Zinc in PDB 3gox: Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta

The structure of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta, PDB code: 3gox was solved by M.Sokolowska, H.Czapinska, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.60 / 1.50
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	90.682, 90.682, 334.933, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 18.6

The structure of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta (pdb code 3gox). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta, PDB code: 3gox:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:13.5 occ:1.00 SG A:CYS68 2.3 14.5 1.0 SG A:CYS100 2.3 17.2 1.0 SG A:CYS71 2.3 14.9 1.0 SG A:CYS97 2.4 15.2 1.0 CB A:CYS68 3.1 14.2 1.0 CB A:CYS100 3.3 16.6 1.0 CB A:CYS71 3.4 14.0 1.0 CB A:CYS97 3.5 14.6 1.0 N A:CYS71 3.7 13.8 1.0 N A:CYS97 3.9 13.7 1.0 O A:HOH293 4.0 23.4 1.0 CA A:CYS71 4.1 14.2 1.0 N A:CYS100 4.2 15.9 1.0 O A:HOH374 4.2 29.1 1.0 CA A:CYS97 4.3 14.1 1.0 CA A:CYS100 4.3 16.2 1.0 CA A:CYS68 4.6 13.7 1.0 NZ A:LYS75 4.6 18.8 1.0 CB A:ILE70 4.7 14.4 1.0 CE A:LYS75 4.8 18.4 1.0 O A:CYS97 4.8 14.4 1.0 C A:ILE70 4.8 14.9 1.0 C A:CYS97 4.9 13.3 1.0 C A:CYS71 5.0 13.2 1.0 N A:ILE70 5.0 14.1 1.0 N A:HIS72 5.0 12.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.5 occ:1.00 SG A:CYS164 2.3 14.8 1.0 SG A:CYS130 2.3 15.2 1.0 SG A:CYS161 2.3 14.9 1.0 SG A:CYS133 2.4 15.0 1.0 CB A:CYS130 3.2 14.0 1.0 CB A:CYS164 3.3 14.4 1.0 CB A:CYS133 3.3 16.7 1.0 CB A:CYS161 3.5 14.3 1.0 N A:CYS133 3.7 16.4 1.0 N A:CYS161 4.0 14.4 1.0 O A:HOH375 4.1 15.6 1.0 CA A:CYS133 4.1 16.1 1.0 O A:HOH356 4.1 15.0 1.0 N A:CYS164 4.2 13.9 1.0 CA A:CYS161 4.3 14.1 1.0 CA A:CYS164 4.3 14.0 1.0 CA A:CYS130 4.6 14.5 1.0 CB A:ILE132 4.7 16.8 1.0 NZ A:LYS135 4.7 16.4 1.0 O A:CYS161 4.7 14.1 1.0 C A:CYS161 4.8 14.1 1.0 C A:ILE132 4.9 17.1 1.0 C A:CYS133 5.0 15.9 1.0 N A:ILE132 5.0 16.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:12.9 occ:1.00 SG B:CYS100 2.3 16.1 1.0 SG B:CYS68 2.3 13.8 1.0 SG B:CYS71 2.4 15.2 1.0 SG B:CYS97 2.4 14.0 1.0 CB B:CYS68 3.2 12.0 1.0 CB B:CYS100 3.3 15.3 1.0 CB B:CYS71 3.4 13.7 1.0 CB B:CYS97 3.5 13.8 1.0 N B:CYS71 3.7 14.0 1.0 O B:HOH257 3.9 23.6 1.0 N B:CYS97 4.0 13.4 1.0 CA B:CYS71 4.1 13.7 1.0 N B:CYS100 4.2 14.8 1.0 O B:HOH252 4.2 26.1 1.0 CA B:CYS97 4.3 13.0 1.0 CA B:CYS100 4.3 15.1 1.0 NZ B:LYS75 4.6 18.7 1.0 CA B:CYS68 4.6 12.5 1.0 CB B:ILE70 4.7 14.3 1.0 CE B:LYS75 4.8 18.3 1.0 C B:ILE70 4.8 14.7 1.0 O B:CYS97 4.9 13.6 1.0 C B:CYS97 4.9 13.5 1.0 C B:CYS71 5.0 12.7 1.0 N B:ILE70 5.0 13.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I in the Absence of Edta within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:12.9 occ:1.00 SG B:CYS164 2.3 15.3 1.0 SG B:CYS130 2.3 15.0 1.0 SG B:CYS161 2.4 14.8 1.0 SG B:CYS133 2.4 15.5 1.0 CB B:CYS130 3.1 15.6 1.0 CB B:CYS164 3.3 14.5 1.0 CB B:CYS133 3.3 16.3 1.0 CB B:CYS161 3.5 15.4 1.0 N B:CYS133 3.7 16.1 1.0 O B:HOH280 4.0 13.0 1.0 N B:CYS161 4.1 15.2 1.0 CA B:CYS133 4.1 15.3 1.0 O B:HOH339 4.2 15.6 1.0 N B:CYS164 4.2 14.0 1.0 CA B:CYS161 4.3 15.1 1.0 CA B:CYS164 4.3 14.3 1.0 CA B:CYS130 4.6 15.3 1.0 CB B:ILE132 4.6 16.7 1.0 NZ B:LYS135 4.7 17.3 1.0 O B:CYS161 4.7 14.5 1.0 C B:ILE132 4.9 16.5 1.0 C B:CYS161 4.9 14.6 1.0 C B:CYS133 5.0 14.9 1.0 N B:ILE132 5.0 16.4 1.0

M.Sokolowska, H.Czapinska, M.Bochtler. Crystal Structure of the Beta Beta Alpha-Me Type II Restriction Endonuclease HPY99I with Target Dna. Nucleic Acids Res. V. 37 3799 2009.
ISSN: ISSN 0305-1048
PubMed: 19380375
DOI: 10.1093/NAR/GKP228