Zinc in PDB 8vmo: Homing Endonuclease I-Ppoi-Dna Complex:Ground State at PH7.0 (K+ Mes) with Na+

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Ground State at PH7.0 (K+ Mes) with Na+, PDB code: 8vmo 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)	49.40 / 1.68
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.083, 114.083, 88.123, 90, 90, 120
R / Rfree (%)	16.9 / 18.9

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Ground State at PH7.0 (K+ Mes) with Na+ also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Homing Endonuclease I-Ppoi-Dna Complex:Ground State at PH7.0 (K+ Mes) with Na+ (pdb code 8vmo). 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:Ground State at PH7.0 (K+ Mes) with Na+, PDB code: 8vmo:
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:Ground State at PH7.0 (K+ Mes) with Na+


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:Ground State at PH7.0 (K+ Mes) with Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:21.4 occ:1.00 ND1 A:HIS134 2.1 18.8 1.0 SG A:CYS125 2.3 22.0 1.0 SG A:CYS132 2.3 21.0 1.0 SG A:CYS138 2.3 19.8 1.0 CE1 A:HIS134 2.9 20.7 1.0 CG A:HIS134 3.2 19.2 1.0 CB A:CYS138 3.3 20.6 1.0 CB A:CYS132 3.3 22.0 1.0 CB A:CYS125 3.3 20.2 1.0 CB A:HIS134 3.6 18.9 1.0 O A:HOH803 3.9 23.6 1.0 N A:CYS138 4.0 19.4 1.0 CA A:CYS132 4.0 22.8 1.0 NE2 A:HIS134 4.1 21.4 1.0 CD2 A:HIS134 4.2 20.8 1.0 CA A:CYS138 4.2 18.3 1.0 N A:HIS134 4.2 20.9 1.0 NH1 A:ARG122 4.3 20.1 1.0 CA A:HIS134 4.6 19.8 1.0 N A:VAL133 4.6 23.4 1.0 C A:CYS132 4.7 25.6 1.0 CA A:CYS125 4.7 19.8 1.0

Zinc binding site 2 out of 4 in the Homing Endonuclease I-Ppoi-Dna Complex:Ground State at PH7.0 (K+ Mes) with Na+


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:Ground State at PH7.0 (K+ Mes) with Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:19.4 occ:1.00 ND1 A:HIS110 2.1 18.3 1.0 SG A:CYS105 2.3 19.0 1.0 SG A:CYS100 2.3 18.6 1.0 SG A:CYS41 2.4 19.8 1.0 CE1 A:HIS110 3.0 18.7 1.0 CB A:CYS105 3.0 17.3 1.0 CB A:CYS100 3.1 18.8 1.0 CG A:HIS110 3.1 16.6 1.0 CB A:CYS41 3.3 21.0 1.0 CB A:HIS110 3.5 18.2 1.0 CA A:CYS41 3.7 18.6 1.0 NE2 A:HIS110 4.1 17.8 1.0 CD2 A:HIS110 4.2 20.2 1.0 CB A:ASN102 4.5 20.9 1.0 N A:CYS41 4.5 19.0 1.0 CA A:CYS105 4.5 18.3 1.0 CA A:CYS100 4.5 20.3 1.0 ND2 A:ASN102 4.6 19.9 1.0 CB A:ASN107 4.6 17.7 1.0 O A:HIS40 4.8 20.0 1.0 C A:CYS41 4.8 20.3 1.0 N A:TYR42 4.9 20.0 1.0 C A:HIS40 4.9 17.8 1.0 O A:ASN102 5.0 20.1 1.0 CG A:ASN102 5.0 22.4 1.0

Zinc binding site 3 out of 4 in the Homing Endonuclease I-Ppoi-Dna Complex:Ground State at PH7.0 (K+ Mes) with Na+


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:Ground State at PH7.0 (K+ Mes) with Na+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:20.9 occ:1.00 ND1 B:HIS334 2.1 21.9 1.0 SG B:CYS332 2.3 19.5 1.0 SG B:CYS325 2.3 21.0 1.0 SG B:CYS338 2.3 19.8 1.0 CE1 B:HIS334 2.9 21.6 1.0 CG B:HIS334 3.2 20.6 1.0 CB B:CYS332 3.2 20.8 1.0 CB B:CYS338 3.3 19.4 1.0 CB B:CYS325 3.3 19.1 1.0 CB B:HIS334 3.6 20.4 1.0 O B:HOH604 3.8 24.6 1.0 CA B:CYS332 3.9 20.8 1.0 N B:CYS338 4.0 20.1 1.0 NE2 B:HIS334 4.1 21.0 1.0 N B:HIS334 4.2 22.1 1.0 CD2 B:HIS334 4.2 22.3 1.0 CA B:CYS338 4.2 20.9 1.0 NH1 B:ARG322 4.3 21.4 1.0 N B:VAL333 4.6 21.2 1.0 CA B:HIS334 4.6 21.2 1.0 C B:CYS332 4.6 23.2 1.0 CA B:CYS325 4.7 18.0 1.0

Zinc binding site 4 out of 4 in the Homing Endonuclease I-Ppoi-Dna Complex:Ground State at PH7.0 (K+ Mes) with Na+


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:Ground State at PH7.0 (K+ Mes) with Na+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:20.3 occ:1.00 ND1 B:HIS310 2.1 20.2 1.0 SG B:CYS305 2.3 20.1 1.0 SG B:CYS300 2.3 19.5 1.0 SG B:CYS241 2.3 20.8 1.0 CE1 B:HIS310 3.0 21.0 1.0 CB B:CYS305 3.1 20.0 1.0 CB B:CYS300 3.1 20.8 1.0 CG B:HIS310 3.1 19.5 1.0 CB B:CYS241 3.2 20.6 1.0 CB B:HIS310 3.5 18.7 1.0 CA B:CYS241 3.7 20.3 1.0 NE2 B:HIS310 4.2 20.4 1.0 CD2 B:HIS310 4.2 19.5 1.0 CB B:ASN302 4.5 21.0 1.0 N B:CYS241 4.5 20.7 1.0 CA B:CYS305 4.6 20.6 1.0 CA B:CYS300 4.6 21.3 1.0 ND2 B:ASN302 4.6 21.0 1.0 CB B:ASN307 4.6 20.3 1.0 C B:CYS241 4.8 23.3 1.0 O B:HIS240 4.9 22.3 1.0 N B:TYR242 4.9 20.7 1.0

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