1.0 CB B:CYS300 3.0 12.9 1.0 CB B:CYS305 3.1 16.0 1.0 CE1 B:HIS310 3.2 13.9 1.0 CB B:CYS241 3.2 17.0 1.0 CG B:HIS310 3.3 16.5 1.0 CB B:HIS310 3.6 16.0 1.0 CA B:CYS241 3.8 15.7 1.0 NE2 B:HIS310 4.3 14.1 1.0 CD2 B:HIS310 4.4 18.8 1.0 CB B:ASN302 4.4 13.5 1.0 CA B:CYS300 4.5 14.2 1.0 N B:CYS241 4.5 17.4 1.0 CA B:CYS305 4.6 15.5 1.0 ND2 B:ASN302 4.6 13.2 1.0 CB B:ASN307 4.8 14.8 1.0 O B:ASN302 4.9 19.7 1.0 C B:CYS241 4.9 16.1 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