Zinc in PDB 8vnu: Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S

The structure of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S, PDB code: 8vnu 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)	47.67 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.574, 113.574, 87.695, 90, 90, 120
R / Rfree (%)	18.3 / 21.9

The structure of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Thallium	(Tl)	2 atoms

The binding sites of Zinc atom in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S (pdb code 8vnu). 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 H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S, PDB code: 8vnu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:33.7 occ:1.00 ND1 A:HIS134 2.0 32.5 1.0 SG A:CYS125 2.3 34.8 1.0 SG A:CYS132 2.3 31.6 1.0 SG A:CYS138 2.3 34.9 1.0 CE1 A:HIS134 2.8 29.9 1.0 CB A:CYS132 3.1 32.6 1.0 CG A:HIS134 3.2 31.5 1.0 CB A:CYS138 3.3 31.7 1.0 CB A:CYS125 3.3 32.7 1.0 CB A:HIS134 3.7 29.4 1.0 O A:HOH775 3.8 35.5 1.0 CA A:CYS132 3.9 34.4 1.0 NE2 A:HIS134 3.9 31.1 1.0 N A:CYS138 4.0 32.1 1.0 CD2 A:HIS134 4.2 28.1 1.0 CA A:CYS138 4.2 34.7 1.0 N A:HIS134 4.2 33.3 1.0 NH1 A:ARG122 4.3 31.1 1.0 N A:VAL133 4.5 35.8 1.0 C A:CYS132 4.6 36.8 1.0 CA A:HIS134 4.6 32.5 1.0 CA A:CYS125 4.7 34.0 1.0 O A:HOH763 5.0 24.0 1.0

Zinc binding site 2 out of 4 in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:29.7 occ:1.00 ND1 A:HIS110 2.1 25.4 1.0 SG A:CYS100 2.3 31.9 1.0 SG A:CYS105 2.3 30.1 1.0 SG A:CYS41 2.3 31.3 1.0 CB A:CYS100 3.0 29.6 1.0 CE1 A:HIS110 3.0 29.1 1.0 CB A:CYS105 3.0 27.9 1.0 CG A:HIS110 3.1 30.0 1.0 CB A:CYS41 3.2 26.1 1.0 CB A:HIS110 3.4 30.2 1.0 CA A:CYS41 3.6 28.1 1.0 NE2 A:HIS110 4.2 28.4 1.0 CD2 A:HIS110 4.2 25.5 1.0 CB A:ASN102 4.4 29.9 1.0 N A:CYS41 4.5 28.1 1.0 ND2 A:ASN102 4.5 34.1 1.0 CA A:CYS100 4.5 31.5 1.0 CA A:CYS105 4.5 29.3 1.0 CB A:ASN107 4.5 25.6 1.0 O A:HIS40 4.7 27.6 1.0 C A:CYS41 4.8 29.4 1.0 CG A:ASN102 4.9 35.3 1.0 C A:HIS40 4.9 26.4 1.0 N A:TYR42 4.9 26.0 1.0 CA A:HIS110 5.0 30.7 1.0 O A:ASN102 5.0 33.1 1.0 N A:CYS100 5.0 29.6 1.0

Zinc binding site 3 out of 4 in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:34.3 occ:1.00 ND1 B:HIS334 2.1 34.2 1.0 SG B:CYS325 2.3 32.6 1.0 SG B:CYS338 2.3 30.0 1.0 SG B:CYS332 2.3 34.4 1.0 CE1 B:HIS334 2.9 33.3 1.0 CG B:HIS334 3.1 33.5 1.0 CB B:CYS332 3.2 30.2 1.0 CB B:CYS338 3.3 32.2 1.0 CB B:CYS325 3.3 29.1 1.0 CB B:HIS334 3.6 32.6 1.0 O B:HOH581 3.7 37.8 1.0 CA B:CYS332 4.0 34.8 1.0 N B:CYS338 4.0 33.0 1.0 NE2 B:HIS334 4.1 33.0 1.0 N B:HIS334 4.2 32.8 1.0 CD2 B:HIS334 4.2 32.9 1.0 CA B:CYS338 4.2 34.2 1.0 NH1 B:ARG322 4.3 28.8 1.0 CA B:HIS334 4.5 35.5 1.0 N B:VAL333 4.5 30.2 1.0 C B:CYS332 4.6 35.7 1.0 CA B:CYS325 4.7 32.1 1.0

Zinc binding site 4 out of 4 in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:30.2 occ:1.00 ND1 B:HIS310 2.1 33.9 1.0 SG B:CYS241 2.3 32.2 1.0 SG B:CYS300 2.3 28.3 1.0 SG B:CYS305 2.3 31.9 1.0 CB B:CYS300 3.0 30.7 1.0 CB B:CYS305 3.0 29.2 1.0 CE1 B:HIS310 3.0 28.9 1.0 CG B:HIS310 3.1 33.2 1.0 CB B:CYS241 3.2 28.7 1.0 CB B:HIS310 3.5 31.5 1.0 CA B:CYS241 3.6 31.9 1.0 NE2 B:HIS310 4.2 29.9 1.0 CD2 B:HIS310 4.2 30.3 1.0 CB B:ASN302 4.5 29.6 1.0 N B:CYS241 4.5 33.0 1.0 CA B:CYS300 4.5 34.8 1.0 CA B:CYS305 4.5 28.5 1.0 ND2 B:ASN302 4.6 28.4 1.0 CB B:ASN307 4.7 29.7 1.0 C B:CYS241 4.8 33.0 1.0 O B:HIS240 4.9 30.8 1.0 N B:TYR242 4.9 28.6 1.0 C B:HIS240 5.0 35.4 1.0 N B:CYS300 5.0 34.1 1.0 CG B:ASN302 5.0 31.8 1.0

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