Zinc in PDB 1evx: Apo Crystal Structure of the Homing Endonuclease, I-Ppoi

The structure of Apo Crystal Structure of the Homing Endonuclease, I-Ppoi, PDB code: 1evx was solved by E.A.Galburt, M.S.Jurica, B.S.Chevalier, D.Erho, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	52.800, 52.800, 278.800, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.9

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

Zinc binding site 1 out of 4 in the Apo Crystal Structure of the Homing Endonuclease, I-Ppoi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Apo Crystal Structure of the Homing Endonuclease, I-Ppoi within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:15.2 occ:1.00 ND1 A:HIS134 2.2 10.0 1.0 SG A:CYS132 2.4 11.9 1.0 SG A:CYS125 2.4 11.3 1.0 SG A:CYS138 2.4 11.6 1.0 CE1 A:HIS134 3.1 6.9 1.0 CB A:CYS138 3.3 8.4 1.0 CB A:CYS132 3.3 10.5 1.0 CG A:HIS134 3.3 7.0 1.0 CB A:CYS125 3.3 11.1 1.0 CB A:HIS134 3.7 6.5 1.0 O A:HOH1033 3.8 6.4 1.0 CA A:CYS132 4.0 12.4 1.0 N A:CYS138 4.0 12.4 1.0 NE2 A:HIS134 4.2 10.7 1.0 CA A:CYS138 4.2 10.8 1.0 N A:HIS134 4.3 9.2 1.0 CD2 A:HIS134 4.3 7.3 1.0 NH1 A:ARG122 4.4 8.2 1.0 N A:VAL133 4.5 12.2 1.0 C A:CYS132 4.6 14.1 1.0 CA A:HIS134 4.6 8.5 1.0 CA A:CYS125 4.8 10.4 1.0

Zinc binding site 2 out of 4 in the Apo Crystal Structure of the Homing Endonuclease, I-Ppoi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Apo Crystal Structure of the Homing Endonuclease, I-Ppoi within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:13.6 occ:1.00 ND1 A:HIS110 2.2 9.8 1.0 SG A:CYS41 2.3 11.7 1.0 SG A:CYS100 2.4 10.8 1.0 SG A:CYS105 2.4 12.3 1.0 CB A:CYS100 3.1 13.3 1.0 CE1 A:HIS110 3.1 9.2 1.0 CB A:CYS105 3.2 11.7 1.0 CB A:CYS41 3.2 10.4 1.0 CG A:HIS110 3.2 11.3 1.0 CB A:HIS110 3.5 8.8 1.0 CA A:CYS41 3.6 11.2 1.0 NE2 A:HIS110 4.2 9.2 1.0 CD2 A:HIS110 4.3 8.0 1.0 N A:CYS41 4.4 11.5 1.0 CB A:ASN102 4.5 13.0 1.0 CA A:CYS100 4.6 12.1 1.0 CB A:ASN107 4.6 8.8 1.0 CA A:CYS105 4.6 11.1 1.0 O A:HIS40 4.8 10.5 1.0 ND2 A:ASN102 4.8 11.5 1.0 C A:CYS41 4.8 13.1 1.0 C A:HIS40 4.9 10.1 1.0 N A:TYR42 4.9 13.4 1.0

Zinc binding site 3 out of 4 in the Apo Crystal Structure of the Homing Endonuclease, I-Ppoi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Apo Crystal Structure of the Homing Endonuclease, I-Ppoi within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:15.4 occ:1.00 ND1 B:HIS134 2.1 4.7 1.0 SG B:CYS132 2.3 12.0 1.0 SG B:CYS125 2.4 12.3 1.0 SG B:CYS138 2.4 14.6 1.0 CE1 B:HIS134 3.0 7.5 1.0 CG B:HIS134 3.2 8.3 1.0 CB B:CYS138 3.2 10.4 1.0 CB B:CYS132 3.3 11.1 1.0 CB B:CYS125 3.4 6.3 1.0 CB B:HIS134 3.6 9.4 1.0 O B:HOH1045 3.8 13.1 1.0 CA B:CYS132 4.0 12.9 1.0 N B:CYS138 4.0 11.3 1.0 CA B:CYS138 4.2 10.6 1.0 NE2 B:HIS134 4.2 8.2 1.0 N B:HIS134 4.3 8.6 1.0 NH1 B:ARG122 4.3 9.1 1.0 CD2 B:HIS134 4.3 7.6 1.0 N B:VAL133 4.5 11.9 1.0 CA B:HIS134 4.6 9.4 1.0 C B:CYS132 4.6 11.8 1.0 CA B:CYS125 4.8 11.6 1.0 CG B:ARG122 5.0 11.9 1.0

Zinc binding site 4 out of 4 in the Apo Crystal Structure of the Homing Endonuclease, I-Ppoi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Apo Crystal Structure of the Homing Endonuclease, I-Ppoi within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:13.1 occ:1.00 ND1 B:HIS110 2.1 5.5 1.0 SG B:CYS105 2.4 10.8 1.0 SG B:CYS41 2.4 9.7 1.0 SG B:CYS100 2.4 11.4 1.0 CB B:CYS100 3.0 9.8 1.0 CE1 B:HIS110 3.0 3.6 1.0 CB B:CYS105 3.1 13.2 1.0 CG B:HIS110 3.1 5.7 1.0 CB B:CYS41 3.3 8.2 1.0 CB B:HIS110 3.5 7.5 1.0 CA B:CYS41 3.7 8.2 1.0 NE2 B:HIS110 4.2 4.6 1.0 CD2 B:HIS110 4.2 4.9 1.0 CB B:ASN102 4.4 10.2 1.0 CA B:CYS100 4.4 11.7 1.0 N B:CYS41 4.5 9.0 1.0 CA B:CYS105 4.6 12.0 1.0 CB B:ASN107 4.7 10.5 1.0 O B:HIS40 4.8 11.2 1.0 C B:CYS41 4.8 11.1 1.0 N B:TYR42 4.9 10.6 1.0 N B:CYS100 4.9 13.3 1.0 ND2 B:ASN102 4.9 10.9 1.0 C B:HIS40 5.0 8.1 1.0 CA B:HIS110 5.0 10.2 1.0

E.A.Galburt, M.S.Chadsey, M.S.Jurica, B.S.Chevalier, D.Erho, W.Tang, R.J.Monnat Jr., B.L.Stoddard. Conformational Changes and Cleavage By the Homing Endonuclease I-Ppoi: A Critical Role For A Leucine Residue in the Active Site. J.Mol.Biol. V. 300 877 2000.
ISSN: ISSN 0022-2836
PubMed: 10891275
DOI: 10.1006/JMBI.2000.3874