Zinc in PDB 2o6m: H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna

The structure of H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna, PDB code: 2o6m was solved by J.H.Eastberg, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.30 / 2.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.850, 113.850, 88.880, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 24.4

The structure of H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna (pdb code 2o6m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna, PDB code: 2o6m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the H98Q Mutant of the Homing 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 H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:15.7 occ:1.00 ND1 A:HIS110 2.0 14.5 1.0 SG A:CYS100 2.3 19.2 1.0 SG A:CYS105 2.3 15.7 1.0 SG A:CYS41 2.3 17.0 1.0 CE1 A:HIS110 2.9 14.5 1.0 CB A:CYS100 3.0 19.2 1.0 CG A:HIS110 3.1 14.5 1.0 CB A:CYS105 3.2 15.7 1.0 CB A:CYS41 3.2 17.0 1.0 CB A:HIS110 3.6 14.5 1.0 CA A:CYS41 3.7 17.9 1.0 NE2 A:HIS110 4.0 14.5 1.0 CD2 A:HIS110 4.2 14.5 1.0 O A:HOH815 4.2 48.5 1.0 NE2 A:GLN98 4.3 38.2 1.0 N A:CYS41 4.4 17.9 1.0 CA A:CYS100 4.5 17.2 1.0 CB A:ASN107 4.5 11.9 1.0 ND2 A:ASN102 4.6 19.7 1.0 CA A:CYS105 4.6 11.2 1.0 CB A:ASN102 4.7 19.7 1.0 O A:HIS40 4.8 18.6 1.0 C A:CYS41 4.9 17.9 1.0 C A:HIS40 4.9 18.6 1.0 N A:TYR42 5.0 16.4 1.0 N A:CYS100 5.0 17.2 1.0

Zinc binding site 2 out of 4 in the H98Q Mutant of the Homing 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 H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:16.6 occ:1.00 ND1 A:HIS134 2.1 12.8 1.0 SG A:CYS125 2.2 16.2 1.0 SG A:CYS138 2.3 16.4 1.0 SG A:CYS132 2.4 13.6 1.0 CE1 A:HIS134 2.8 12.8 1.0 CG A:HIS134 3.2 12.8 1.0 CB A:CYS132 3.2 13.6 1.0 CB A:CYS125 3.2 16.2 1.0 CB A:CYS138 3.3 16.4 1.0 CB A:HIS134 3.7 12.8 1.0 O A:HOH745 3.8 17.9 1.0 N A:CYS138 4.0 16.7 1.0 NE2 A:HIS134 4.0 12.8 1.0 CA A:CYS132 4.0 16.7 1.0 CD2 A:HIS134 4.2 12.8 1.0 CA A:CYS138 4.2 16.7 1.0 N A:HIS134 4.3 21.9 1.0 NH2 A:ARG122 4.4 13.4 1.0 N A:VAL133 4.6 20.6 1.0 C A:CYS132 4.6 16.7 1.0 CA A:CYS125 4.7 17.2 1.0 CA A:HIS134 4.7 21.9 1.0

Zinc binding site 3 out of 4 in the H98Q Mutant of the Homing 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 H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:17.2 occ:1.00 ND1 B:HIS334 2.2 13.6 1.0 SG B:CYS338 2.3 14.8 1.0 SG B:CYS325 2.3 14.3 1.0 SG B:CYS332 2.3 20.5 1.0 CE1 B:HIS334 3.0 13.6 1.0 CB B:CYS338 3.2 14.8 1.0 CB B:CYS332 3.2 20.5 1.0 CB B:CYS325 3.3 14.3 1.0 CG B:HIS334 3.3 13.6 1.0 O B:HOH777 3.7 23.1 1.0 CB B:HIS334 3.8 13.6 1.0 N B:CYS338 4.0 13.1 1.0 CA B:CYS332 4.0 25.5 1.0 CA B:CYS338 4.2 13.1 1.0 NE2 B:HIS334 4.2 13.6 1.0 NH2 B:ARG322 4.3 10.7 1.0 N B:HIS334 4.3 19.8 1.0 CD2 B:HIS334 4.4 13.6 1.0 N B:VAL333 4.6 16.3 1.0 C B:CYS332 4.6 25.5 1.0 CA B:HIS334 4.7 19.8 1.0 CA B:CYS325 4.7 13.5 1.0

Zinc binding site 4 out of 4 in the H98Q Mutant of the Homing 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 H98Q Mutant of the Homing Endonuclease I-Ppoi Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:15.8 occ:1.00 ND1 B:HIS310 2.0 23.3 1.0 SG B:CYS300 2.3 14.0 1.0 SG B:CYS305 2.3 15.8 1.0 SG B:CYS241 2.3 13.3 1.0 CE1 B:HIS310 2.9 23.3 1.0 CB B:CYS300 3.0 14.0 1.0 CB B:CYS305 3.1 15.8 1.0 CB B:CYS241 3.1 13.3 1.0 CG B:HIS310 3.2 23.3 1.0 CB B:HIS310 3.6 23.3 1.0 CA B:CYS241 3.6 22.1 1.0 NE2 B:HIS310 4.1 23.3 1.0 CD2 B:HIS310 4.2 23.3 1.0 N B:CYS241 4.4 22.1 1.0 NE2 B:GLN298 4.4 38.6 1.0 CA B:CYS300 4.5 16.7 1.0 CA B:CYS305 4.6 17.0 1.0 ND2 B:ASN302 4.6 18.3 1.0 CB B:ASN302 4.7 18.3 1.0 CB B:ASN307 4.7 18.8 1.0 O B:HIS240 4.8 16.6 1.0 C B:CYS241 4.8 22.1 1.0 C B:HIS240 4.9 16.6 1.0 N B:TYR242 5.0 16.3 1.0 O B:ASN302 5.0 11.9 1.0

J.H.Eastberg, J.Eklund, R.Monnat, B.L.Stoddard. Mutability of An Hnh Nuclease Imidazole General Base and Exchange of A Deprotonation Mechanism. Biochemistry V. 46 7215 2007.
ISSN: ISSN 0006-2960
PubMed: 17516660
DOI: 10.1021/BI700418D