Zinc in PDB 8vnp: Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate

The structure of Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate, PDB code: 8vnp was solved by C.Chang, Y.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.28 / 1.79
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.695, 113.695, 87.994, 90, 90, 120
R / Rfree (%)	17.1 / 19

The structure of Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate (pdb code 8vnp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate, PDB code: 8vnp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:15.2 occ:1.00 ND1 A:HIS134 2.1 12.5 1.0 SG A:CYS125 2.3 14.6 1.0 SG A:CYS132 2.3 13.7 1.0 SG A:CYS138 2.3 12.4 1.0 CE1 A:HIS134 3.0 14.4 1.0 CG A:HIS134 3.2 12.7 1.0 CB A:CYS132 3.3 13.3 1.0 CB A:CYS138 3.3 12.4 1.0 CB A:CYS125 3.3 11.0 1.0 CB A:HIS134 3.6 11.2 1.0 O A:HOH790 3.8 15.1 1.0 N A:CYS138 4.0 13.7 1.0 CA A:CYS132 4.0 14.4 1.0 NE2 A:HIS134 4.1 13.8 1.0 N A:HIS134 4.2 13.0 1.0 CA A:CYS138 4.2 10.8 1.0 CD2 A:HIS134 4.3 14.0 1.0 NH1 A:ARG122 4.3 13.0 1.0 N A:VAL133 4.6 14.7 1.0 CA A:HIS134 4.6 12.3 1.0 C A:CYS132 4.6 15.7 1.0 CA A:CYS125 4.7 12.7 1.0

Zinc binding site 2 out of 4 in the Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:13.5 occ:1.00 ND1 A:HIS110 2.1 12.6 1.0 SG A:CYS105 2.3 12.2 1.0 SG A:CYS100 2.3 12.0 1.0 SG A:CYS41 2.3 13.3 1.0 CB A:CYS105 3.0 10.9 1.0 CB A:CYS100 3.0 13.2 1.0 CE1 A:HIS110 3.0 11.7 1.0 CG A:HIS110 3.1 10.5 1.0 CB A:CYS41 3.3 13.2 1.0 CB A:HIS110 3.5 10.9 1.0 CA A:CYS41 3.7 11.7 1.0 NE2 A:HIS110 4.2 11.9 1.0 CD2 A:HIS110 4.2 12.3 1.0 CB A:ASN102 4.5 15.2 1.0 CA A:CYS105 4.5 12.9 1.0 CA A:CYS100 4.5 12.8 1.0 N A:CYS41 4.5 11.1 1.0 CB A:ASN107 4.6 11.5 1.0 ND2 A:ASN102 4.6 13.7 1.0 O A:HIS40 4.8 13.1 1.0 C A:CYS41 4.8 13.4 1.0 N A:TYR42 4.9 13.9 1.0 C A:HIS40 4.9 11.5 1.0 O A:ASN102 4.9 13.1 1.0 CG A:ASN102 5.0 16.2 1.0 N A:CYS100 5.0 12.9 1.0

Zinc binding site 3 out of 4 in the Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:14.5 occ:1.00 ND1 B:HIS334 2.1 13.2 1.0 SG B:CYS325 2.3 13.2 1.0 SG B:CYS332 2.3 12.4 1.0 SG B:CYS338 2.3 12.6 1.0 CE1 B:HIS334 2.9 14.9 1.0 CB B:CYS332 3.2 14.1 1.0 CG B:HIS334 3.2 13.7 1.0 CB B:CYS338 3.3 11.7 1.0 CB B:CYS325 3.3 10.7 1.0 CB B:HIS334 3.6 12.7 1.0 O B:HOH600 3.8 16.6 1.0 CA B:CYS332 3.9 12.7 1.0 N B:CYS338 4.0 13.6 1.0 NE2 B:HIS334 4.1 14.6 1.0 N B:HIS334 4.2 13.6 1.0 CA B:CYS338 4.2 13.4 1.0 CD2 B:HIS334 4.2 13.1 1.0 NH1 B:ARG322 4.4 12.2 1.0 CA B:HIS334 4.6 13.4 1.0 N B:VAL333 4.6 12.9 1.0 C B:CYS332 4.6 15.9 1.0 CA B:CYS325 4.7 10.3 1.0

Zinc binding site 4 out of 4 in the Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:13.5 occ:1.00 ND1 B:HIS310 2.1 12.3 1.0 SG B:CYS305 2.3 11.7 1.0 SG B:CYS241 2.3 12.1 1.0 SG B:CYS300 2.3 12.3 1.0 CB B:CYS305 3.0 12.0 1.0 CE1 B:HIS310 3.0 12.3 1.0 CB B:CYS300 3.0 13.2 1.0 CG B:HIS310 3.1 12.6 1.0 CB B:CYS241 3.2 12.6 1.0 CB B:HIS310 3.5 10.5 1.0 CA B:CYS241 3.6 13.2 1.0 NE2 B:HIS310 4.2 13.7 1.0 CD2 B:HIS310 4.2 13.3 1.0 N B:CYS241 4.5 12.0 1.0 CA B:CYS305 4.5 11.2 1.0 CB B:ASN302 4.5 13.5 1.0 CA B:CYS300 4.5 11.3 1.0 ND2 B:ASN302 4.6 14.5 1.0 CB B:ASN307 4.6 11.0 1.0 C B:CYS241 4.8 12.8 1.0 O B:HIS240 4.8 12.6 1.0 N B:TYR242 4.9 12.9 1.0 C B:HIS240 5.0 13.2 1.0 O B:ASN302 5.0 12.9 1.0 CG B:ASN302 5.0 13.5 1.0

C.Chang, Y.Gao. Homing Endonuclease I-Ppoi-Dna Complex:Reaction with 500 Um MG2+ For 160S To Be Published.