Zinc in PDB 1evw: L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna.

The structure of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna., PDB code: 1evw 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 / 3.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	182.000, 73.100, 92.700, 90.00, 95.40, 90.00
R / Rfree (%)	27.3 / 32

The structure of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. (pdb code 1evw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna., PDB code: 1evw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:16.4 occ:1.00 SG A:CYS138 2.2 36.5 1.0 SG A:CYS125 2.3 2.2 1.0 ND1 A:HIS134 2.3 26.7 1.0 SG A:CYS132 2.5 4.7 1.0 CB A:CYS138 3.1 36.5 1.0 CE1 A:HIS134 3.2 26.7 1.0 CB A:CYS125 3.2 2.2 1.0 CB A:CYS132 3.3 4.7 1.0 CG A:HIS134 3.4 26.7 1.0 CB A:HIS134 3.7 26.7 1.0 N A:CYS138 4.0 3.2 1.0 CA A:CYS138 4.1 3.2 1.0 CA A:CYS132 4.3 2.0 1.0 NH2 A:ARG122 4.3 4.6 1.0 NE2 A:HIS134 4.3 26.7 1.0 CD2 A:HIS134 4.5 26.7 1.0 N A:HIS134 4.5 18.7 1.0 CA A:CYS125 4.7 18.9 1.0 CG A:ARG122 4.7 4.6 1.0 CA A:HIS134 4.8 18.7 1.0 N A:VAL133 4.8 10.6 1.0 C A:CYS132 4.9 2.0 1.0

Zinc binding site 2 out of 8 in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:16.4 occ:1.00 SG A:CYS100 2.2 17.4 1.0 SG A:CYS41 2.2 3.8 1.0 ND1 A:HIS110 2.3 5.2 1.0 SG A:CYS105 2.3 10.4 1.0 CB A:CYS100 3.0 17.4 1.0 CG A:HIS110 3.1 5.2 1.0 CB A:CYS105 3.2 10.4 1.0 CB A:HIS110 3.2 5.2 1.0 CE1 A:HIS110 3.3 5.2 1.0 CB A:CYS41 3.4 3.8 1.0 CA A:CYS41 3.8 16.5 1.0 CD2 A:HIS110 4.3 5.2 1.0 NE2 A:HIS110 4.4 5.2 1.0 CA A:CYS100 4.5 2.0 1.0 N A:CYS41 4.6 16.5 1.0 CB A:ASN102 4.6 18.1 1.0 CA A:CYS105 4.7 8.2 1.0 O A:HIS40 4.7 5.5 1.0 CA A:HIS110 4.8 12.0 1.0 CB A:ASN107 4.8 2.0 1.0 N A:CYS100 4.9 2.0 1.0 C A:HIS40 4.9 2.0 1.0 O A:HIS110 5.0 5.2 1.0 O A:ASN102 5.0 18.1 1.0

Zinc binding site 3 out of 8 in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:16.4 occ:1.00 ND1 B:HIS134 2.0 13.5 1.0 SG B:CYS132 2.2 11.3 1.0 SG B:CYS125 2.3 18.8 1.0 SG B:CYS138 2.6 30.3 1.0 CE1 B:HIS134 2.9 13.5 1.0 CG B:HIS134 3.0 13.5 1.0 CB B:CYS138 3.3 30.3 1.0 CB B:CYS132 3.3 11.3 1.0 CB B:HIS134 3.4 13.5 1.0 CB B:CYS125 3.5 18.8 1.0 N B:CYS138 4.0 19.6 1.0 NE2 B:HIS134 4.1 13.5 1.0 CD2 B:HIS134 4.1 13.5 1.0 N B:HIS134 4.2 29.0 1.0 CA B:CYS138 4.2 19.6 1.0 CA B:CYS132 4.2 14.3 1.0 NH2 B:ARG122 4.4 2.0 1.0 CA B:HIS134 4.4 29.0 1.0 N B:VAL133 4.6 25.3 1.0 CG B:ARG122 4.7 2.0 1.0 C B:CYS132 4.8 14.3 1.0 CA B:CYS125 4.9 8.7 1.0 C B:VAL137 4.9 9.6 1.0

Zinc binding site 4 out of 8 in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:16.4 occ:1.00 ND1 B:HIS110 2.0 2.0 1.0 SG B:CYS41 2.1 8.3 1.0 SG B:CYS105 2.7 2.0 1.0 SG B:CYS100 2.8 37.2 1.0 CE1 B:HIS110 2.9 2.0 1.0 CG B:HIS110 3.0 2.0 1.0 CB B:CYS100 3.1 37.2 1.0 CB B:CYS41 3.2 8.3 1.0 CB B:HIS110 3.4 2.0 1.0 CA B:CYS41 3.5 17.7 1.0 CB B:CYS105 3.7 2.0 1.0 NE2 B:HIS110 4.0 2.0 1.0 CD2 B:HIS110 4.1 2.0 1.0 N B:CYS41 4.1 17.7 1.0 O B:HIS40 4.2 6.6 1.0 C B:HIS40 4.4 24.9 1.0 CA B:CYS100 4.6 19.5 1.0 CB B:ASN107 4.8 18.5 1.0 C B:CYS41 4.8 17.7 1.0 CB B:ASN102 4.9 2.8 1.0 CA B:HIS110 4.9 6.4 1.0

Zinc binding site 5 out of 8 in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn505 b:16.4 occ:1.00 ND1 C:HIS134 1.8 41.8 1.0 SG C:CYS132 2.3 11.9 1.0 SG C:CYS138 2.4 7.7 1.0 SG C:CYS125 2.6 23.7 1.0 CG C:HIS134 2.8 41.8 1.0 CE1 C:HIS134 2.8 41.8 1.0 CB C:HIS134 3.2 41.8 1.0 CB C:CYS138 3.4 7.7 1.0 CB C:CYS125 3.5 23.7 1.0 CB C:CYS132 3.6 11.9 1.0 NE2 C:HIS134 3.9 41.8 1.0 CD2 C:HIS134 3.9 41.8 1.0 N C:CYS138 4.0 3.2 1.0 NH2 C:ARG122 4.1 22.2 1.0 N C:HIS134 4.1 2.0 1.0 CA C:CYS138 4.2 3.2 1.0 CA C:HIS134 4.3 2.0 1.0 CA C:CYS132 4.5 19.4 1.0 CG C:ARG122 4.5 22.2 1.0 N C:VAL133 4.7 2.0 1.0 C C:VAL137 4.9 2.0 1.0 C C:CYS132 5.0 19.4 1.0

Zinc binding site 6 out of 8 in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn506 b:16.4 occ:1.00 SG C:CYS100 2.1 2.0 1.0 SG C:CYS105 2.2 13.0 1.0 ND1 C:HIS110 2.3 2.0 1.0 SG C:CYS41 2.3 9.0 1.0 CB C:CYS100 3.0 2.0 1.0 CG C:HIS110 3.1 2.0 1.0 CB C:HIS110 3.2 2.0 1.0 CB C:CYS105 3.3 13.0 1.0 CE1 C:HIS110 3.4 2.0 1.0 CB C:CYS41 3.5 9.0 1.0 CA C:CYS41 3.9 3.2 1.0 CD2 C:HIS110 4.3 2.0 1.0 NE2 C:HIS110 4.4 2.0 1.0 CA C:CYS100 4.5 17.0 1.0 CA C:HIS110 4.7 2.0 1.0 O C:HIS40 4.7 2.8 1.0 N C:CYS41 4.7 3.2 1.0 CB C:ASN102 4.7 4.8 1.0 CA C:CYS105 4.8 2.0 1.0 CB C:ASN107 4.8 7.0 1.0 N C:CYS100 4.8 17.0 1.0 O C:HIS110 4.9 2.0 1.0 O C:ASN102 5.0 4.8 1.0

Zinc binding site 7 out of 8 in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn507 b:16.4 occ:1.00 ND1 D:HIS134 2.0 6.0 1.0 SG D:CYS132 2.3 5.2 1.0 SG D:CYS125 2.3 37.0 1.0 SG D:CYS138 2.4 5.2 1.0 CE1 D:HIS134 2.8 6.0 1.0 CB D:CYS138 3.1 5.2 1.0 CG D:HIS134 3.1 6.0 1.0 CB D:CYS125 3.2 37.0 1.0 CB D:CYS132 3.6 5.2 1.0 CB D:HIS134 3.6 6.0 1.0 NE2 D:HIS134 4.0 6.0 1.0 N D:CYS138 4.1 2.0 1.0 CA D:CYS138 4.1 2.0 1.0 CD2 D:HIS134 4.1 6.0 1.0 NH2 D:ARG122 4.3 5.2 1.0 CG D:ARG122 4.3 5.2 1.0 CA D:CYS132 4.5 5.4 1.0 N D:HIS134 4.6 25.8 1.0 CA D:CYS125 4.7 2.0 1.0 CA D:HIS134 4.7 25.8 1.0 CA D:ARG122 4.9 26.7 1.0 N D:VAL133 5.0 19.1 1.0

Zinc binding site 8 out of 8 in the L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of L116A Mutant of the Homing Endonuclease I-Ppoi Complexed to Homing Site Dna. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn508 b:16.4 occ:1.00 ND1 D:HIS110 1.9 2.0 1.0 SG D:CYS105 2.3 12.3 1.0 SG D:CYS41 2.4 24.7 1.0 SG D:CYS100 2.4 4.8 1.0 CG D:HIS110 2.7 2.0 1.0 CB D:HIS110 2.9 2.0 1.0 CE1 D:HIS110 3.0 2.0 1.0 CB D:CYS100 3.2 4.8 1.0 CB D:CYS105 3.5 12.3 1.0 CB D:CYS41 3.6 24.7 1.0 CA D:CYS41 3.9 32.2 1.0 CD2 D:HIS110 3.9 2.0 1.0 NE2 D:HIS110 4.0 2.0 1.0 CA D:HIS110 4.5 2.0 1.0 O D:HIS40 4.5 2.0 1.0 CB D:ASN107 4.6 4.3 1.0 N D:CYS41 4.6 32.2 1.0 CA D:CYS100 4.7 2.0 1.0 C D:HIS40 4.8 46.3 1.0 O D:HIS110 4.8 2.0 1.0 CA D:CYS105 4.9 9.1 1.0 O D:ASN107 4.9 4.3 1.0 N D:CYS100 5.0 2.0 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