Zinc in PDB 1a73: Intron-Encoded Endonuclease I-Ppoi Complexed with Dna

The structure of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna, PDB code: 1a73 was solved by K.E.Flick, R.J.Monnat Junior, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.700, 113.700, 88.400, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 29.7

The structure of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna (pdb code 1a73). 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 Endonuclease I-Ppoi Complexed with Dna, PDB code: 1a73:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:18.9 occ:1.00 ND1 A:HIS134 2.2 15.7 1.0 SG A:CYS125 2.4 18.4 1.0 SG A:CYS138 2.4 17.2 1.0 SG A:CYS132 2.5 17.5 1.0 CE1 A:HIS134 3.1 15.7 1.0 CG A:HIS134 3.3 15.6 1.0 CB A:CYS125 3.3 16.5 1.0 CB A:CYS132 3.3 17.3 1.0 CB A:CYS138 3.3 16.0 1.0 CB A:HIS134 3.7 15.2 1.0 O A:HOH344 3.9 18.2 1.0 N A:CYS138 4.0 15.6 1.0 CA A:CYS132 4.0 19.0 1.0 NE2 A:HIS134 4.2 15.3 1.0 CA A:CYS138 4.3 15.8 1.0 NH1 A:ARG122 4.3 10.9 1.0 N A:HIS134 4.3 16.5 1.0 CD2 A:HIS134 4.3 15.8 1.0 N A:VAL133 4.6 17.3 1.0 C A:CYS132 4.7 18.7 1.0 CA A:HIS134 4.7 15.7 1.0 CA A:CYS125 4.7 16.2 1.0 O A:HOH442 5.0 14.2 1.0

Zinc binding site 2 out of 4 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:12.8 occ:1.00 ND1 A:HIS110 2.2 10.8 1.0 SG A:CYS41 2.3 12.5 1.0 SG A:CYS105 2.4 12.6 1.0 SG A:CYS100 2.4 12.0 1.0 CE1 A:HIS110 3.1 10.9 1.0 CB A:CYS100 3.1 13.7 1.0 CB A:CYS105 3.1 10.0 1.0 CG A:HIS110 3.2 9.8 1.0 CB A:CYS41 3.3 10.8 1.0 CB A:HIS110 3.5 10.2 1.0 CA A:CYS41 3.7 11.0 1.0 NE2 A:HIS110 4.2 10.2 1.0 CD2 A:HIS110 4.3 9.2 1.0 CB A:ASN102 4.4 13.3 1.0 N A:CYS41 4.5 11.0 1.0 CA A:CYS100 4.6 12.8 1.0 CA A:CYS105 4.6 11.8 1.0 CB A:ASN107 4.6 9.4 1.0 ND2 A:ASN102 4.6 14.5 1.0 O A:HIS40 4.7 10.9 1.0 C A:CYS41 4.8 9.8 1.0 C A:HIS40 4.9 10.5 1.0 N A:TYR42 4.9 11.0 1.0 CG A:ASN102 5.0 12.7 1.0 O A:ASN102 5.0 14.5 1.0

Zinc binding site 3 out of 4 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:17.5 occ:1.00 ND1 B:HIS134 2.2 15.3 1.0 SG B:CYS125 2.4 16.1 1.0 SG B:CYS138 2.4 14.0 1.0 SG B:CYS132 2.4 15.4 1.0 CE1 B:HIS134 3.1 15.1 1.0 CG B:HIS134 3.2 14.5 1.0 CB B:CYS132 3.3 16.0 1.0 CB B:CYS138 3.3 14.2 1.0 CB B:CYS125 3.3 14.8 1.0 CB B:HIS134 3.6 14.1 1.0 O B:HOH476 3.9 15.6 1.0 CA B:CYS132 4.0 16.3 1.0 N B:CYS138 4.1 14.5 1.0 NE2 B:HIS134 4.2 12.1 1.0 N B:HIS134 4.2 14.6 1.0 CA B:CYS138 4.3 13.9 1.0 CD2 B:HIS134 4.3 12.6 1.0 NH1 B:ARG122 4.4 11.9 1.0 CA B:HIS134 4.6 14.3 1.0 N B:VAL133 4.6 14.1 1.0 C B:CYS132 4.7 16.8 1.0 CA B:CYS125 4.7 12.7 1.0

Zinc binding site 4 out of 4 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:12.2 occ:1.00 ND1 B:HIS110 2.2 12.2 1.0 SG B:CYS41 2.3 12.4 1.0 SG B:CYS105 2.3 10.5 1.0 SG B:CYS100 2.4 12.3 1.0 CB B:CYS100 3.1 12.1 1.0 CB B:CYS105 3.1 11.5 1.0 CE1 B:HIS110 3.1 11.2 1.0 CG B:HIS110 3.2 11.6 1.0 CB B:CYS41 3.2 9.7 1.0 CB B:HIS110 3.5 11.9 1.0 CA B:CYS41 3.7 10.8 1.0 NE2 B:HIS110 4.2 11.3 1.0 CD2 B:HIS110 4.3 11.6 1.0 CB B:ASN102 4.4 11.7 1.0 N B:CYS41 4.5 10.7 1.0 CA B:CYS100 4.5 11.7 1.0 CA B:CYS105 4.6 11.8 1.0 ND2 B:ASN102 4.6 12.2 1.0 CB B:ASN107 4.7 10.8 1.0 O B:HIS40 4.8 10.4 1.0 C B:CYS41 4.8 10.6 1.0 C B:HIS40 4.9 11.2 1.0 O B:ASN102 4.9 12.6 1.0 N B:TYR42 5.0 11.7 1.0 CG B:ASN102 5.0 11.8 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