Zinc in PDB 8vnq: Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 1800S

The structure of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 1800S, PDB code: 8vnq 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)	48.20 / 1.93
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.646, 114.646, 89.057, 90, 90, 120
R / Rfree (%)	19.3 / 21

The structure of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 1800S also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 1800S (pdb code 8vnq). 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 1 Mm MN2+ For 1800S, PDB code: 8vnq:
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 1 Mm MN2+ 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 1 Mm MN2+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:24.0 occ:1.00 ND1 A:HIS134 2.1 23.3 1.0 SG A:CYS125 2.3 24.0 1.0 SG A:CYS132 2.3 25.1 1.0 SG A:CYS138 2.3 24.0 1.0 CE1 A:HIS134 2.9 23.3 1.0 CG A:HIS134 3.2 25.5 1.0 CB A:CYS138 3.3 23.7 1.0 CB A:CYS132 3.3 26.3 1.0 CB A:CYS125 3.4 22.2 1.0 CB A:HIS134 3.7 22.1 1.0 O A:HOH778 3.7 27.6 1.0 N A:CYS138 4.0 23.7 1.0 CA A:CYS132 4.1 28.4 1.0 NE2 A:HIS134 4.1 23.3 1.0 CD2 A:HIS134 4.2 25.6 1.0 CA A:CYS138 4.3 25.3 1.0 N A:HIS134 4.3 25.0 1.0 NH1 A:ARG122 4.3 21.8 1.0 CA A:HIS134 4.6 22.4 1.0 N A:VAL133 4.7 26.3 1.0 C A:CYS132 4.7 29.4 1.0 CA A:CYS125 4.8 26.5 1.0

Zinc binding site 2 out of 4 in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ 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 1 Mm MN2+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:22.9 occ:1.00 ND1 A:HIS110 2.1 20.9 1.0 SG A:CYS105 2.3 22.1 1.0 SG A:CYS100 2.4 22.4 1.0 SG A:CYS41 2.4 23.8 1.0 CE1 A:HIS110 3.0 24.1 1.0 CB A:CYS105 3.0 20.7 1.0 CB A:CYS100 3.1 21.8 1.0 CG A:HIS110 3.2 19.3 1.0 CB A:CYS41 3.3 22.6 1.0 CB A:HIS110 3.6 21.0 1.0 CA A:CYS41 3.7 21.4 1.0 NE2 A:HIS110 4.2 21.9 1.0 CD2 A:HIS110 4.3 23.8 1.0 CA A:CYS105 4.5 23.5 1.0 N A:CYS41 4.6 22.1 1.0 CA A:CYS100 4.6 21.4 1.0 ND2 A:ASN102 4.6 30.1 1.0 CB A:ASN102 4.6 25.5 1.0 CB A:ASN107 4.6 19.1 1.0 O A:HIS40 4.8 21.3 1.0 C A:CYS41 4.9 24.9 1.0 N A:TYR42 5.0 23.5 1.0 C A:HIS40 5.0 21.9 1.0

Zinc binding site 3 out of 4 in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ 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 1 Mm MN2+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:24.9 occ:1.00 ND1 B:HIS334 2.2 26.8 1.0 SG B:CYS332 2.3 24.5 1.0 SG B:CYS325 2.3 23.4 1.0 SG B:CYS338 2.4 23.9 1.0 CE1 B:HIS334 3.0 23.3 1.0 CB B:CYS332 3.2 27.4 1.0 CG B:HIS334 3.2 25.9 1.0 CB B:CYS338 3.3 23.1 1.0 CB B:CYS325 3.3 24.9 1.0 CB B:HIS334 3.7 23.6 1.0 O B:HOH590 3.9 28.7 1.0 CA B:CYS332 4.0 25.3 1.0 N B:CYS338 4.1 21.3 1.0 NE2 B:HIS334 4.2 24.6 1.0 N B:HIS334 4.2 24.3 1.0 CA B:CYS338 4.3 23.4 1.0 CD2 B:HIS334 4.3 24.1 1.0 NH1 B:ARG322 4.4 24.2 1.0 CA B:HIS334 4.6 24.5 1.0 N B:VAL333 4.6 24.9 1.0 C B:CYS332 4.6 30.8 1.0 CA B:CYS325 4.8 23.4 1.0

Zinc binding site 4 out of 4 in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ 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 1 Mm MN2+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:23.6 occ:1.00 ND1 B:HIS310 2.1 24.3 1.0 SG B:CYS241 2.3 22.7 1.0 SG B:CYS300 2.3 22.9 1.0 SG B:CYS305 2.3 23.4 1.0 CE1 B:HIS310 3.0 23.3 1.0 CB B:CYS300 3.1 22.4 1.0 CB B:CYS305 3.1 23.2 1.0 CG B:HIS310 3.2 25.3 1.0 CB B:CYS241 3.3 25.7 1.0 CB B:HIS310 3.6 25.7 1.0 CA B:CYS241 3.8 23.3 1.0 NE2 B:HIS310 4.2 25.4 1.0 CD2 B:HIS310 4.3 29.9 1.0 CA B:CYS300 4.5 24.0 1.0 CA B:CYS305 4.6 23.1 1.0 N B:CYS241 4.6 26.7 1.0 CB B:ASN302 4.6 22.9 1.0 ND2 B:ASN302 4.7 26.3 1.0 CB B:ASN307 4.7 26.9 1.0 C B:CYS241 4.9 26.7 1.0

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